diff --git a/config.json b/config.json
index 474c2d7..419ef98 100644
--- a/config.json
+++ b/config.json
@@ -1,328 +1,6 @@
{
- "aggregateTextSearchAdapters" : [
- {
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/names/"
- },
- "textSearchAdapterId" : "b_malayi_PRJNA10729_generate-names-index",
- "assemblyNames" : [
- "b_malayi_PRJNA10729"
- ],
- "type" : "JBrowse1TextSearchAdapter"
- },
- {
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_angaria_PRJNA51225/names/"
- },
- "assemblyNames" : [
- "c_angaria_PRJNA51225"
- ],
- "type" : "JBrowse1TextSearchAdapter",
- "textSearchAdapterId" : "c_angaria_PRJNA51225_generate-names-index"
- },
- {
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_becei_PRJEB28243/names/"
- },
- "textSearchAdapterId" : "c_becei_PRJEB28243_generate-names-index",
- "assemblyNames" : [
- "c_becei_PRJEB28243"
- ],
- "type" : "JBrowse1TextSearchAdapter"
- },
- {
- "assemblyNames" : [
- "c_bovis_PRJEB34497"
- ],
- "type" : "JBrowse1TextSearchAdapter",
- "textSearchAdapterId" : "c_bovis_PRJEB34497_generate-names-index",
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_bovis_PRJEB34497/names/"
- }
- },
- {
- "type" : "JBrowse1TextSearchAdapter",
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
- ],
- "textSearchAdapterId" : "c_brenneri_PRJNA20035_generate-names-index",
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/names/"
- }
- },
- {
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/names/"
- },
- "assemblyNames" : [
- "c_briggsae_PRJNA10731"
- ],
- "type" : "JBrowse1TextSearchAdapter",
- "textSearchAdapterId" : "c_briggsae_PRJNA10731_generate-names-index"
- },
- {
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/names/"
- },
- "textSearchAdapterId" : "c_elegans_PRJEB28388_generate-names-index",
- "assemblyNames" : [
- "c_elegans_PRJEB28388"
- ],
- "type" : "JBrowse1TextSearchAdapter"
- },
- {
- "type" : "JBrowse1TextSearchAdapter",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "textSearchAdapterId" : "c_elegans_PRJNA13758_generate-names-index",
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/names/"
- }
- },
- {
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/names/"
- },
- "textSearchAdapterId" : "c_elegans_PRJNA275000_generate-names-index",
- "assemblyNames" : [
- "c_elegans_PRJNA275000"
- ],
- "type" : "JBrowse1TextSearchAdapter"
- },
- {
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_inopinata_PRJDB5687/names/"
- },
- "assemblyNames" : [
- "c_inopinata_PRJDB5687"
- ],
- "type" : "JBrowse1TextSearchAdapter",
- "textSearchAdapterId" : "c_inopinata_PRJDB5687_generate-names-index"
- },
- {
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/names/"
- },
- "textSearchAdapterId" : "c_japonica_PRJNA12591_generate-names-index",
- "type" : "JBrowse1TextSearchAdapter",
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ]
- },
- {
- "textSearchAdapterId" : "c_latens_PRJNA248912_generate-names-index",
- "assemblyNames" : [
- "c_latens_PRJNA248912"
- ],
- "type" : "JBrowse1TextSearchAdapter",
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_latens_PRJNA248912/names/"
- }
- },
- {
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_nigoni_PRJNA384657/names/"
- },
- "type" : "JBrowse1TextSearchAdapter",
- "assemblyNames" : [
- "c_nigoni_PRJNA384657"
- ],
- "textSearchAdapterId" : "c_nigoni_PRJNA384657_generate-names-index"
- },
- {
- "type" : "JBrowse1TextSearchAdapter",
- "assemblyNames" : [
- "c_panamensis_PRJEB28259"
- ],
- "textSearchAdapterId" : "c_panamensis_PRJEB28259_generate-names-index",
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_panamensis_PRJEB28259/names/"
- }
- },
- {
- "type" : "JBrowse1TextSearchAdapter",
- "assemblyNames" : [
- "c_parvicauda_PRJEB12595"
- ],
- "textSearchAdapterId" : "c_parvicauda_PRJEB12595_generate-names-index",
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_parvicauda_PRJEB12595/names/"
- }
- },
- {
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_quiockensis_PRJEB11354/names/"
- },
- "textSearchAdapterId" : "c_quiockensis_PRJEB11354_generate-names-index",
- "type" : "JBrowse1TextSearchAdapter",
- "assemblyNames" : [
- "c_quiockensis_PRJEB11354"
- ]
- },
- {
- "textSearchAdapterId" : "c_remanei_PRJNA53967_generate-names-index",
- "type" : "JBrowse1TextSearchAdapter",
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ],
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/names/"
- }
- },
- {
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA577507/names/"
- },
- "textSearchAdapterId" : "c_remanei_PRJNA577507_generate-names-index",
- "assemblyNames" : [
- "c_remanei_PRJNA577507"
- ],
- "type" : "JBrowse1TextSearchAdapter"
- },
- {
- "textSearchAdapterId" : "c_sinica_PRJNA194557_generate-names-index",
- "type" : "JBrowse1TextSearchAdapter",
- "assemblyNames" : [
- "c_sinica_PRJNA194557"
- ],
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sinica_PRJNA194557/names/"
- }
- },
- {
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sulstoni_PRJEB12601/names/"
- },
- "assemblyNames" : [
- "c_sulstoni_PRJEB12601"
- ],
- "type" : "JBrowse1TextSearchAdapter",
- "textSearchAdapterId" : "c_sulstoni_PRJEB12601_generate-names-index"
- },
- {
- "type" : "JBrowse1TextSearchAdapter",
- "assemblyNames" : [
- "c_tribulationis_PRJEB12608"
- ],
- "textSearchAdapterId" : "c_tribulationis_PRJEB12608_generate-names-index",
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tribulationis_PRJEB12608/names/"
- }
- },
- {
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/names/"
- },
- "type" : "JBrowse1TextSearchAdapter",
- "assemblyNames" : [
- "c_tropicalis_PRJNA53597"
- ],
- "textSearchAdapterId" : "c_tropicalis_PRJNA53597_generate-names-index"
- },
- {
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_uteleia_PRJEB12600/names/"
- },
- "type" : "JBrowse1TextSearchAdapter",
- "assemblyNames" : [
- "c_uteleia_PRJEB12600"
- ],
- "textSearchAdapterId" : "c_uteleia_PRJEB12600_generate-names-index"
- },
- {
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_waitukubuli_PRJEB12602/names/"
- },
- "textSearchAdapterId" : "c_waitukubuli_PRJEB12602_generate-names-index",
- "assemblyNames" : [
- "c_waitukubuli_PRJEB12602"
- ],
- "type" : "JBrowse1TextSearchAdapter"
- },
- {
- "type" : "JBrowse1TextSearchAdapter",
- "assemblyNames" : [
- "c_zanzibari_PRJEB12596"
- ],
- "textSearchAdapterId" : "c_zanzibari_PRJEB12596_generate-names-index",
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_zanzibari_PRJEB12596/names/"
- }
- },
- {
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_tipulae_PRJEB15512/names/"
- },
- "assemblyNames" : [
- "o_tipulae_PRJEB15512"
- ],
- "type" : "JBrowse1TextSearchAdapter",
- "textSearchAdapterId" : "o_tipulae_PRJEB15512_generate-names-index"
- },
- {
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/names/"
- },
- "assemblyNames" : [
- "o_volvulus_PRJEB513"
- ],
- "type" : "JBrowse1TextSearchAdapter",
- "textSearchAdapterId" : "o_volvulus_PRJEB513_generate-names-index"
- },
- {
- "textSearchAdapterId" : "p_pacificus_PRJNA12644_generate-names-index",
- "assemblyNames" : [
- "p_pacificus_PRJNA12644"
- ],
- "type" : "JBrowse1TextSearchAdapter",
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/names/"
- }
- },
- {
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/names/"
- },
- "assemblyNames" : [
- "p_redivivus_PRJNA186477"
- ],
- "type" : "JBrowse1TextSearchAdapter",
- "textSearchAdapterId" : "p_redivivus_PRJNA186477_generate-names-index"
- },
- {
- "type" : "JBrowse1TextSearchAdapter",
- "assemblyNames" : [
- "s_ratti_PRJEB125"
- ],
- "textSearchAdapterId" : "s_ratti_PRJEB125_generate-names-index",
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/names/"
- }
- },
- {
- "namesIndexLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/names/"
- },
- "textSearchAdapterId" : "t_muris_PRJEB126_generate-names-index",
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ],
- "type" : "JBrowse1TextSearchAdapter"
- }
- ],
"tracks" : [
{
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Curated_Genes/{refseq}/trackData.jsonz"
- }
- },
- "name" : "Curated Genes",
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
"category" : [
"Genes",
"Curated Genes"
@@ -330,28 +8,37 @@
"assemblyNames" : [
"b_malayi_PRJNA10729"
],
+ "type" : "FeatureTrack",
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
"trackId" : "b_malayi_PRJNA10729_curated_genes",
+ "name" : "Curated Genes",
"formatDetails" : {
"feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
},
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
+ "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
},
- "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
"maxHeight" : 5000,
+ "type" : "SvgFeatureRenderer",
"color3" : "#965567"
},
- "type" : "LinearBasicDisplay",
"displayId" : "curated_genes-b_malayi_PRJNA10729-LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Curated_Genes/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -359,88 +46,78 @@
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Curated Genes (noncoding)/{refseq}/trackData.jsonz"
}
},
- "name" : "Curated Genes (noncoding)",
- "description" : "Non-coding curated gene models, including ncRNA, tRNA, miRNA, snRNA, snoRNA, piRNA, lincRNA and antisense RNA.",
- "assemblyNames" : [
- "b_malayi_PRJNA10729"
- ],
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "trackId" : "b_malayi_PRJNA10729_curated_genes_noncoding",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
"displays" : [
{
- "displayId" : "curated_genes_(noncoding)-b_malayi_PRJNA10729-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"color1" : "gray",
+ "height" : 6,
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "curated_genes_(noncoding)-b_malayi_PRJNA10729-LinearBasicDisplay"
}
- ]
- },
- {
- "description" : "This track shows the extent of predicted protein motifs. Note these spans correspond to amino acid coordinates interpolated onto the physical map. Included are signal peptide (signalp), coiled coil (ncoils) and transmembrane (tmhmm) domains, regions of low complexity (seg), and Pfam annotated motif homologies.",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Protein motifs/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "Protein motifs",
+ ],
"formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
- "displays" : [
- {
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "jexl:parent(feature)=='undefined'?'purple':get(parent(feature),'predictiontype')=='tmhmm'?'magenta':get(parent(feature),'predictiontype')=='seg'?'lightseagreen':get(parent(feature),'predictiontype')=='signalp'?'aquamarine':get(parent(feature),'predictiontype')=='ncoils'?'chartreuse':\nget(parent(feature),'predictiontype')=='pfam'?'lightsalmon':'purple'",
- "height" : 7
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "protein_motifs-b_malayi_PRJNA10729-LinearBasicDisplay"
- }
- ],
+ "description" : "Non-coding curated gene models, including ncRNA, tRNA, miRNA, snRNA, snoRNA, piRNA, lincRNA and antisense RNA.",
+ "trackId" : "b_malayi_PRJNA10729_curated_genes_noncoding",
+ "name" : "Curated Genes (noncoding)",
"category" : [
- "Sequence Features",
- "Translated Features"
+ "Genes",
+ "Curated Genes"
],
"assemblyNames" : [
"b_malayi_PRJNA10729"
],
- "trackId" : "b_malayi_PRJNA10729_protein_motifs"
+ "type" : "FeatureTrack"
},
{
"assemblyNames" : [
"b_malayi_PRJNA10729"
],
+ "type" : "FeatureTrack",
"category" : [
- "Genes",
- "Curated Genes"
+ "Sequence Features",
+ "Translated Features"
],
- "trackId" : "b_malayi_PRJNA10729_dicistronic_mrnas",
+ "trackId" : "b_malayi_PRJNA10729_protein_motifs",
+ "name" : "Protein motifs",
+ "description" : "This track shows the extent of predicted protein motifs. Note these spans correspond to amino acid coordinates interpolated onto the physical map. Included are signal peptide (signalp), coiled coil (ncoils) and transmembrane (tmhmm) domains, regions of low complexity (seg), and Pfam annotated motif homologies.",
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
"displays" : [
{
- "displayId" : "dicistronic_mrnas-b_malayi_PRJNA10729-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "protein_motifs-b_malayi_PRJNA10729-LinearBasicDisplay",
"renderer" : {
- "color1" : "darkgreen",
+ "color1" : "jexl:parent(feature)=='undefined'?'purple':get(parent(feature),'predictiontype')=='tmhmm'?'magenta':get(parent(feature),'predictiontype')=='seg'?'lightseagreen':get(parent(feature),'predictiontype')=='signalp'?'aquamarine':get(parent(feature),'predictiontype')=='ncoils'?'chartreuse':\nget(parent(feature),'predictiontype')=='pfam'?'lightsalmon':'purple'",
+ "height" : 7,
"type" : "SvgFeatureRenderer"
}
}
],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Protein motifs/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ }
+ },
+ {
+ "trackId" : "b_malayi_PRJNA10729_dicistronic_mrnas",
+ "name" : "Dicistronic mRNAs",
+ "description" : "Dicistronic mRNA operons - manually observed by curators",
+ "assemblyNames" : [
+ "b_malayi_PRJNA10729"
+ ],
"type" : "FeatureTrack",
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -448,81 +125,93 @@
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Dicistronic mRNAs/{refseq}/trackData.jsonz"
}
},
- "name" : "Dicistronic mRNAs",
- "description" : "Dicistronic mRNA operons - manually observed by curators"
- },
- {
"displays" : [
{
- "displayId" : "polya_sites_and_signal_sequences-b_malayi_PRJNA10729-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "labels" : {
- "description" : "jexl:get(feature,'type') || get(feature,'description')"
- },
- "color1" : "purple"
- }
+ "color1" : "darkgreen"
+ },
+ "displayId" : "dicistronic_mrnas-b_malayi_PRJNA10729-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
- "trackId" : "b_malayi_PRJNA10729_polya_sites_and_signal_sequences",
+ }
+ },
+ {
"assemblyNames" : [
"b_malayi_PRJNA10729"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Features",
"Signals & Motifs"
],
- "description" : "High-confidence polyadenylation signal sequences and sites calculated by an algorithm trained with verified sites from full-length mRNAs. Signals are indicated with a diamond; sites with a triangle.",
+ "trackId" : "b_malayi_PRJNA10729_polya_sites_and_signal_sequences",
"name" : "PolyA sites and signal sequences",
- "type" : "FeatureTrack",
+ "description" : "High-confidence polyadenylation signal sequences and sites calculated by an algorithm trained with verified sites from full-length mRNAs. Signals are indicated with a diamond; sites with a triangle.",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "purple",
+ "labels" : {
+ "description" : "jexl:get(feature,'type') || get(feature,'description')"
+ }
+ },
+ "displayId" : "polya_sites_and_signal_sequences-b_malayi_PRJNA10729-LinearBasicDisplay"
+ }
+ ],
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/PolyA sites and signal sequences/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "NCListAdapter"
}
},
{
- "name" : "Curated Genes (protein coding)",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "NCListAdapter"
+ },
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
- "trackId" : "b_malayi_PRJNA10729_curated_genes_protein_coding",
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "assemblyNames" : [
- "b_malayi_PRJNA10729"
- ],
"displays" : [
{
+ "displayId" : "curated_genes_(protein_coding)-b_malayi_PRJNA10729-LinearBasicDisplay",
"renderer" : {
- "maxHeight" : 5000,
"color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
"type" : "SvgFeatureRenderer",
+ "maxHeight" : 5000,
"color3" : "#965567"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "curated_genes_(protein_coding)-b_malayi_PRJNA10729-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- }
+ "trackId" : "b_malayi_PRJNA10729_curated_genes_protein_coding",
+ "name" : "Curated Genes (protein coding)",
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
+ "assemblyNames" : [
+ "b_malayi_PRJNA10729"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ]
},
{
+ "type" : "FeatureTrack",
"assemblyNames" : [
"b_malayi_PRJNA10729"
],
@@ -530,7 +219,9 @@
"Sequence Features",
"Signals & Motifs"
],
+ "name" : "Trans-spliced acceptor",
"trackId" : "b_malayi_PRJNA10729_trans-spliced_acceptor",
+ "description" : "This track contains SL1 and SL2 trans-spliced acceptors from a variety of sources: SL1 and SL2 trans-spliced acceptors published by Blumenthal et al, Nature (2002), Trans-Spliced Exon Coupled RNA End Determination (TEC-RED) Hwang et al, PNAS (2004), EST/mRNA sequence data, RNASeq read data from ENA. SL1 acceptors are show in red, SL2 in green. Direction of transcription is indicated by arrow direction.",
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
@@ -538,39 +229,31 @@
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"labels" : {
"description" : "jexl:get(feature,'source') || get(feature,'description')"
},
- "color1" : "jexl:get(feature,'source')=='SL1'?'red':get(feature,'source')=='SL2'?'green':'black'"
+ "color1" : "jexl:get(feature,'source')=='SL1'?'red':get(feature,'source')=='SL2'?'green':'black'",
+ "type" : "SvgFeatureRenderer"
},
"displayId" : "trans-spliced_acceptor-b_malayi_PRJNA10729-LinearBasicDisplay"
}
],
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Trans-spliced acceptor/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "Trans-spliced acceptor",
- "description" : "This track contains SL1 and SL2 trans-spliced acceptors from a variety of sources: SL1 and SL2 trans-spliced acceptors published by Blumenthal et al, Nature (2002), Trans-Spliced Exon Coupled RNA End Determination (TEC-RED) Hwang et al, PNAS (2004), EST/mRNA sequence data, RNASeq read data from ENA. SL1 acceptors are show in red, SL2 in green. Direction of transcription is indicated by arrow direction."
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Trans-spliced acceptor/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
- "trackId" : "b_malayi_PRJNA10729_curated_genes_pseudogenes",
- "assemblyNames" : [
- "b_malayi_PRJNA10729"
- ],
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "displays" : [
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
+ "displays" : [
{
- "displayId" : "curated_genes_(pseudogenes)-b_malayi_PRJNA10729-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "curated_genes_(pseudogenes)-b_malayi_PRJNA10729-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"color1" : "gray",
@@ -578,119 +261,124 @@
}
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
- "name" : "Curated Genes (pseudogenes)",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Curated Genes (pseudogenes)/{refseq}/trackData.jsonz"
- }
- },
- "type" : "FeatureTrack",
- "description" : "A subset of the full Curated Genes set limited to pseudogenes only. Pseudogenes of tRNA are lighter gray and pseudogenes of rRNA are darker gray than pseudogenes of protein coding genes."
- },
- {
- "description" : "These are transposon spans reviewed by WormBase curators.",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Transposon Genes/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
+ "assemblyNames" : [
+ "b_malayi_PRJNA10729"
+ ],
"type" : "FeatureTrack",
- "name" : "Transposon Genes",
+ "description" : "A subset of the full Curated Genes set limited to pseudogenes only. Pseudogenes of tRNA are lighter gray and pseudogenes of rRNA are darker gray than pseudogenes of protein coding genes.",
+ "trackId" : "b_malayi_PRJNA10729_curated_genes_pseudogenes",
+ "name" : "Curated Genes (pseudogenes)"
+ },
+ {
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "transposon_genes-b_malayi_PRJNA10729-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
- "color1" : "gray",
"type" : "SvgFeatureRenderer",
"labels" : {
"description" : "jexl:get(feature,'type')=='pseudogenic_transcript'?'transposon pseudogene':'transposon mRNA'"
- }
- },
- "type" : "LinearBasicDisplay"
+ },
+ "color1" : "gray",
+ "height" : 6
+ }
}
],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Transposon Genes/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"assemblyNames" : [
"b_malayi_PRJNA10729"
],
+ "type" : "FeatureTrack",
"category" : [
"Genes",
"Curated Genes"
],
- "trackId" : "b_malayi_PRJNA10729_transposon_genes"
+ "trackId" : "b_malayi_PRJNA10729_transposon_genes",
+ "name" : "Transposon Genes",
+ "description" : "These are transposon spans reviewed by WormBase curators."
},
{
- "name" : "mRNAs/ncRNAs (best)",
- "type" : "FeatureTrack",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
+ "displays" : [
+ {
+ "displayId" : "mrnas/ncrnas_(best)-b_malayi_PRJNA10729-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "outline" : "black",
+ "height" : 6,
+ "color1" : "jexl:startsWith(get(feature,'source'),'BLAT_mRNA_')==true?'yellow':'gray'"
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/mRNAs_ncRNAs (best)/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/mRNAs_ncRNAs (best)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "description" : "Native (same species) full length cDNAs and ncRNAs aligned to the genome using BLAT. This track shows the best unique location for each cDNA.",
- "trackId" : "b_malayi_PRJNA10729_mrnas/ncrnas_(best)",
"category" : [
"Genes",
"Supporting Evidence"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"b_malayi_PRJNA10729"
],
- "displays" : [
- {
- "renderer" : {
- "color1" : "jexl:startsWith(get(feature,'source'),'BLAT_mRNA_')==true?'yellow':'gray'",
- "outline" : "black",
- "type" : "SvgFeatureRenderer",
- "height" : 6
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "mrnas/ncrnas_(best)-b_malayi_PRJNA10729-LinearBasicDisplay"
- }
- ],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- }
+ "description" : "Native (same species) full length cDNAs and ncRNAs aligned to the genome using BLAT. This track shows the best unique location for each cDNA.",
+ "name" : "mRNAs/ncRNAs (best)",
+ "trackId" : "b_malayi_PRJNA10729_mrnas/ncrnas_(best)"
},
{
"name" : "YACs, Fosmids, & Cosmids",
+ "trackId" : "b_malayi_PRJNA10729_yacs_fosmids_cosmids",
+ "description" : "This track shows the locations of the cosmids, fosmids, and YACs used for the physical mapping and sequencing of the C. elegans genome. The clone termini do not necessarily correspond to the termini of submitted GenBank/EMBL entries. In some cases the exact termini of the clones is not known. For example, YACs were sequenced using PCR amplification across gaps in the cosmid maps. When a clone end is not known, it is shown as an arrow extending to the end of the display. Such data is to be treated with caution. The Vancouver fosmids can be ordered directly from GeneService.",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "b_malayi_PRJNA10729"
+ ],
+ "category" : [
+ "Reagents"
+ ],
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/YACs, Fosmids, & Cosmids/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "NCListAdapter"
},
- "description" : "This track shows the locations of the cosmids, fosmids, and YACs used for the physical mapping and sequencing of the C. elegans genome. The clone termini do not necessarily correspond to the termini of submitted GenBank/EMBL entries. In some cases the exact termini of the clones is not known. For example, YACs were sequenced using PCR amplification across gaps in the cosmid maps. When a clone end is not known, it is shown as an arrow extending to the end of the display. Such data is to be treated with caution. The Vancouver fosmids can be ordered directly from GeneService.",
- "trackId" : "b_malayi_PRJNA10729_yacs_fosmids_cosmids",
- "category" : [
- "Reagents"
- ],
- "assemblyNames" : [
- "b_malayi_PRJNA10729"
- ],
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "yacs,_fosmids,_&_cosmids-b_malayi_PRJNA10729-LinearBasicDisplay",
"renderer" : {
"height" : 3,
"color1" : "black",
"type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay"
+ }
}
],
"formatDetails" : {
@@ -698,207 +386,208 @@
}
},
{
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
+ "assemblyNames" : [
+ "b_malayi_PRJNA10729"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Historical gene predictions.",
+ "trackId" : "b_malayi_PRJNA10729_gene_models_(historical)",
+ "name" : "Gene Models (historical)",
"displays" : [
{
- "displayId" : "gene_models_(historical)-b_malayi_PRJNA10729-LinearBasicDisplay",
"renderer" : {
"color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
- "type" : "SvgFeatureRenderer",
"labels" : {
"description" : "jexl:get(feature,'type')"
- }
+ },
+ "type" : "SvgFeatureRenderer"
},
+ "displayId" : "gene_models_(historical)-b_malayi_PRJNA10729-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "assemblyNames" : [
- "b_malayi_PRJNA10729"
- ],
- "trackId" : "b_malayi_PRJNA10729_gene_models_(historical)",
- "description" : "Historical gene predictions.",
- "type" : "FeatureTrack",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
"adapter" : {
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Gene Models (historical)/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
- },
- "name" : "Gene Models (historical)"
+ }
},
{
- "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "b_malayi_PRJNA10729_C_japonica_proteins",
"name" : "C. japonica proteins",
+ "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "assemblyNames" : [
+ "b_malayi_PRJNA10729"
+ ],
"type" : "FeatureTrack",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/C. japonica proteins/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/C. japonica proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
"displays" : [
{
- "type" : "LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"color1" : "orange",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"height" : 4
},
- "displayId" : "C_japonica_proteins-b_malayi_PRJNA10729-LinearBasicDisplay"
+ "displayId" : "C_japonica_proteins-b_malayi_PRJNA10729-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ],
- "trackId" : "b_malayi_PRJNA10729_C_japonica_proteins",
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "b_malayi_PRJNA10729"
]
},
{
"description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"name" : "Other UniProt proteins",
+ "trackId" : "b_malayi_PRJNA10729_other_uniprot_proteins",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "b_malayi_PRJNA10729"
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Other UniProt proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Other UniProt proteins/{refseq}/trackData.jsonz"
}
},
"displays" : [
{
- "displayId" : "other_uniprot_proteins-b_malayi_PRJNA10729-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "other_uniprot_proteins-b_malayi_PRJNA10729-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "showDescriptions" : false,
"color1" : "orange",
"showLabels" : false,
+ "height" : 4,
+ "showDescriptions" : false,
"type" : "SvgFeatureRenderer"
}
}
- ],
- "trackId" : "b_malayi_PRJNA10729_other_uniprot_proteins",
- "assemblyNames" : [
- "b_malayi_PRJNA10729"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
]
},
{
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display.",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/RNASeq introns/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ }
},
- "type" : "FeatureTrack",
- "name" : "RNASeq introns",
"displays" : [
{
"displayId" : "rnaseq_introns-b_malayi_PRJNA10729-LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'score')+' reads'",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "green",
+ "height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)",
"showDescriptions" : false,
- "height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)"
+ "showLabels" : false
},
+ "mouseover" : "jexl:get(feature,'score')+' reads'",
"type" : "LinearBasicDisplay"
}
],
+ "name" : "RNASeq introns",
+ "trackId" : "b_malayi_PRJNA10729_rnaseq_introns",
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"b_malayi_PRJNA10729"
],
"category" : [
"Expression"
- ],
- "trackId" : "b_malayi_PRJNA10729_rnaseq_introns"
+ ]
},
{
- "displays" : [
- {
- "renderer" : {
- "showDescriptions" : false,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))"
- },
- "mouseover" : "jexl:get(feature,'score')+' reads'",
- "type" : "LinearBasicDisplay",
- "displayId" : "rnaseq_splice_junctions_(common)-b_malayi_PRJNA10729-LinearBasicDisplay"
- }
- ],
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
+ "trackId" : "b_malayi_PRJNA10729_rnaseq_splice_junctions_(common)",
+ "name" : "RNASeq Splice Junctions (common)",
"category" : [
"Expression"
],
"assemblyNames" : [
"b_malayi_PRJNA10729"
],
- "trackId" : "b_malayi_PRJNA10729_rnaseq_splice_junctions_(common)",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
+ "type" : "FeatureTrack",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/RNASeq Splice Junctions (common)/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ }
},
- "type" : "FeatureTrack",
- "name" : "RNASeq Splice Junctions (common)"
- },
- {
- "category" : [
- "Expression"
- ],
- "assemblyNames" : [
- "b_malayi_PRJNA10729"
- ],
- "trackId" : "b_malayi_PRJNA10729_rnaseq_splice_junctions_(rare)",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "maxHeight" : 5000,
"color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
+ "showDescriptions" : false,
"showLabels" : false,
- "height" : "jexl:4",
"type" : "SvgFeatureRenderer"
},
"mouseover" : "jexl:get(feature,'score')+' reads'",
- "displayId" : "rnaseq_splice_junctions_(rare)-b_malayi_PRJNA10729-LinearBasicDisplay"
+ "displayId" : "rnaseq_splice_junctions_(common)-b_malayi_PRJNA10729-LinearBasicDisplay"
}
+ ]
+ },
+ {
+ "trackId" : "b_malayi_PRJNA10729_rnaseq_splice_junctions_(rare)",
+ "name" : "RNASeq Splice Junctions (rare)",
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
+ "assemblyNames" : [
+ "b_malayi_PRJNA10729"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Expression"
],
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "name" : "RNASeq Splice Junctions (rare)",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads."
+ "displays" : [
+ {
+ "displayId" : "rnaseq_splice_junctions_(rare)-b_malayi_PRJNA10729-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'score')+' reads'",
+ "renderer" : {
+ "color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
+ "showDescriptions" : false,
+ "height" : "jexl:4",
+ "showLabels" : false,
+ "maxHeight" : 5000,
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
+ "type" : "FeatureTrack",
"assemblyNames" : [
"b_malayi_PRJNA10729"
],
@@ -906,62 +595,61 @@
"Sequence Similarity",
"Proteins"
],
+ "name" : "C. elegans proteins",
"trackId" : "b_malayi_PRJNA10729_C_elegans_proteins",
+ "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"displays" : [
{
- "displayId" : "C_elegans_proteins-b_malayi_PRJNA10729-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
+ "height" : 4,
"showLabels" : false,
- "height" : 4
+ "color1" : "orange"
},
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay"
+ "displayId" : "C_elegans_proteins-b_malayi_PRJNA10729-LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/C. elegans proteins/{refseq}/trackData.jsonz"
- }
- },
- "name" : "C. elegans proteins",
- "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/C. elegans proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz"
}
},
- "type" : "FeatureTrack",
- "name" : "Repeat Region (RepeatMasker)",
- "description" : "Repetitive regions identified by RepeatMasker.",
- "category" : [
- "Genome Structure",
- "Repeats"
- ],
- "assemblyNames" : [
- "b_malayi_PRJNA10729"
- ],
- "trackId" : "b_malayi_PRJNA10729_repeat_region_(repeatmasker)",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
+ "showLabels" : false,
"showDescriptions" : false,
"height" : 4,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "bisque"
+ "color1" : "bisque",
+ "type" : "SvgFeatureRenderer"
},
"displayId" : "repeat_region_(repeatmasker)-b_malayi_PRJNA10729-LinearBasicDisplay"
}
+ ],
+ "description" : "Repetitive regions identified by RepeatMasker.",
+ "name" : "Repeat Region (RepeatMasker)",
+ "trackId" : "b_malayi_PRJNA10729_repeat_region_(repeatmasker)",
+ "category" : [
+ "Genome Structure",
+ "Repeats"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "b_malayi_PRJNA10729"
]
},
{
@@ -969,9 +657,9 @@
{
"displayId" : "ests-b_malayi_PRJNA10729-LinearBasicDisplay",
"renderer" : {
- "maxHeight" : 5000,
"color1" : "jexl:parent(feature)=='undefined'?'red':get(parent(feature),'has_mate')==1?'limegreen':get(parent(feature),'has_mate')==2?'green':get(parent(feature),'has_mate')==0?'gold':'black'",
- "type" : "SvgFeatureRenderer"
+ "type" : "SvgFeatureRenderer",
+ "maxHeight" : 5000
},
"type" : "LinearBasicDisplay"
}
@@ -979,171 +667,181 @@
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "trackId" : "b_malayi_PRJNA10729_ests",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/ESTs (best)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"assemblyNames" : [
"b_malayi_PRJNA10729"
],
+ "type" : "FeatureTrack",
"category" : [
"Genes",
"Supporting Evidence"
],
- "description" : "Native (same-species) Expressed Sequence Tags (ESTs), aligned to the genome using BLAT. This track shows the best unique location for each EST. The paired 5' and 3' ESTs from the same cDNA clone are connected by a dashed line and a colored light green. ESTs with no mate are yellow, and ESTs with a mate that is 'far away' are dark green.",
+ "trackId" : "b_malayi_PRJNA10729_ests",
"name" : "ESTs",
+ "description" : "Native (same-species) Expressed Sequence Tags (ESTs), aligned to the genome using BLAT. This track shows the best unique location for each EST. The paired 5' and 3' ESTs from the same cDNA clone are connected by a dashed line and a colored light green. ESTs with no mate are yellow, and ESTs with a mate that is 'far away' are dark green."
+ },
+ {
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "height" : 4,
+ "showLabels" : false,
+ "color1" : "orange"
+ },
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "C_briggsae_proteins-b_malayi_PRJNA10729-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/ESTs (best)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/C. briggsae proteins/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack"
- },
- {
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "b_malayi_PRJNA10729"
+ ],
"description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"name" : "C. briggsae proteins",
+ "trackId" : "b_malayi_PRJNA10729_C_briggsae_proteins"
+ },
+ {
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/C. briggsae proteins/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/B. malayi proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
"displays" : [
{
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
+ "color1" : "orange",
+ "height" : 4,
"showLabels" : false
},
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
- "displayId" : "C_briggsae_proteins-b_malayi_PRJNA10729-LinearBasicDisplay"
+ "displayId" : "B_malayi_proteins-b_malayi_PRJNA10729-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "b_malayi_PRJNA10729_C_briggsae_proteins",
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "b_malayi_PRJNA10729"
- ]
- },
- {
+ "name" : "B. malayi proteins",
"trackId" : "b_malayi_PRJNA10729_B_malayi_proteins",
+ "description" : "Matches to WormBase B. malayi proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"b_malayi_PRJNA10729"
],
"category" : [
"Sequence Similarity",
"Proteins"
- ],
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "orange",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "height" : 4
- },
- "mouseover" : "jexl:get(feature,'clone')",
- "displayId" : "B_malayi_proteins-b_malayi_PRJNA10729-LinearBasicDisplay"
- }
- ],
- "name" : "B. malayi proteins",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/B. malayi proteins/{refseq}/trackData.jsonz"
- }
- },
- "type" : "FeatureTrack",
- "description" : "Matches to WormBase B. malayi proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ ]
},
{
- "description" : "Matches to WormBase S. ratti proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "S. ratti proteins",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/S. ratti proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
+ }
},
"displays" : [
{
- "displayId" : "S_ratti_proteins-b_malayi_PRJNA10729-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"color1" : "orange",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"height" : 4
- }
+ },
+ "displayId" : "S_ratti_proteins-b_malayi_PRJNA10729-LinearBasicDisplay"
}
],
+ "name" : "S. ratti proteins",
"trackId" : "b_malayi_PRJNA10729_S_ratti_proteins",
+ "description" : "Matches to WormBase S. ratti proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "b_malayi_PRJNA10729"
+ ],
"category" : [
"Sequence Similarity",
"Proteins"
- ],
- "assemblyNames" : [
- "b_malayi_PRJNA10729"
]
},
{
"displays" : [
{
- "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
+ "showLabels" : false,
"height" : 4,
"color1" : "orange",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "O_volvulus_proteins-b_malayi_PRJNA10729-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "O_volvulus_proteins-b_malayi_PRJNA10729-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "b_malayi_PRJNA10729_O_volvulus_proteins",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/O. volvulus proteins/{refseq}/trackData.jsonz"
+ }
+ },
"assemblyNames" : [
"b_malayi_PRJNA10729"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "description" : "Matches to WormBase O. volvulus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "b_malayi_PRJNA10729_O_volvulus_proteins",
"name" : "O. volvulus proteins",
+ "description" : "Matches to WormBase O. volvulus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ },
+ {
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/O. volvulus proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/C. remanei proteins/{refseq}/trackData.jsonz"
+ }
},
- "type" : "FeatureTrack"
- },
- {
"displays" : [
{
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "color1" : "orange",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "height" : 4
+ "color1" : "orange",
+ "height" : 4,
+ "showLabels" : false
},
- "type" : "LinearBasicDisplay",
- "displayId" : "C_remanei_proteins-b_malayi_PRJNA10729-LinearBasicDisplay"
+ "displayId" : "C_remanei_proteins-b_malayi_PRJNA10729-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
+ "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "b_malayi_PRJNA10729_C_remanei_proteins",
+ "name" : "C. remanei proteins",
"category" : [
"Sequence Similarity",
"Proteins"
@@ -1151,152 +849,156 @@
"assemblyNames" : [
"b_malayi_PRJNA10729"
],
- "trackId" : "b_malayi_PRJNA10729_C_remanei_proteins",
- "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/C. remanei proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "C. remanei proteins"
+ "type" : "FeatureTrack"
},
{
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "b_malayi_PRJNA10729"
+ ],
+ "category" : [
+ "Genes",
+ "Supporting Evidence"
+ ],
+ "name" : "Nanopore matches",
+ "trackId" : "b_malayi_PRJNA10729_nanopore_matches",
+ "description" : "This Nanopore transcript data is from the paper 'The full-length transcriptome of C. elegans using direct RNA sequencing' Roach et al. https://doi.org/10.1101/598763. Where several transcripts are nearly identical, they are represented by a single transcript and the number of transcripts is recorded in the read coverage. Sequencing is from 3' to 5' and randomly terminates, so the 5' end of transcripts is often incomplete.",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "nanopore_matches-b_malayi_PRJNA10729-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
"color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA'?'lightblue':'green'",
+ "height" : 4,
+ "showLabels" : false,
"maxHeight" : 5000,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "type" : "LinearBasicDisplay"
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "category" : [
- "Genes",
- "Supporting Evidence"
- ],
- "assemblyNames" : [
- "b_malayi_PRJNA10729"
- ],
- "trackId" : "b_malayi_PRJNA10729_nanopore_matches",
- "description" : "This Nanopore transcript data is from the paper 'The full-length transcriptome of C. elegans using direct RNA sequencing' Roach et al. https://doi.org/10.1101/598763. Where several transcripts are nearly identical, they are represented by a single transcript and the number of transcripts is recorded in the read coverage. Sequencing is from 3' to 5' and randomly terminates, so the 5' end of transcripts is often incomplete.",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Nanopore matches/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Nanopore matches/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
- },
- "name" : "Nanopore matches"
+ }
},
{
+ "description" : "Low-complexity regions identified by Dust.",
+ "trackId" : "b_malayi_PRJNA10729_low_complextity_region_(dust)",
+ "name" : "Low complextity region (Dust)",
+ "category" : [
+ "Genome Structure",
+ "Repeats"
+ ],
+ "assemblyNames" : [
+ "b_malayi_PRJNA10729"
+ ],
"type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "name" : "Low complextity region (Dust)",
- "description" : "Low-complexity regions identified by Dust.",
- "assemblyNames" : [
- "b_malayi_PRJNA10729"
- ],
- "category" : [
- "Genome Structure",
- "Repeats"
- ],
- "trackId" : "b_malayi_PRJNA10729_low_complextity_region_(dust)",
"displays" : [
{
- "displayId" : "low_complextity_region_(dust)-b_malayi_PRJNA10729-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "low_complextity_region_(dust)-b_malayi_PRJNA10729-LinearBasicDisplay",
"renderer" : {
+ "color1" : "bisque",
+ "showLabels" : false,
"height" : 4,
"showDescriptions" : false,
- "color1" : "bisque",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "type" : "SvgFeatureRenderer"
}
}
]
},
{
+ "category" : [
+ "Expression"
+ ],
+ "assemblyNames" : [
+ "b_malayi_PRJNA10729"
+ ],
+ "type" : "FeatureTrack",
"description" : "These boxes indicate alignments of short read sequences from all available RNASeq projects. The number of reads has been normalised by averaging over the number of libraries. The height of all boxes indicates the relative score of the feature.",
+ "trackId" : "b_malayi_PRJNA10729_rnaseq",
"name" : "RNASeq",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/RNASeq/{refseq}/trackData.jsonz"
- }
- },
- "type" : "FeatureTrack",
"displays" : [
{
"displayId" : "rnaseq-b_malayi_PRJNA10729-LinearBasicDisplay",
+ "mouseover" : "jexl:'Score: '+get(feature,'score')",
"renderer" : {
- "displayMode" : "collapse",
- "showDescriptions" : false,
+ "color1" : "black",
"height" : "jexl:get(feature,'score')>100?50:floor(get(feature,'score')/2)>4?floor(get(feature,'score')/2):4",
- "type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
"showLabels" : false,
- "color1" : "black"
+ "displayMode" : "collapse",
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:'Score: '+get(feature,'score')",
"type" : "LinearBasicDisplay"
}
],
- "trackId" : "b_malayi_PRJNA10729_rnaseq",
- "category" : [
- "Expression"
- ],
- "assemblyNames" : [
- "b_malayi_PRJNA10729"
- ]
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/RNASeq/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/RNASeq Asymmetries/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "displayId" : "rnaseq_asymmetries-b_malayi_PRJNA10729-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "rnaseq_asymmetries-b_malayi_PRJNA10729-LinearBasicDisplay",
+ "mouseover" : "jexl:'Score: '+get(feature,'score')",
"renderer" : {
- "displayMode" : "collapse",
+ "color1" : "jexl:get(feature,'source')=='RNASeq_R_asymmetry'?'red': get(feature,'source')=='RNASeq_F_asymmetry'?'green':'black'",
"height" : 24,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "jexl:get(feature,'source')=='RNASeq_R_asymmetry'?'red': get(feature,'source')=='RNASeq_F_asymmetry'?'green':'black'"
- },
- "mouseover" : "jexl:'Score: '+get(feature,'score')"
+ "displayMode" : "collapse",
+ "type" : "SvgFeatureRenderer"
+ }
}
],
+ "description" : "Red boxes indicate regions where there are more than 2 times as many forward sense RNASeq reads aligned to the genome as reverse sense reads. This asymmetrical signal has been found empirically to be a sensitive marker for the ends of transcripts. Green boxes indicate regions where there are more than 2 times as many reverse sense RNASeq reads aligned to the genome as forward sense reads. This asymmetrical signal has been found empirically to be sensitive marker for the ends of transcripts. The height of all boxes indicates the relative score of the feature.",
+ "name" : "RNASeq Asymmetries",
"trackId" : "b_malayi_PRJNA10729_rnaseq_asymmetries",
"category" : [
"Expression"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"b_malayi_PRJNA10729"
- ],
- "description" : "Red boxes indicate regions where there are more than 2 times as many forward sense RNASeq reads aligned to the genome as reverse sense reads. This asymmetrical signal has been found empirically to be a sensitive marker for the ends of transcripts. Green boxes indicate regions where there are more than 2 times as many reverse sense RNASeq reads aligned to the genome as forward sense reads. This asymmetrical signal has been found empirically to be sensitive marker for the ends of transcripts. The height of all boxes indicates the relative score of the feature.",
- "name" : "RNASeq Asymmetries",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/RNASeq Asymmetries/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- }
+ ]
},
{
+ "displays" : [
+ {
+ "displayId" : "contig_submissions-b_malayi_PRJNA10729-LinearBasicDisplay",
+ "renderer" : {
+ "height" : 7,
+ "color1" : "sienna",
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"adapter" : {
"rootUrlTemplate" : {
"locationType" : "UriLocation",
@@ -1304,36 +1006,19 @@
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "name" : "Contig submissions",
- "description" : "This track shows the location and coordinates of contigs (mostly cosmids) submitted to GenBank/EMBL.",
"assemblyNames" : [
"b_malayi_PRJNA10729"
],
+ "type" : "FeatureTrack",
"category" : [
"Genome Structure",
"Assembly & Curation"
],
"trackId" : "b_malayi_PRJNA10729_contig_submissions",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
- "displays" : [
- {
- "displayId" : "contig_submissions-b_malayi_PRJNA10729-LinearBasicDisplay",
- "renderer" : {
- "height" : 7,
- "color1" : "sienna",
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay"
- }
- ]
+ "name" : "Contig submissions",
+ "description" : "This track shows the location and coordinates of contigs (mostly cosmids) submitted to GenBank/EMBL."
},
{
- "description" : "Matches to WormBase T. muris proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "T. muris proteins",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/T. muris proteins/{refseq}/trackData.jsonz",
@@ -1343,172 +1028,185 @@
},
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "T_muris_proteins-b_malayi_PRJNA10729-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "orange",
+ "showLabels" : false,
"height" : 4
},
"mouseover" : "jexl:get(feature,'clone')",
- "displayId" : "T_muris_proteins-b_malayi_PRJNA10729-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
+ "name" : "T. muris proteins",
"trackId" : "b_malayi_PRJNA10729_T_muris_proteins",
+ "description" : "Matches to WormBase T. muris proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "b_malayi_PRJNA10729"
+ ],
"category" : [
"Sequence Similarity",
"Proteins"
- ],
- "assemblyNames" : [
- "b_malayi_PRJNA10729"
]
},
{
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Collapsed IsoSeq structures/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA_BEST'?'lightblue':'green'",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
+ "showDescriptions" : false,
"height" : 4,
- "showDescriptions" : false
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "collapsed_isoseq_structures-b_malayi_PRJNA10729-LinearBasicDisplay"
+ "displayId" : "collapsed_isoseq_structures-b_malayi_PRJNA10729-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
+ "description" : "Aligned and filtered full-length non-chimeric IsoSeq reads with similar alignments collapsed into one representative structure.",
+ "name" : "Collapsed IsoSeq structures",
"trackId" : "b_malayi_PRJNA10729_collapsed_isoseq_structures",
- "assemblyNames" : [
- "b_malayi_PRJNA10729"
- ],
"category" : [
"Genes",
"Supporting Evidence"
],
- "description" : "Aligned and filtered full-length non-chimeric IsoSeq reads with similar alignments collapsed into one representative structure.",
- "name" : "Collapsed IsoSeq structures",
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Collapsed IsoSeq structures/{refseq}/trackData.jsonz"
- }
- }
- },
- {
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
"assemblyNames" : [
"b_malayi_PRJNA10729"
- ],
- "trackId" : "b_malayi_PRJNA10729_S_cerevisiae_proteins",
+ ]
+ },
+ {
"displays" : [
{
- "displayId" : "S_cerevisiae_proteins-b_malayi_PRJNA10729-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
"color1" : "orange",
+ "height" : 4,
"showLabels" : false,
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "S_cerevisiae_proteins-b_malayi_PRJNA10729-LinearBasicDisplay"
}
],
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
+ "assemblyNames" : [
+ "b_malayi_PRJNA10729"
+ ],
"type" : "FeatureTrack",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "trackId" : "b_malayi_PRJNA10729_S_cerevisiae_proteins",
"name" : "S. cerevisiae proteins",
"description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
},
{
- "name" : "Mass spec peptides",
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "mass_spec_peptides-b_malayi_PRJNA10729-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "red",
+ "height" : 7
+ }
+ }
+ ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Mass spec peptides/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ }
},
+ "category" : [
+ "Sequence Features",
+ "Translated Features"
+ ],
+ "assemblyNames" : [
+ "b_malayi_PRJNA10729"
+ ],
+ "type" : "FeatureTrack",
"description" : "This track shows peptides identified in mass spec proteomics experiments.",
"trackId" : "b_malayi_PRJNA10729_mass_spec_peptides",
+ "name" : "Mass spec peptides"
+ },
+ {
+ "trackId" : "wormbase_nematode_mrnas/ests_(best)-b_malayi_PRJNA10729",
+ "name" : "WormBase nematode mRNAs/ESTs (best)",
+ "description" : "ESTs and mRNAs from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each cDNA sequence. mRNAs are shown in light blue; ESTs in green.",
"assemblyNames" : [
"b_malayi_PRJNA10729"
],
+ "type" : "FeatureTrack",
"category" : [
- "Sequence Features",
- "Translated Features"
+ "Sequence Similarity",
+ "Nucleotide"
],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/WormBase nematode mRNAs_ESTs (best)/{refseq}/trackData.jsonz"
+ }
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "wormbase_nematode_mrnas/ests_(best)-b_malayi_PRJNA10729-LinearBasicDisplay",
"renderer" : {
- "color1" : "red",
"type" : "SvgFeatureRenderer",
- "height" : 7
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "mass_spec_peptides-b_malayi_PRJNA10729-LinearBasicDisplay"
+ "height" : 4,
+ "labels" : {
+ "name" : "jexl:get(feature,'species') || get(feature,'id')"
+ },
+ "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA_BEST'?'lightblue':get(feature,'source')=='BLAT_Caen_EST_BEST'?'green':'black'"
+ }
}
- ],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- }
+ ]
},
{
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 4,
- "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA_BEST'?'lightblue':get(feature,'source')=='BLAT_Caen_EST_BEST'?'green':'black'",
- "labels" : {
- "name" : "jexl:get(feature,'species') || get(feature,'id')"
- },
- "type" : "SvgFeatureRenderer"
+ "color1" : "black"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "wormbase_nematode_mrnas/ests_(best)-b_malayi_PRJNA10729-LinearBasicDisplay"
+ "displayId" : "links_and_superlinks-b_malayi_PRJNA10729-LinearBasicDisplay"
}
],
- "trackId" : "wormbase_nematode_mrnas/ests_(best)-b_malayi_PRJNA10729",
- "category" : [
- "Sequence Similarity",
- "Nucleotide"
- ],
- "assemblyNames" : [
- "b_malayi_PRJNA10729"
- ],
- "description" : "ESTs and mRNAs from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each cDNA sequence. mRNAs are shown in light blue; ESTs in green.",
- "name" : "WormBase nematode mRNAs/ESTs (best)",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/WormBase nematode mRNAs_ESTs (best)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- }
- },
- {
- "name" : "Links and Superlinks",
- "type" : "FeatureTrack",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Links and Superlinks/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Links and Superlinks/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
},
- "description" : "This track shows the location and coordinates of contigs created during the assembly of the C. elegans genome.",
- "trackId" : "b_malayi_PRJNA10729_links_and_superlinks",
"category" : [
"Genome Structure",
"Assembly & Curation"
@@ -1516,23 +1214,23 @@
"assemblyNames" : [
"b_malayi_PRJNA10729"
],
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "height" : 4,
- "color1" : "black",
- "type" : "SvgFeatureRenderer"
- },
- "displayId" : "links_and_superlinks-b_malayi_PRJNA10729-LinearBasicDisplay"
- }
- ],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- }
+ "type" : "FeatureTrack",
+ "description" : "This track shows the location and coordinates of contigs created during the assembly of the C. elegans genome.",
+ "trackId" : "b_malayi_PRJNA10729_links_and_superlinks",
+ "name" : "Links and Superlinks"
},
{
+ "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "P. pacificus proteins",
+ "trackId" : "b_malayi_PRJNA10729_P_pacificus_proteins",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "b_malayi_PRJNA10729"
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -1540,44 +1238,41 @@
"locationType" : "UriLocation"
}
},
- "name" : "P. pacificus proteins",
- "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "assemblyNames" : [
- "b_malayi_PRJNA10729"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "trackId" : "b_malayi_PRJNA10729_P_pacificus_proteins",
"displays" : [
{
- "displayId" : "P_pacificus_proteins-b_malayi_PRJNA10729-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 4,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "orange"
},
- "mouseover" : "jexl:get(feature,'clone')"
+ "displayId" : "P_pacificus_proteins-b_malayi_PRJNA10729-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
]
},
{
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "color1" : "orange",
+ "height" : 4,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 4
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
"displayId" : "H_sapiens_proteins-b_malayi_PRJNA10729-LinearBasicDisplay"
}
],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/H. sapiens proteins/{refseq}/trackData.jsonz"
+ }
+ },
"category" : [
"Sequence Similarity",
"Proteins"
@@ -1585,117 +1280,121 @@
"assemblyNames" : [
"b_malayi_PRJNA10729"
],
- "trackId" : "b_malayi_PRJNA10729_H_sapiens_proteins",
- "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/H. sapiens proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
+ "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "b_malayi_PRJNA10729_H_sapiens_proteins",
"name" : "H. sapiens proteins"
},
{
- "description" : "IsoSeq from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each IsoSeqsequence.",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Non-C. elegans Isoseq collection (best)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "Non-C. elegans Isoseq collection (best)",
"displays" : [
{
- "displayId" : "non-c._elegans_isoseq_collection_(best)-b_malayi_PRJNA10729-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"color1" : "green",
"height" : 4
- }
+ },
+ "displayId" : "non-c._elegans_isoseq_collection_(best)-b_malayi_PRJNA10729-LinearBasicDisplay"
}
],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Non-C. elegans Isoseq collection (best)/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"category" : [
"Sequence Similarity",
"Nucleotide"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"b_malayi_PRJNA10729"
],
+ "description" : "IsoSeq from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each IsoSeqsequence.",
+ "name" : "Non-C. elegans Isoseq collection (best)",
"trackId" : "non-c._elegans_isoseq_collection_(best)-b_malayi_PRJNA10729"
},
{
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/C. brenneri proteins/{refseq}/trackData.jsonz"
- }
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/C. brenneri proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
},
- "name" : "C. brenneri proteins",
- "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "b_malayi_PRJNA10729"
- ],
- "trackId" : "b_malayi_PRJNA10729_C_brenneri_proteins",
"displays" : [
{
- "displayId" : "C_brenneri_proteins-b_malayi_PRJNA10729-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
+ "showLabels" : false,
+ "height" : 4,
"color1" : "orange"
},
- "mouseover" : "jexl:get(feature,'clone')"
+ "displayId" : "C_brenneri_proteins-b_malayi_PRJNA10729-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
+ ],
+ "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "C. brenneri proteins",
+ "trackId" : "b_malayi_PRJNA10729_C_brenneri_proteins",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "b_malayi_PRJNA10729"
]
},
{
+ "assemblyNames" : [
+ "b_malayi_PRJNA10729"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "trackId" : "b_malayi_PRJNA10729_D_melanogaster_proteins",
+ "name" : "D. melanogaster proteins",
+ "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
+ "height" : 4,
"color1" : "orange",
- "height" : 4
+ "type" : "SvgFeatureRenderer"
},
"mouseover" : "jexl:get(feature,'clone')",
"displayId" : "D_melanogaster_proteins-b_malayi_PRJNA10729-LinearBasicDisplay"
}
],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "b_malayi_PRJNA10729"
- ],
- "trackId" : "b_malayi_PRJNA10729_D_melanogaster_proteins",
- "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"adapter" : {
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "D. melanogaster proteins"
+ }
},
{
- "name" : "Tandem and Inverted Repeats",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "color1" : "bisque",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "tandem_and_inverted_repeats-b_malayi_PRJNA10729-LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -1703,40 +1402,39 @@
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "description" : "Exact tandem and inverted repetitive elements.",
- "trackId" : "b_malayi_PRJNA10729_tandem_and_inverted_repeats",
"category" : [
"Genome Structure",
"Repeats"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"b_malayi_PRJNA10729"
],
+ "description" : "Exact tandem and inverted repetitive elements.",
+ "name" : "Tandem and Inverted Repeats",
+ "trackId" : "b_malayi_PRJNA10729_tandem_and_inverted_repeats"
+ },
+ {
"displays" : [
{
- "displayId" : "tandem_and_inverted_repeats-b_malayi_PRJNA10729-LinearBasicDisplay",
+ "displayId" : "trinity-assembled_rnaseq-b_malayi_PRJNA10729-LinearBasicDisplay",
"renderer" : {
- "color1" : "bisque",
- "type" : "SvgFeatureRenderer",
+ "color1" : "mediumpurple",
"showLabels" : false,
- "showDescriptions" : false
+ "height" : 5,
+ "type" : "SvgFeatureRenderer"
},
"type" : "LinearBasicDisplay"
}
- ]
- },
- {
- "type" : "FeatureTrack",
+ ],
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Trinity-assembled RNAseq/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/Trinity-assembled RNAseq/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
},
- "name" : "Trinity-assembled RNAseq",
- "description" : "Native (same species) RNAseq data was assembled with Trinity and then aligned to the genome with BLAT",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"b_malayi_PRJNA10729"
],
@@ -1744,94 +1442,118 @@
"Genes",
"Supporting Evidence"
],
+ "name" : "Trinity-assembled RNAseq",
"trackId" : "b_malayi_PRJNA10729_trinity-assembled_rnaseq",
+ "description" : "Native (same species) RNAseq data was assembled with Trinity and then aligned to the genome with BLAT"
+ },
+ {
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
+ "name" : "Cas12e TTCN PAM sites",
+ "trackId" : "b_malayi_PRJNA10729_TTCN_sequence_search",
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "b_malayi_PRJNA10729"
+ ],
+ "adapter" : {
+ "search" : "TTC.",
+ "type" : "SequenceSearchAdapter",
+ "sequenceAdapter" : {
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/b_malayi.PRJNA10729.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
+ },
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/b_malayi.PRJNA10729.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
+ },
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/b_malayi.PRJNA10729.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BgzipFastaAdapter"
+ }
+ },
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 5,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "mediumpurple"
+ "showDescriptions" : false,
+ "height" : 4,
+ "color1" : "SlateBlue",
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "trinity-assembled_rnaseq-b_malayi_PRJNA10729-LinearBasicDisplay"
+ "displayId" : "TTCN_sequence_search_b_malayi_PRJNA10729-LinearBasicDisplay"
}
]
},
{
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
- "name" : "Cas12e TTCN PAM sites",
"adapter" : {
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
"type" : "BgzipFastaAdapter",
"gziLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/b_malayi.PRJNA10729.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
},
- "faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/b_malayi.PRJNA10729.WS284.genomic.fa.gz.fai"
- },
"fastaLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/b_malayi.PRJNA10729.WS284.genomic.fa.gz"
+ },
+ "faiLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/b_malayi.PRJNA10729.WS284.genomic.fa.gz.fai"
}
},
- "search" : "TTC.",
- "type" : "SequenceSearchAdapter"
+ "search" : "TT."
},
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "TTCN_sequence_search_b_malayi_PRJNA10729-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showLabels" : false,
"height" : 4,
"showDescriptions" : false,
- "color1" : "SlateBlue",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "color1" : "Indigo"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "TTN_sequence_search_b_malayi_PRJNA10729-LinearBasicDisplay"
}
],
- "trackId" : "b_malayi_PRJNA10729_TTCN_sequence_search",
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
+ "name" : "Cas12a TTN PAM sites",
+ "trackId" : "b_malayi_PRJNA10729_TTN_sequence_search",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"b_malayi_PRJNA10729"
]
},
{
- "assemblyNames" : [
- "b_malayi_PRJNA10729"
- ],
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
+ "trackId" : "b_malayi_PRJNA10729_NNGRRT_sequence_search",
+ "name" : "SaCas9 NNGRRT PAM sites",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "trackId" : "b_malayi_PRJNA10729_TTN_sequence_search",
- "displays" : [
- {
- "displayId" : "TTN_sequence_search_b_malayi_PRJNA10729-LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "Indigo",
- "showDescriptions" : false,
- "height" : 4
- },
- "type" : "LinearBasicDisplay"
- }
+ "assemblyNames" : [
+ "b_malayi_PRJNA10729"
],
+ "type" : "FeatureTrack",
"adapter" : {
- "search" : "TT.",
"sequenceAdapter" : {
"type" : "BgzipFastaAdapter",
"gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/b_malayi.PRJNA10729.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/b_malayi.PRJNA10729.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
},
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/b_malayi.PRJNA10729.WS284.genomic.fa.gz",
@@ -1842,80 +1564,24 @@
"locationType" : "UriLocation"
}
},
- "type" : "SequenceSearchAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "Cas12a TTN PAM sites",
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time."
- },
- {
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
- "adapter" : {
- "sequenceAdapter" : {
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/b_malayi.PRJNA10729.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
- },
- "faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/b_malayi.PRJNA10729.WS284.genomic.fa.gz.fai"
- },
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/b_malayi.PRJNA10729.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
- },
- "type" : "BgzipFastaAdapter"
- },
- "search" : "..G[AG][AG]T",
- "type" : "SequenceSearchAdapter"
+ "type" : "SequenceSearchAdapter",
+ "search" : "..G[AG][AG]T"
},
- "type" : "FeatureTrack",
- "name" : "SaCas9 NNGRRT PAM sites",
"displays" : [
{
"displayId" : "NNGRRT_sequence_search_b_malayi_PRJNA10729-LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showLabels" : false,
"height" : 4,
"showDescriptions" : false,
- "color1" : "DarkViolet",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "color1" : "DarkViolet"
},
"type" : "LinearBasicDisplay"
}
- ],
- "assemblyNames" : [
- "b_malayi_PRJNA10729"
- ],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "trackId" : "b_malayi_PRJNA10729_NNGRRT_sequence_search"
+ ]
},
{
- "trackId" : "b_malayi_PRJNA10729_NGG_sequence_search",
- "assemblyNames" : [
- "b_malayi_PRJNA10729"
- ],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "displays" : [
- {
- "displayId" : "NGG_sequence_search_b_malayi_PRJNA10729-LinearBasicDisplay",
- "renderer" : {
- "height" : 4,
- "showDescriptions" : false,
- "color1" : "RebeccaPurple",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay"
- }
- ],
- "name" : "SpCas9 NGG PAM sites",
"adapter" : {
"sequenceAdapter" : {
"type" : "BgzipFastaAdapter",
@@ -1932,148 +1598,88 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/b_malayi.PRJNA10729.WS284.genomic.fa.gz.fai"
}
},
- "search" : ".GG",
- "type" : "SequenceSearchAdapter"
+ "type" : "SequenceSearchAdapter",
+ "search" : ".GG"
},
- "type" : "FeatureTrack",
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time."
- },
- {
- "trackId" : "b_malayi_PRJNA10729_rnaseq_introns",
- "category" : [
- "Expression"
- ],
- "assemblyNames" : [
- "b_malayi_PRJNA10729"
- ],
"displays" : [
{
- "displayId" : "rnaseq_introns-b_malayi_PRJNA10729-LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "green"
+ "showLabels" : false,
+ "height" : 4,
+ "showDescriptions" : false,
+ "color1" : "RebeccaPurple"
},
- "mouseover" : "jexl:get(feature,'score')+' reads'",
+ "displayId" : "NGG_sequence_search_b_malayi_PRJNA10729-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
- "name" : "RNASeq introns",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/RNASeq introns/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display."
- },
- {
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/RNASeq Splice Junctions (common)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "name" : "RNASeq Splice Junctions (common)",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
- "category" : [
- "Expression"
- ],
+ "trackId" : "b_malayi_PRJNA10729_NGG_sequence_search",
+ "name" : "SpCas9 NGG PAM sites",
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
"assemblyNames" : [
"b_malayi_PRJNA10729"
],
- "trackId" : "b_malayi_PRJNA10729_rnaseq_splice_junctions_(common)",
- "displays" : [
- {
- "mouseover" : "jexl:get(feature,'score')+' reads'",
- "renderer" : {
- "showDescriptions" : false,
- "color1" : "jexl:get(feature,'score')>1000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/1000))))+'00'+hex(round(255-(140*(get(feature,'score')/1000)))):'#00'+hex(round(255-(140*(get(feature,'score')/1000))))+hex(round(255-(140*(get(feature,'score')/1000))))",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "rnaseq_splice_junctions_(common)-b_malayi_PRJNA10729-LinearBasicDisplay"
- }
+ "type" : "FeatureTrack",
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
]
},
{
- "name" : "RNASeq Splice Junctions (rare)",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
+ "name" : "Curated Genes (protein coding)",
+ "trackId" : "c_angaria_PRJNA51225_curated_genes_protein_coding",
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
"type" : "FeatureTrack",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
- "trackId" : "b_malayi_PRJNA10729_rnaseq_splice_junctions_(rare)",
"assemblyNames" : [
- "b_malayi_PRJNA10729"
+ "c_angaria_PRJNA51225"
],
"category" : [
- "Expression"
+ "Genes",
+ "Curated Genes"
],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_angaria_PRJNA51225/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "displayId" : "rnaseq_splice_junctions_(rare)-b_malayi_PRJNA10729-LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'score')+' reads'",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "jexl:get(feature,'score')>1000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/1000))))+'00'+hex(round(255-(140*(get(feature,'score')/1000)))):'#00'+hex(round(255-(140*(get(feature,'score')/1000))))+hex(round(255-(140*(get(feature,'score')/1000))))",
"maxHeight" : 5000,
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "height" : "jexl:4",
- "showDescriptions" : false
+ "color3" : "#965567",
+ "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "curated_genes_(protein_coding)-c_angaria_PRJNA51225-LinearBasicDisplay"
}
- ]
+ ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ }
},
{
- "trackId" : "c_angaria_PRJNA51225_curated_genes_protein_coding",
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "assemblyNames" : [
- "c_angaria_PRJNA51225"
- ],
+ "formatDetails" : {
+ "feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
+ },
"displays" : [
{
- "displayId" : "curated_genes_(protein_coding)-c_angaria_PRJNA51225-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
"color3" : "#965567",
+ "type" : "SvgFeatureRenderer",
"maxHeight" : 5000,
- "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
- "type" : "SvgFeatureRenderer"
- }
+ "labels" : {
+ "name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
+ },
+ "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'"
+ },
+ "displayId" : "curated_genes-c_angaria_PRJNA51225-LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
- "name" : "Curated Genes (protein coding)",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_angaria_PRJNA51225/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track."
- },
- {
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
"locationType" : "UriLocation",
@@ -2081,37 +1687,29 @@
},
"type" : "NCListAdapter"
},
- "name" : "Curated Genes",
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_angaria_PRJNA51225"
+ ],
"category" : [
"Genes",
"Curated Genes"
],
- "assemblyNames" : [
- "c_angaria_PRJNA51225"
- ],
+ "name" : "Curated Genes",
"trackId" : "c_angaria_PRJNA51225_curated_genes",
- "formatDetails" : {
- "feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
- },
- "displays" : [
- {
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "labels" : {
- "name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
- },
- "maxHeight" : 5000,
- "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
- "color3" : "#965567"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "curated_genes-c_angaria_PRJNA51225-LinearBasicDisplay"
- }
- ]
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes."
},
{
+ "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_angaria_PRJNA51225_D_melanogaster_proteins",
"name" : "D. melanogaster proteins",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "assemblyNames" : [
+ "c_angaria_PRJNA51225"
+ ],
"type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
@@ -2120,64 +1718,64 @@
},
"type" : "NCListAdapter"
},
- "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "trackId" : "c_angaria_PRJNA51225_D_melanogaster_proteins",
- "assemblyNames" : [
- "c_angaria_PRJNA51225"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "D_melanogaster_proteins-c_angaria_PRJNA51225-LinearBasicDisplay",
"renderer" : {
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
+ "height" : 4,
"color1" : "orange",
- "height" : 4
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')",
- "displayId" : "D_melanogaster_proteins-c_angaria_PRJNA51225-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')"
}
]
},
{
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "S_cerevisiae_proteins-c_angaria_PRJNA51225-LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
"showLabels" : false,
- "height" : 4
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "S_cerevisiae_proteins-c_angaria_PRJNA51225-LinearBasicDisplay"
+ "height" : 4,
+ "color1" : "orange"
+ }
}
],
- "trackId" : "c_angaria_PRJNA51225_S_cerevisiae_proteins",
- "assemblyNames" : [
- "c_angaria_PRJNA51225"
- ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_angaria_PRJNA51225/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_angaria_PRJNA51225"
+ ],
"description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"name" : "S. cerevisiae proteins",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_angaria_PRJNA51225/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- }
+ "trackId" : "c_angaria_PRJNA51225_S_cerevisiae_proteins"
},
{
"description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_angaria_PRJNA51225_C_japonica_proteins",
+ "name" : "C. japonica proteins",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "assemblyNames" : [
+ "c_angaria_PRJNA51225"
+ ],
"type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
@@ -2186,360 +1784,350 @@
},
"type" : "NCListAdapter"
},
- "name" : "C. japonica proteins",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "C_japonica_proteins-c_angaria_PRJNA51225-LinearBasicDisplay",
"renderer" : {
+ "height" : 4,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "orange",
- "height" : 4
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')",
- "displayId" : "C_japonica_proteins-c_angaria_PRJNA51225-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')"
}
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
+ ]
+ },
+ {
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_angaria_PRJNA51225"
],
- "trackId" : "c_angaria_PRJNA51225_C_japonica_proteins"
- },
- {
"category" : [
"Genome Structure",
"Repeats"
],
- "assemblyNames" : [
- "c_angaria_PRJNA51225"
- ],
+ "name" : "Low complextity region (Dust)",
"trackId" : "c_angaria_PRJNA51225_low_complextity_region_(dust)",
+ "description" : "Low-complexity regions identified by Dust.",
"displays" : [
{
- "displayId" : "low_complextity_region_(dust)-c_angaria_PRJNA51225-LinearBasicDisplay",
"renderer" : {
- "color1" : "bisque",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
+ "color1" : "bisque",
"height" : 4,
- "showDescriptions" : false
+ "showDescriptions" : false,
+ "showLabels" : false
},
+ "displayId" : "low_complextity_region_(dust)-c_angaria_PRJNA51225-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_angaria_PRJNA51225/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "Low complextity region (Dust)",
- "description" : "Low-complexity regions identified by Dust."
+ }
+ }
},
{
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_angaria_PRJNA51225/tracks/C. remanei proteins/{refseq}/trackData.jsonz"
+ }
+ },
"displays" : [
{
- "displayId" : "C_remanei_proteins-c_angaria_PRJNA51225-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
"color1" : "orange",
- "height" : 4
+ "height" : 4,
+ "showLabels" : false
},
"mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay"
+ "displayId" : "C_remanei_proteins-c_angaria_PRJNA51225-LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_angaria_PRJNA51225"
- ],
+ "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "C. remanei proteins",
+ "trackId" : "c_angaria_PRJNA51225_C_remanei_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "trackId" : "c_angaria_PRJNA51225_C_remanei_proteins",
- "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_angaria_PRJNA51225"
+ ]
+ },
+ {
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_angaria_PRJNA51225/tracks/C. remanei proteins/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_angaria_PRJNA51225/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ }
},
- "type" : "FeatureTrack",
- "name" : "C. remanei proteins"
- },
- {
"displays" : [
{
- "displayId" : "repeat_region_(repeatmasker)-c_angaria_PRJNA51225-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "bisque",
"showDescriptions" : false,
- "height" : 4
+ "height" : 4,
+ "color1" : "bisque",
+ "type" : "SvgFeatureRenderer"
},
+ "displayId" : "repeat_region_(repeatmasker)-c_angaria_PRJNA51225-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
+ "name" : "Repeat Region (RepeatMasker)",
"trackId" : "c_angaria_PRJNA51225_repeat_region_(repeatmasker)",
- "category" : [
- "Genome Structure",
- "Repeats"
- ],
+ "description" : "Repetitive regions identified by RepeatMasker.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_angaria_PRJNA51225"
],
- "description" : "Repetitive regions identified by RepeatMasker.",
- "name" : "Repeat Region (RepeatMasker)",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_angaria_PRJNA51225/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack"
+ "category" : [
+ "Genome Structure",
+ "Repeats"
+ ]
},
{
- "description" : "cDNAs from this species from INSDC that have been aligned to the genome using STAR.",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/$ASEMBLY/tracks/INSDC nematode cDNAs/{refseq}/trackData.jsonz"
- }
- },
- "name" : "INSDC nematode cDNAs",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 4,
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "grey"
+ "color1" : "grey",
+ "height" : 4,
+ "showDescriptions" : false,
+ "showLabels" : false
},
"displayId" : "$ASEMBLY_insdc_nematode_cdnas-LinearBasicDisplay"
}
],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/$ASEMBLY/tracks/INSDC nematode cDNAs/{refseq}/trackData.jsonz"
+ }
+ },
"category" : [
"Sequence Similarity",
"Nucleotide"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"$ASEMBLY"
],
+ "description" : "cDNAs from this species from INSDC that have been aligned to the genome using STAR.",
+ "name" : "INSDC nematode cDNAs",
"trackId" : "$ASEMBLY_insdc_nematode_cdnas"
},
{
"name" : "C. brenneri proteins",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_angaria_PRJNA51225/tracks/C. brenneri proteins/{refseq}/trackData.jsonz"
- }
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_angaria_PRJNA51225/tracks/C. brenneri proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"trackId" : "c_angaria_PRJNA51225_C_brenneri_proteins",
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
+ "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_angaria_PRJNA51225"
],
"displays" : [
{
- "displayId" : "C_brenneri_proteins-c_angaria_PRJNA51225-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
+ "type" : "SvgFeatureRenderer",
"color1" : "orange",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
- }
+ "height" : 4
+ },
+ "displayId" : "C_brenneri_proteins-c_angaria_PRJNA51225-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
+ ],
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
]
},
{
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_angaria_PRJNA51225"
+ ],
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "name" : "P. pacificus proteins",
+ "trackId" : "c_angaria_PRJNA51225_P_pacificus_proteins",
+ "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"displays" : [
{
- "mouseover" : "jexl:get(feature,'clone')",
+ "type" : "LinearBasicDisplay",
"renderer" : {
+ "showLabels" : false,
"height" : 4,
"color1" : "orange",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"displayId" : "P_pacificus_proteins-c_angaria_PRJNA51225-LinearBasicDisplay"
}
],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "c_angaria_PRJNA51225"
- ],
- "trackId" : "c_angaria_PRJNA51225_P_pacificus_proteins",
- "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_angaria_PRJNA51225/tracks/P. pacificus proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
},
"type" : "NCListAdapter"
- },
- "name" : "P. pacificus proteins"
+ }
},
{
- "displays" : [
- {
- "renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "bisque",
- "showDescriptions" : false
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "tandem_and_inverted_repeats-c_angaria_PRJNA51225-LinearBasicDisplay"
- }
- ],
"trackId" : "c_angaria_PRJNA51225_tandem_and_inverted_repeats",
+ "name" : "Tandem and Inverted Repeats",
+ "description" : "Exact tandem and inverted repetitive elements.",
"assemblyNames" : [
"c_angaria_PRJNA51225"
],
+ "type" : "FeatureTrack",
"category" : [
"Genome Structure",
"Repeats"
],
- "description" : "Exact tandem and inverted repetitive elements.",
- "name" : "Tandem and Inverted Repeats",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_angaria_PRJNA51225/tracks/Tandem and Inverted Repeats/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "NCListAdapter"
},
- "type" : "FeatureTrack"
- },
- {
- "trackId" : "c_angaria_PRJNA51225_H_sapiens_proteins",
- "assemblyNames" : [
- "c_angaria_PRJNA51225"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
"displays" : [
{
- "displayId" : "H_sapiens_proteins-c_angaria_PRJNA51225-LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "tandem_and_inverted_repeats-c_angaria_PRJNA51225-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "orange"
+ "showDescriptions" : false,
+ "color1" : "bisque",
+ "type" : "SvgFeatureRenderer"
},
"type" : "LinearBasicDisplay"
}
- ],
- "name" : "H. sapiens proteins",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_angaria_PRJNA51225/tracks/H. sapiens proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ ]
},
{
+ "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "H. sapiens proteins",
+ "trackId" : "c_angaria_PRJNA51225_H_sapiens_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_angaria_PRJNA51225"
],
- "trackId" : "c_angaria_PRJNA51225_other_uniprot_proteins",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_angaria_PRJNA51225/tracks/H. sapiens proteins/{refseq}/trackData.jsonz"
+ }
+ },
"displays" : [
{
- "displayId" : "other_uniprot_proteins-c_angaria_PRJNA51225-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
"height" : 4,
"showLabels" : false,
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
+ },
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "H_sapiens_proteins-c_angaria_PRJNA51225-LinearBasicDisplay"
+ }
+ ]
+ },
+ {
+ "displays" : [
+ {
+ "renderer" : {
"type" : "SvgFeatureRenderer",
- "color1" : "orange"
- }
+ "color1" : "orange",
+ "showDescriptions" : false,
+ "height" : 4,
+ "showLabels" : false
+ },
+ "displayId" : "other_uniprot_proteins-c_angaria_PRJNA51225-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_angaria_PRJNA51225/tracks/Other UniProt proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_angaria_PRJNA51225/tracks/Other UniProt proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
},
+ "assemblyNames" : [
+ "c_angaria_PRJNA51225"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "trackId" : "c_angaria_PRJNA51225_other_uniprot_proteins",
"name" : "Other UniProt proteins",
"description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation)."
},
{
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_angaria_PRJNA51225/tracks/C. elegans proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "name" : "C. elegans proteins",
- "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "assemblyNames" : [
- "c_angaria_PRJNA51225"
- ],
"category" : [
"Sequence Similarity",
"Proteins"
],
- "trackId" : "c_angaria_PRJNA51225_C_elegans_proteins",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_angaria_PRJNA51225"
+ ],
"displays" : [
{
- "displayId" : "C_elegans_proteins-c_angaria_PRJNA51225-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "orange",
- "height" : 4
+ "showLabels" : false,
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')"
+ "displayId" : "C_elegans_proteins-c_angaria_PRJNA51225-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "C. elegans proteins",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_angaria_PRJNA51225/tracks/C. elegans proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
+ "trackId" : "c_angaria_PRJNA51225_C_elegans_proteins"
},
{
- "trackId" : "c_angaria_PRJNA51225_C_briggsae_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
@@ -2547,147 +2135,138 @@
"assemblyNames" : [
"c_angaria_PRJNA51225"
],
+ "type" : "FeatureTrack",
+ "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_angaria_PRJNA51225_C_briggsae_proteins",
+ "name" : "C. briggsae proteins",
"displays" : [
{
"displayId" : "C_briggsae_proteins-c_angaria_PRJNA51225-LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "color1" : "orange",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 4
+ "height" : 4,
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
},
+ "mouseover" : "jexl:get(feature,'clone')",
"type" : "LinearBasicDisplay"
}
],
- "name" : "C. briggsae proteins",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_angaria_PRJNA51225/tracks/C. briggsae proteins/{refseq}/trackData.jsonz"
}
- },
- "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ }
},
{
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "SlateBlue",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
"height" : 4,
- "showDescriptions" : false
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "TTCN_sequence_search_c_angaria_PRJNA51225-LinearBasicDisplay"
+ "displayId" : "TTCN_sequence_search_c_angaria_PRJNA51225-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "assemblyNames" : [
- "c_angaria_PRJNA51225"
- ],
- "trackId" : "c_angaria_PRJNA51225_TTCN_sequence_search",
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
"adapter" : {
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
- "gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_angaria.PRJNA51225.WS284.genomic.fa.gz.gzi"
- },
"faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_angaria.PRJNA51225.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_angaria.PRJNA51225.WS284.genomic.fa.gz.fai"
},
"fastaLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_angaria.PRJNA51225.WS284.genomic.fa.gz"
+ },
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_angaria.PRJNA51225.WS284.genomic.fa.gz.gzi"
}
},
- "search" : "TTC.",
- "type" : "SequenceSearchAdapter"
+ "search" : "TTC."
},
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
+ "assemblyNames" : [
+ "c_angaria_PRJNA51225"
+ ],
"type" : "FeatureTrack",
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
+ "trackId" : "c_angaria_PRJNA51225_TTCN_sequence_search",
"name" : "Cas12e TTCN PAM sites"
},
{
+ "name" : "Cas12a TTN PAM sites",
"adapter" : {
"type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_angaria.PRJNA51225.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_angaria.PRJNA51225.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ },
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_angaria.PRJNA51225.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
},
"fastaLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_angaria.PRJNA51225.WS284.genomic.fa.gz"
- },
- "faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_angaria.PRJNA51225.WS284.genomic.fa.gz.fai"
- },
- "type" : "BgzipFastaAdapter"
+ }
},
"search" : "TT."
},
- "type" : "FeatureTrack",
- "name" : "Cas12a TTN PAM sites",
+ "trackId" : "c_angaria_PRJNA51225_TTN_sequence_search",
"description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_angaria_PRJNA51225"
],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "trackId" : "c_angaria_PRJNA51225_TTN_sequence_search",
"displays" : [
{
- "displayId" : "TTN_sequence_search_c_angaria_PRJNA51225-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "Indigo",
"type" : "SvgFeatureRenderer",
"showLabels" : false,
"height" : 4,
- "showDescriptions" : false
- }
+ "showDescriptions" : false,
+ "color1" : "Indigo"
+ },
+ "displayId" : "TTN_sequence_search_c_angaria_PRJNA51225-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
+ ],
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
]
},
{
"displays" : [
{
- "displayId" : "NNGRRT_sequence_search_c_angaria_PRJNA51225-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 4,
+ "showLabels" : false,
"showDescriptions" : false,
+ "height" : 4,
"color1" : "DarkViolet",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "NNGRRT_sequence_search_c_angaria_PRJNA51225-LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_angaria_PRJNA51225"
- ],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "trackId" : "c_angaria_PRJNA51225_NNGRRT_sequence_search",
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
"adapter" : {
"type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_angaria.PRJNA51225.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
@@ -2699,39 +2278,42 @@
"gziLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_angaria.PRJNA51225.WS284.genomic.fa.gz.gzi"
- }
+ },
+ "type" : "BgzipFastaAdapter"
},
"search" : "..G[AG][AG]T"
},
"type" : "FeatureTrack",
- "name" : "SaCas9 NNGRRT PAM sites"
+ "assemblyNames" : [
+ "c_angaria_PRJNA51225"
+ ],
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
+ "name" : "SaCas9 NNGRRT PAM sites",
+ "trackId" : "c_angaria_PRJNA51225_NNGRRT_sequence_search",
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time."
},
{
"trackId" : "c_angaria_PRJNA51225_NGG_sequence_search",
+ "name" : "SpCas9 NGG PAM sites",
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
"assemblyNames" : [
"c_angaria_PRJNA51225"
],
+ "type" : "FeatureTrack",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "RebeccaPurple",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 4,
- "showDescriptions" : false
- },
- "displayId" : "NGG_sequence_search_c_angaria_PRJNA51225-LinearBasicDisplay"
- }
- ],
- "name" : "SpCas9 NGG PAM sites",
"adapter" : {
"search" : ".GG",
"sequenceAdapter" : {
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_angaria.PRJNA51225.WS284.genomic.fa.gz.gzi"
+ },
"type" : "BgzipFastaAdapter",
"fastaLocation" : {
"locationType" : "UriLocation",
@@ -2740,48 +2322,55 @@
"faiLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_angaria.PRJNA51225.WS284.genomic.fa.gz.fai"
- },
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_angaria.PRJNA51225.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
}
},
"type" : "SequenceSearchAdapter"
},
- "type" : "FeatureTrack",
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time."
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "height" : 4,
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "color1" : "RebeccaPurple"
+ },
+ "displayId" : "NGG_sequence_search_c_angaria_PRJNA51225-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
- "name" : "Curated Genes",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_becei_PRJEB28243/tracks/Curated_Genes/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
"description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
+ "name" : "Curated Genes",
"trackId" : "c_becei_PRJEB28243_curated_genes",
"category" : [
"Genes",
"Curated Genes"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_becei_PRJEB28243"
],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_becei_PRJEB28243/tracks/Curated_Genes/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "color3" : "#965567",
- "maxHeight" : 5000,
"color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
- "type" : "SvgFeatureRenderer",
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
- }
+ },
+ "color3" : "#965567",
+ "type" : "SvgFeatureRenderer",
+ "maxHeight" : 5000
},
- "type" : "LinearBasicDisplay",
"displayId" : "curated_genes-c_becei_PRJEB28243-LinearBasicDisplay"
}
],
@@ -2791,108 +2380,105 @@
},
{
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_becei_PRJEB28243/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ }
},
- "type" : "FeatureTrack",
- "name" : "Curated Genes (protein coding)",
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
- "assemblyNames" : [
- "c_becei_PRJEB28243"
- ],
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "trackId" : "c_becei_PRJEB28243_curated_genes_protein_coding",
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "curated_genes_(protein_coding)-c_becei_PRJEB28243-LinearBasicDisplay",
"renderer" : {
"maxHeight" : 5000,
- "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
"type" : "SvgFeatureRenderer",
- "color3" : "#965567"
- },
- "type" : "LinearBasicDisplay"
+ "color3" : "#965567",
+ "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'"
+ }
}
- ]
+ ],
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
+ "trackId" : "c_becei_PRJEB28243_curated_genes_protein_coding",
+ "name" : "Curated Genes (protein coding)",
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
+ "assemblyNames" : [
+ "c_becei_PRJEB28243"
+ ],
+ "type" : "FeatureTrack"
},
{
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_becei_PRJEB28243/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz"
+ }
+ },
"displays" : [
{
- "displayId" : "low_complextity_region_(dust)-c_becei_PRJEB28243-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "bisque",
+ "showLabels" : false,
"showDescriptions" : false,
- "height" : 4
- }
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "low_complextity_region_(dust)-c_becei_PRJEB28243-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
"trackId" : "c_becei_PRJEB28243_low_complextity_region_(dust)",
+ "name" : "Low complextity region (Dust)",
+ "description" : "Low-complexity regions identified by Dust.",
"assemblyNames" : [
"c_becei_PRJEB28243"
],
+ "type" : "FeatureTrack",
"category" : [
"Genome Structure",
"Repeats"
- ],
- "description" : "Low-complexity regions identified by Dust.",
- "name" : "Low complextity region (Dust)",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_becei_PRJEB28243/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- }
+ ]
},
{
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "displayId" : "TTCN_sequence_search_c_becei_PRJEB28243-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "SlateBlue",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 4
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
+ "search" : "TTC.",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
+ "fastaLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz"
},
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz",
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
- },
- "type" : "BgzipFastaAdapter"
- },
- "search" : "TTC.",
- "type" : "SequenceSearchAdapter"
- },
- "name" : "Cas12e TTCN PAM sites",
- "displays" : [
- {
- "renderer" : {
- "showDescriptions" : false,
- "height" : 4,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "SlateBlue"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "TTCN_sequence_search_c_becei_PRJEB28243-LinearBasicDisplay"
+ }
}
- ],
+ },
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
@@ -2900,9 +2486,13 @@
"assemblyNames" : [
"c_becei_PRJEB28243"
],
- "trackId" : "c_becei_PRJEB28243_TTCN_sequence_search"
+ "type" : "FeatureTrack",
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
+ "trackId" : "c_becei_PRJEB28243_TTCN_sequence_search",
+ "name" : "Cas12e TTCN PAM sites"
},
{
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_becei_PRJEB28243"
],
@@ -2910,152 +2500,159 @@
"Externally Sourced Resources",
"CRISPR predictions"
],
+ "name" : "Cas12a TTN PAM sites",
"trackId" : "c_becei_PRJEB28243_TTN_sequence_search",
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "TTN_sequence_search_c_becei_PRJEB28243-LinearBasicDisplay",
"renderer" : {
- "color1" : "Indigo",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
+ "showLabels" : false,
"height" : 4,
- "showDescriptions" : false
- },
- "type" : "LinearBasicDisplay"
+ "showDescriptions" : false,
+ "color1" : "Indigo"
+ }
}
],
- "type" : "FeatureTrack",
"adapter" : {
"type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz",
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
- "faiLocation" : {
+ "fastaLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz.fai"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz"
},
"gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz.gzi"
},
"type" : "BgzipFastaAdapter"
},
"search" : "TT."
- },
- "name" : "Cas12a TTN PAM sites",
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time."
+ }
},
{
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
+ "name" : "SaCas9 NNGRRT PAM sites",
"trackId" : "c_becei_PRJEB28243_NNGRRT_sequence_search",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_becei_PRJEB28243"
],
- "displays" : [
- {
- "displayId" : "NNGRRT_sequence_search_c_becei_PRJEB28243-LinearBasicDisplay",
- "renderer" : {
- "height" : 4,
- "showDescriptions" : false,
- "color1" : "DarkViolet",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "type" : "LinearBasicDisplay"
- }
- ],
- "name" : "SaCas9 NNGRRT PAM sites",
"adapter" : {
+ "search" : "..G[AG][AG]T",
"sequenceAdapter" : {
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
+ "faiLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz.fai"
},
"fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
},
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz.fai",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
},
"type" : "BgzipFastaAdapter"
},
- "search" : "..G[AG][AG]T",
"type" : "SequenceSearchAdapter"
},
- "type" : "FeatureTrack",
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time."
- },
- {
"displays" : [
{
- "displayId" : "NGG_sequence_search_c_becei_PRJEB28243-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "RebeccaPurple",
+ "height" : 4,
"showDescriptions" : false,
- "height" : 4
- }
+ "color1" : "DarkViolet",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "NNGRRT_sequence_search_c_becei_PRJEB28243-LinearBasicDisplay"
}
- ],
+ ]
+ },
+ {
+ "name" : "SpCas9 NGG PAM sites",
"trackId" : "c_becei_PRJEB28243_NGG_sequence_search",
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_becei_PRJEB28243"
+ ],
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "assemblyNames" : [
- "c_becei_PRJEB28243"
- ],
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
- "name" : "SpCas9 NGG PAM sites",
- "type" : "FeatureTrack",
"adapter" : {
"sequenceAdapter" : {
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz.gzi"
},
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
- },
- "type" : "BgzipFastaAdapter"
+ "faiLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz.fai"
+ }
},
- "search" : ".GG",
- "type" : "SequenceSearchAdapter"
- }
+ "type" : "SequenceSearchAdapter",
+ "search" : ".GG"
+ },
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "NGG_sequence_search_c_becei_PRJEB28243-LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "RebeccaPurple",
+ "showDescriptions" : false,
+ "height" : 4,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
+ }
+ }
+ ]
},
{
- "formatDetails" : {
- "feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
- },
"displays" : [
{
- "displayId" : "curated_genes-c_bovis_PRJEB34497-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "curated_genes-c_bovis_PRJEB34497-LinearBasicDisplay",
"renderer" : {
- "maxHeight" : 5000,
- "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
},
+ "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
"type" : "SvgFeatureRenderer",
+ "maxHeight" : 5000,
"color3" : "#965567"
}
}
],
+ "formatDetails" : {
+ "feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
+ },
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_bovis_PRJEB34497/tracks/Curated_Genes/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_bovis_PRJEB34497"
],
@@ -3063,17 +2660,9 @@
"Genes",
"Curated Genes"
],
+ "name" : "Curated Genes",
"trackId" : "c_bovis_PRJEB34497_curated_genes",
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_bovis_PRJEB34497/tracks/Curated_Genes/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "Curated Genes"
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes."
},
{
"category" : [
@@ -3083,117 +2672,173 @@
"assemblyNames" : [
"c_bovis_PRJEB34497"
],
+ "type" : "FeatureTrack",
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
"trackId" : "c_bovis_PRJEB34497_curated_genes_protein_coding",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
+ "name" : "Curated Genes (protein coding)",
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
"color3" : "#965567",
"type" : "SvgFeatureRenderer",
- "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
- "maxHeight" : 5000
+ "maxHeight" : 5000,
+ "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'"
},
- "displayId" : "curated_genes_(protein_coding)-c_bovis_PRJEB34497-LinearBasicDisplay"
+ "displayId" : "curated_genes_(protein_coding)-c_bovis_PRJEB34497-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_bovis_PRJEB34497/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz"
}
- },
- "name" : "Curated Genes (protein coding)",
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track."
+ }
},
{
+ "name" : "Low complextity region (Dust)",
+ "trackId" : "c_bovis_PRJEB34497_low_complextity_region_(dust)",
+ "description" : "Low-complexity regions identified by Dust.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_bovis_PRJEB34497"
+ ],
+ "category" : [
+ "Genome Structure",
+ "Repeats"
+ ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_bovis_PRJEB34497/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
"displayId" : "low_complextity_region_(dust)-c_bovis_PRJEB34497-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showLabels" : false,
"showDescriptions" : false,
"height" : 4,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "bisque"
- }
+ },
+ "type" : "LinearBasicDisplay"
}
+ ]
+ },
+ {
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
],
"assemblyNames" : [
"c_bovis_PRJEB34497"
],
- "category" : [
- "Genome Structure",
- "Repeats"
- ],
- "trackId" : "c_bovis_PRJEB34497_low_complextity_region_(dust)",
- "description" : "Low-complexity regions identified by Dust.",
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_bovis_PRJEB34497/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
+ "trackId" : "c_bovis_PRJEB34497_TTCN_sequence_search",
+ "name" : "Cas12e TTCN PAM sites",
+ "displays" : [
+ {
+ "renderer" : {
+ "showDescriptions" : false,
+ "height" : 4,
+ "showLabels" : false,
+ "color1" : "SlateBlue",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "TTCN_sequence_search_c_bovis_PRJEB34497-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- },
- "name" : "Low complextity region (Dust)"
- },
- {
- "type" : "FeatureTrack",
+ ],
"adapter" : {
- "type" : "SequenceSearchAdapter",
+ "search" : "TTC.",
"sequenceAdapter" : {
"type" : "BgzipFastaAdapter",
"gziLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_bovis.PRJEB34497.WS284.genomic.fa.gz.gzi"
},
- "fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_bovis.PRJEB34497.WS284.genomic.fa.gz"
- },
"faiLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_bovis.PRJEB34497.WS284.genomic.fa.gz.fai"
+ },
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_bovis.PRJEB34497.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
}
},
- "search" : "TTC."
- },
- "name" : "Cas12e TTCN PAM sites",
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
+ "type" : "SequenceSearchAdapter"
+ }
+ },
+ {
+ "trackId" : "c_bovis_PRJEB34497_TTN_sequence_search",
+ "name" : "Cas12a TTN PAM sites",
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
"assemblyNames" : [
"c_bovis_PRJEB34497"
],
+ "type" : "FeatureTrack",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "trackId" : "c_bovis_PRJEB34497_TTCN_sequence_search",
+ "adapter" : {
+ "search" : "TT.",
+ "type" : "SequenceSearchAdapter",
+ "sequenceAdapter" : {
+ "fastaLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_bovis.PRJEB34497.WS284.genomic.fa.gz"
+ },
+ "faiLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_bovis.PRJEB34497.WS284.genomic.fa.gz.fai"
+ },
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_bovis.PRJEB34497.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BgzipFastaAdapter"
+ }
+ },
"displays" : [
{
- "displayId" : "TTCN_sequence_search_c_bovis_PRJEB34497-LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 4,
"showDescriptions" : false,
- "color1" : "SlateBlue",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "color1" : "Indigo"
},
+ "displayId" : "TTN_sequence_search_c_bovis_PRJEB34497-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
]
},
{
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
- "name" : "Cas12a TTN PAM sites",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 4,
+ "color1" : "DarkViolet",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "NNGRRT_sequence_search_c_bovis_PRJEB34497-LinearBasicDisplay"
+ }
+ ],
"adapter" : {
+ "search" : "..G[AG][AG]T",
"type" : "SequenceSearchAdapter",
- "search" : "TT.",
"sequenceAdapter" : {
"faiLocation" : {
"locationType" : "UriLocation",
@@ -3210,131 +2855,67 @@
"type" : "BgzipFastaAdapter"
}
},
- "type" : "FeatureTrack",
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "height" : 4,
- "showDescriptions" : false,
- "color1" : "Indigo",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
- },
- "displayId" : "TTN_sequence_search_c_bovis_PRJEB34497-LinearBasicDisplay"
- }
- ],
- "trackId" : "c_bovis_PRJEB34497_TTN_sequence_search",
- "assemblyNames" : [
- "c_bovis_PRJEB34497"
- ],
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
- ]
- },
- {
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
- "adapter" : {
- "sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_bovis.PRJEB34497.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
- },
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_bovis.PRJEB34497.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
- },
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_bovis.PRJEB34497.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
- }
- },
- "search" : "..G[AG][AG]T",
- "type" : "SequenceSearchAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "SaCas9 NNGRRT PAM sites",
- "displays" : [
- {
- "displayId" : "NNGRRT_sequence_search_c_bovis_PRJEB34497-LinearBasicDisplay",
- "renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "DarkViolet",
- "showDescriptions" : false,
- "height" : 4
- },
- "type" : "LinearBasicDisplay"
- }
],
"assemblyNames" : [
"c_bovis_PRJEB34497"
],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "trackId" : "c_bovis_PRJEB34497_NNGRRT_sequence_search"
+ "type" : "FeatureTrack",
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
+ "trackId" : "c_bovis_PRJEB34497_NNGRRT_sequence_search",
+ "name" : "SaCas9 NNGRRT PAM sites"
},
{
- "displays" : [
- {
- "renderer" : {
- "height" : 4,
- "showDescriptions" : false,
- "color1" : "RebeccaPurple",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "NGG_sequence_search_c_bovis_PRJEB34497-LinearBasicDisplay"
- }
- ],
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
+ "name" : "SpCas9 NGG PAM sites",
"trackId" : "c_bovis_PRJEB34497_NGG_sequence_search",
- "assemblyNames" : [
- "c_bovis_PRJEB34497"
- ],
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
- "name" : "SpCas9 NGG PAM sites",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_bovis_PRJEB34497"
+ ],
"adapter" : {
- "search" : ".GG",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_bovis.PRJEB34497.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
"fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_bovis.PRJEB34497.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_bovis.PRJEB34497.WS284.genomic.fa.gz"
},
"gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_bovis.PRJEB34497.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_bovis.PRJEB34497.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
},
"type" : "BgzipFastaAdapter"
},
- "type" : "SequenceSearchAdapter"
+ "search" : ".GG"
},
- "type" : "FeatureTrack"
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "NGG_sequence_search_c_bovis_PRJEB34497-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "RebeccaPurple",
+ "height" : 4,
+ "showDescriptions" : false,
+ "showLabels" : false
+ }
+ }
+ ]
},
{
- "name" : "Curated Genes (protein coding)",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
"description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
"trackId" : "c_brenneri_PRJNA20035_curated_genes_protein_coding",
+ "name" : "Curated Genes (protein coding)",
"category" : [
"Genes",
"Curated Genes"
@@ -3342,16 +2923,24 @@
"assemblyNames" : [
"c_brenneri_PRJNA20035"
],
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
"renderer" : {
"type" : "SvgFeatureRenderer",
"maxHeight" : 5000,
- "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
- "color3" : "#965567"
+ "color3" : "#965567",
+ "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "curated_genes_(protein_coding)-c_brenneri_PRJNA20035-LinearBasicDisplay"
+ "displayId" : "curated_genes_(protein_coding)-c_brenneri_PRJNA20035-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
"formatDetails" : {
@@ -3359,33 +2948,33 @@
}
},
{
- "name" : "Curated Genes (pseudogenes)",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Curated Genes (pseudogenes)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
"description" : "A subset of the full Curated Genes set limited to pseudogenes only. Pseudogenes of tRNA are lighter gray and pseudogenes of rRNA are darker gray than pseudogenes of protein coding genes.",
"trackId" : "c_brenneri_PRJNA20035_curated_genes_pseudogenes",
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
- ],
+ "name" : "Curated Genes (pseudogenes)",
"category" : [
"Genes",
"Curated Genes"
],
+ "assemblyNames" : [
+ "c_brenneri_PRJNA20035"
+ ],
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Curated Genes (pseudogenes)/{refseq}/trackData.jsonz"
+ }
+ },
"displays" : [
{
"renderer" : {
+ "color1" : "gray",
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "gray"
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "curated_genes_(pseudogenes)-c_brenneri_PRJNA20035-LinearBasicDisplay"
+ "displayId" : "curated_genes_(pseudogenes)-c_brenneri_PRJNA20035-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
"formatDetails" : {
@@ -3393,275 +2982,265 @@
}
},
{
- "name" : "YACs, Fosmids, & Cosmids",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/YACs, Fosmids, & Cosmids/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "This track shows the locations of the cosmids, fosmids, and YACs used for the physical mapping and sequencing of the C. elegans genome. The clone termini do not necessarily correspond to the termini of submitted GenBank/EMBL entries. In some cases the exact termini of the clones is not known. For example, YACs were sequenced using PCR amplification across gaps in the cosmid maps. When a clone end is not known, it is shown as an arrow extending to the end of the display. Such data is to be treated with caution. The Vancouver fosmids can be ordered directly from GeneService.",
- "trackId" : "c_brenneri_PRJNA20035_yacs_fosmids_cosmids",
- "category" : [
- "Reagents"
- ],
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
- ],
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "yacs,_fosmids,_&_cosmids-c_brenneri_PRJNA20035-LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 3,
- "color1" : "black",
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay"
+ "color1" : "black"
+ }
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- }
- },
- {
- "type" : "FeatureTrack",
+ },
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Gene Models (historical)/{refseq}/trackData.jsonz"
- }
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/YACs, Fosmids, & Cosmids/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
},
- "name" : "Gene Models (historical)",
- "description" : "Historical gene predictions.",
"assemblyNames" : [
"c_brenneri_PRJNA20035"
],
+ "type" : "FeatureTrack",
"category" : [
- "Genes",
- "Curated Genes"
+ "Reagents"
],
- "trackId" : "c_brenneri_PRJNA20035_gene_models_(historical)",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
+ "trackId" : "c_brenneri_PRJNA20035_yacs_fosmids_cosmids",
+ "name" : "YACs, Fosmids, & Cosmids",
+ "description" : "This track shows the locations of the cosmids, fosmids, and YACs used for the physical mapping and sequencing of the C. elegans genome. The clone termini do not necessarily correspond to the termini of submitted GenBank/EMBL entries. In some cases the exact termini of the clones is not known. For example, YACs were sequenced using PCR amplification across gaps in the cosmid maps. When a clone end is not known, it is shown as an arrow extending to the end of the display. Such data is to be treated with caution. The Vancouver fosmids can be ordered directly from GeneService."
+ },
+ {
"displays" : [
{
"displayId" : "gene_models_(historical)-c_brenneri_PRJNA20035-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
+ "type" : "SvgFeatureRenderer",
"labels" : {
"description" : "jexl:get(feature,'type')"
},
- "type" : "SvgFeatureRenderer"
- }
- }
- ]
- },
- {
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
- "displays" : [
- {
- "displayId" : "curated_genes_(noncoding)-c_brenneri_PRJNA20035-LinearBasicDisplay",
- "renderer" : {
- "color1" : "gray",
- "type" : "SvgFeatureRenderer",
- "height" : 6
+ "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'"
},
"type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
- ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Gene Models (historical)/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"category" : [
"Genes",
"Curated Genes"
],
- "trackId" : "c_brenneri_PRJNA20035_curated_genes_noncoding",
- "description" : "Non-coding curated gene models, including ncRNA, tRNA, miRNA, snRNA, snoRNA, piRNA, lincRNA and antisense RNA.",
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Curated Genes (noncoding)/{refseq}/trackData.jsonz"
- }
- },
- "name" : "Curated Genes (noncoding)"
+ "assemblyNames" : [
+ "c_brenneri_PRJNA20035"
+ ],
+ "description" : "Historical gene predictions.",
+ "name" : "Gene Models (historical)",
+ "trackId" : "c_brenneri_PRJNA20035_gene_models_(historical)"
},
{
- "description" : "Data from 'genBlastG: using BLAST searches to build homologous gene models' (WBPaper00040677).",
- "name" : "genBlastG CDS predictions",
+ "trackId" : "c_brenneri_PRJNA20035_curated_genes_noncoding",
+ "name" : "Curated Genes (noncoding)",
+ "description" : "Non-coding curated gene models, including ncRNA, tRNA, miRNA, snRNA, snoRNA, piRNA, lincRNA and antisense RNA.",
+ "assemblyNames" : [
+ "c_brenneri_PRJNA20035"
+ ],
"type" : "FeatureTrack",
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/genBlastG CDS predictions/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Curated Genes (noncoding)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "curated_genes_(noncoding)-c_brenneri_PRJNA20035-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "height" : 7
- },
- "displayId" : "genblastg_cds_predictions-c_brenneri_PRJNA20035-LinearBasicDisplay"
+ "color1" : "gray",
+ "height" : 6
+ }
}
],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ }
+ },
+ {
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "trackId" : "c_brenneri_PRJNA20035_genblastg_cds_predictions",
+ "displays" : [
+ {
+ "displayId" : "genblastg_cds_predictions-c_brenneri_PRJNA20035-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "height" : 7
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/genBlastG CDS predictions/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_brenneri_PRJNA20035"
],
"category" : [
"Genes",
"Ab-initio predictions"
- ]
+ ],
+ "name" : "genBlastG CDS predictions",
+ "trackId" : "c_brenneri_PRJNA20035_genblastg_cds_predictions",
+ "description" : "Data from 'genBlastG: using BLAST searches to build homologous gene models' (WBPaper00040677)."
},
{
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/mRNAs_ncRNAs (best)/{refseq}/trackData.jsonz"
- }
- },
"name" : "mRNAs/ncRNAs (best)",
+ "trackId" : "c_brenneri_PRJNA20035_mrnas/ncrnas_(best)",
"description" : "Native (same species) full length cDNAs and ncRNAs aligned to the genome using BLAT. This track shows the best unique location for each cDNA.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_brenneri_PRJNA20035"
+ ],
"category" : [
"Genes",
"Supporting Evidence"
],
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
- ],
- "trackId" : "c_brenneri_PRJNA20035_mrnas/ncrnas_(best)",
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/mRNAs_ncRNAs (best)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
"displays" : [
{
- "displayId" : "mrnas/ncrnas_(best)-c_brenneri_PRJNA20035-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "mrnas/ncrnas_(best)-c_brenneri_PRJNA20035-LinearBasicDisplay",
"renderer" : {
"height" : 6,
- "type" : "SvgFeatureRenderer",
"outline" : "black",
- "color1" : "jexl:startsWith(get(feature,'source'),'BLAT_mRNA_')==true?'yellow':'gray'"
+ "color1" : "jexl:startsWith(get(feature,'source'),'BLAT_mRNA_')==true?'yellow':'gray'",
+ "type" : "SvgFeatureRenderer"
}
}
]
},
{
"description" : "This track shows the extent of predicted protein motifs. Note these spans correspond to amino acid coordinates interpolated onto the physical map. Included are signal peptide (signalp), coiled coil (ncoils) and transmembrane (tmhmm) domains, regions of low complexity (seg), and Pfam annotated motif homologies.",
+ "name" : "Protein motifs",
+ "trackId" : "c_brenneri_PRJNA20035_protein_motifs",
+ "category" : [
+ "Sequence Features",
+ "Translated Features"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_brenneri_PRJNA20035"
+ ],
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Protein motifs/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
+ }
},
- "type" : "FeatureTrack",
- "name" : "Protein motifs",
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 7,
"type" : "SvgFeatureRenderer",
- "color1" : "jexl:parent(feature)=='undefined'?'purple':get(parent(feature),'predictiontype')=='tmhmm'?'magenta':get(parent(feature),'predictiontype')=='seg'?'lightseagreen':get(parent(feature),'predictiontype')=='signalp'?'aquamarine':get(parent(feature),'predictiontype')=='ncoils'?'chartreuse':\nget(parent(feature),'predictiontype')=='pfam'?'lightsalmon':'purple'"
+ "color1" : "jexl:parent(feature)=='undefined'?'purple':get(parent(feature),'predictiontype')=='tmhmm'?'magenta':get(parent(feature),'predictiontype')=='seg'?'lightseagreen':get(parent(feature),'predictiontype')=='signalp'?'aquamarine':get(parent(feature),'predictiontype')=='ncoils'?'chartreuse':\nget(parent(feature),'predictiontype')=='pfam'?'lightsalmon':'purple'",
+ "height" : 7
},
- "displayId" : "protein_motifs-c_brenneri_PRJNA20035-LinearBasicDisplay"
+ "displayId" : "protein_motifs-c_brenneri_PRJNA20035-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ],
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
- ],
- "category" : [
- "Sequence Features",
- "Translated Features"
- ],
- "trackId" : "c_brenneri_PRJNA20035_protein_motifs"
+ ]
},
{
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Curated_Genes/{refseq}/trackData.jsonz"
- }
- },
- "type" : "FeatureTrack",
- "name" : "Curated Genes",
"formatDetails" : {
"feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
},
"displays" : [
{
- "displayId" : "curated_genes-c_brenneri_PRJNA20035-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "color3" : "#965567",
"type" : "SvgFeatureRenderer",
+ "maxHeight" : 5000,
+ "color3" : "#965567",
+ "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
- },
- "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
- "maxHeight" : 5000
+ }
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "curated_genes-c_brenneri_PRJNA20035-LinearBasicDisplay"
}
],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Curated_Genes/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
+ "assemblyNames" : [
+ "c_brenneri_PRJNA20035"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"Genes",
"Curated Genes"
],
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
- ],
- "trackId" : "c_brenneri_PRJNA20035_curated_genes"
+ "trackId" : "c_brenneri_PRJNA20035_curated_genes",
+ "name" : "Curated Genes",
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes."
},
{
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "jexl:get(feature,'source')=='SL1'?'red':get(feature,'source')=='SL2'?'green':'black'",
"type" : "SvgFeatureRenderer",
"labels" : {
"description" : "jexl:get(feature,'source') || get(feature,'description')"
- }
+ },
+ "color1" : "jexl:get(feature,'source')=='SL1'?'red':get(feature,'source')=='SL2'?'green':'black'"
},
- "type" : "LinearBasicDisplay",
"displayId" : "trans-spliced_acceptor-c_brenneri_PRJNA20035-LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "trackId" : "c_brenneri_PRJNA20035_trans-spliced_acceptor",
- "category" : [
- "Sequence Features",
- "Signals & Motifs"
- ],
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
- ],
- "description" : "This track contains SL1 and SL2 trans-spliced acceptors from a variety of sources: SL1 and SL2 trans-spliced acceptors published by Blumenthal et al, Nature (2002), Trans-Spliced Exon Coupled RNA End Determination (TEC-RED) Hwang et al, PNAS (2004), EST/mRNA sequence data, RNASeq read data from ENA. SL1 acceptors are show in red, SL2 in green. Direction of transcription is indicated by arrow direction.",
- "name" : "Trans-spliced acceptor",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -3669,201 +3248,211 @@
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack"
+ "assemblyNames" : [
+ "c_brenneri_PRJNA20035"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Sequence Features",
+ "Signals & Motifs"
+ ],
+ "trackId" : "c_brenneri_PRJNA20035_trans-spliced_acceptor",
+ "name" : "Trans-spliced acceptor",
+ "description" : "This track contains SL1 and SL2 trans-spliced acceptors from a variety of sources: SL1 and SL2 trans-spliced acceptors published by Blumenthal et al, Nature (2002), Trans-Spliced Exon Coupled RNA End Determination (TEC-RED) Hwang et al, PNAS (2004), EST/mRNA sequence data, RNASeq read data from ENA. SL1 acceptors are show in red, SL2 in green. Direction of transcription is indicated by arrow direction."
},
{
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "assemblyNames" : [
+ "c_brenneri_PRJNA20035"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_brenneri_PRJNA20035_C_briggsae_proteins",
+ "name" : "C. briggsae proteins",
"displays" : [
{
- "displayId" : "C_briggsae_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "C_briggsae_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "orange"
+ "color1" : "orange",
+ "height" : 4,
+ "showLabels" : false
}
}
],
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "trackId" : "c_brenneri_PRJNA20035_C_briggsae_proteins",
- "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"adapter" : {
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/C. briggsae proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
},
"type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "C. briggsae proteins"
+ }
},
{
- "description" : "Matches to WormBase B. malayi proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/B. malayi proteins/{refseq}/trackData.jsonz"
- }
- },
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "assemblyNames" : [
+ "c_brenneri_PRJNA20035"
+ ],
"type" : "FeatureTrack",
+ "description" : "Matches to WormBase B. malayi proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_brenneri_PRJNA20035_B_malayi_proteins",
"name" : "B. malayi proteins",
"displays" : [
{
- "type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
"color1" : "orange",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 4
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "B_malayi_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "B_malayi_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
- ],
- "trackId" : "c_brenneri_PRJNA20035_B_malayi_proteins"
- },
- {
- "name" : "C. japonica proteins",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/C. japonica proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "trackId" : "c_brenneri_PRJNA20035_C_japonica_proteins",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/B. malayi proteins/{refseq}/trackData.jsonz"
+ }
+ }
+ },
+ {
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_brenneri_PRJNA20035"
],
+ "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "C. japonica proteins",
+ "trackId" : "c_brenneri_PRJNA20035_C_japonica_proteins",
"displays" : [
{
- "displayId" : "C_japonica_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
+ "height" : 4,
"color1" : "orange",
- "height" : 4
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "C_japonica_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ]
- },
- {
- "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "type" : "FeatureTrack",
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/C. japonica proteins/{refseq}/trackData.jsonz"
}
- },
- "name" : "D. melanogaster proteins",
+ }
+ },
+ {
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "D_melanogaster_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
"color1" : "orange",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "height" : 4,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
- "displayId" : "D_melanogaster_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')"
}
],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
+ "assemblyNames" : [
+ "c_brenneri_PRJNA20035"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
- ],
- "trackId" : "c_brenneri_PRJNA20035_D_melanogaster_proteins"
+ "trackId" : "c_brenneri_PRJNA20035_D_melanogaster_proteins",
+ "name" : "D. melanogaster proteins",
+ "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
},
{
- "description" : "Matches to WormBase O. volvulus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/O. volvulus proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "NCListAdapter"
},
- "name" : "O. volvulus proteins",
"displays" : [
{
- "displayId" : "O_volvulus_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "O_volvulus_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay",
"renderer" : {
- "color1" : "orange",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "height" : 4
- }
+ "color1" : "orange",
+ "height" : 4,
+ "showLabels" : false
+ },
+ "mouseover" : "jexl:get(feature,'clone')"
}
],
+ "name" : "O. volvulus proteins",
+ "trackId" : "c_brenneri_PRJNA20035_O_volvulus_proteins",
+ "description" : "Matches to WormBase O. volvulus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_brenneri_PRJNA20035"
],
"category" : [
"Sequence Similarity",
"Proteins"
- ],
- "trackId" : "c_brenneri_PRJNA20035_O_volvulus_proteins"
+ ]
},
{
+ "trackId" : "c_brenneri_PRJNA20035_ests",
"name" : "ESTs",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/ESTs (best)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
"description" : "Native (same-species) Expressed Sequence Tags (ESTs), aligned to the genome using BLAT. This track shows the best unique location for each EST. The paired 5' and 3' ESTs from the same cDNA clone are connected by a dashed line and a colored light green. ESTs with no mate are yellow, and ESTs with a mate that is 'far away' are dark green.",
- "trackId" : "c_brenneri_PRJNA20035_ests",
"assemblyNames" : [
"c_brenneri_PRJNA20035"
],
+ "type" : "FeatureTrack",
"category" : [
"Genes",
"Supporting Evidence"
],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/ESTs (best)/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "ests-c_brenneri_PRJNA20035-LinearBasicDisplay",
"renderer" : {
"color1" : "jexl:parent(feature)=='undefined'?'red':get(parent(feature),'has_mate')==1?'limegreen':get(parent(feature),'has_mate')==2?'green':get(parent(feature),'has_mate')==0?'gold':'black'",
"maxHeight" : 5000,
"type" : "SvgFeatureRenderer"
- },
- "displayId" : "ests-c_brenneri_PRJNA20035-LinearBasicDisplay"
+ }
}
],
"formatDetails" : {
@@ -3871,28 +3460,6 @@
}
},
{
- "trackId" : "c_brenneri_PRJNA20035_tandem_and_inverted_repeats",
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
- ],
- "category" : [
- "Genome Structure",
- "Repeats"
- ],
- "displays" : [
- {
- "displayId" : "tandem_and_inverted_repeats-c_brenneri_PRJNA20035-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "showDescriptions" : false,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "bisque"
- }
- }
- ],
- "name" : "Tandem and Inverted Repeats",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -3900,166 +3467,188 @@
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Tandem and Inverted Repeats/{refseq}/trackData.jsonz"
}
},
- "description" : "Exact tandem and inverted repetitive elements."
- },
- {
"displays" : [
{
- "displayId" : "T_muris_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "color1" : "orange",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "height" : 4
- }
+ "color1" : "bisque",
+ "showLabels" : false,
+ "showDescriptions" : false
+ },
+ "displayId" : "tandem_and_inverted_repeats-c_brenneri_PRJNA20035-LinearBasicDisplay"
}
],
- "trackId" : "c_brenneri_PRJNA20035_T_muris_proteins",
+ "description" : "Exact tandem and inverted repetitive elements.",
+ "trackId" : "c_brenneri_PRJNA20035_tandem_and_inverted_repeats",
+ "name" : "Tandem and Inverted Repeats",
"category" : [
- "Sequence Similarity",
- "Proteins"
+ "Genome Structure",
+ "Repeats"
],
"assemblyNames" : [
"c_brenneri_PRJNA20035"
],
- "description" : "Matches to WormBase T. muris proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "T. muris proteins",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/T. muris proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- }
+ "type" : "FeatureTrack"
},
{
- "description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Other UniProt proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/T. muris proteins/{refseq}/trackData.jsonz"
+ }
},
- "type" : "FeatureTrack",
- "name" : "Other UniProt proteins",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "T_muris_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "showDescriptions" : false,
- "height" : 4,
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "orange"
+ "color1" : "orange",
+ "height" : 4,
+ "showLabels" : false
},
- "displayId" : "other_uniprot_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
+ "trackId" : "c_brenneri_PRJNA20035_T_muris_proteins",
+ "name" : "T. muris proteins",
+ "description" : "Matches to WormBase T. muris proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"assemblyNames" : [
"c_brenneri_PRJNA20035"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
- ],
- "trackId" : "c_brenneri_PRJNA20035_other_uniprot_proteins"
+ ]
},
{
- "trackId" : "c_brenneri_PRJNA20035_H_sapiens_proteins",
+ "description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "Other UniProt proteins",
+ "trackId" : "c_brenneri_PRJNA20035_other_uniprot_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_brenneri_PRJNA20035"
],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Other UniProt proteins/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
- "displayId" : "H_sapiens_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "orange"
+ "color1" : "orange",
+ "showLabels" : false,
+ "height" : 4,
+ "showDescriptions" : false
},
- "mouseover" : "jexl:get(feature,'clone')"
+ "displayId" : "other_uniprot_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay"
}
- ],
+ ]
+ },
+ {
+ "trackId" : "c_brenneri_PRJNA20035_H_sapiens_proteins",
"name" : "H. sapiens proteins",
+ "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "assemblyNames" : [
+ "c_brenneri_PRJNA20035"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/H. sapiens proteins/{refseq}/trackData.jsonz"
- }
+ },
+ "type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ "displays" : [
+ {
+ "displayId" : "H_sapiens_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showLabels" : false,
+ "height" : 4,
+ "color1" : "orange"
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
- "description" : "Low-complexity regions identified by Dust.",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "name" : "Low complextity region (Dust)",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "showDescriptions" : false,
- "color1" : "bisque",
"type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "color1" : "bisque",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 4
},
"displayId" : "low_complextity_region_(dust)-c_brenneri_PRJNA20035-LinearBasicDisplay"
}
],
- "category" : [
- "Genome Structure",
- "Repeats"
- ],
+ "trackId" : "c_brenneri_PRJNA20035_low_complextity_region_(dust)",
+ "name" : "Low complextity region (Dust)",
+ "description" : "Low-complexity regions identified by Dust.",
"assemblyNames" : [
"c_brenneri_PRJNA20035"
],
- "trackId" : "c_brenneri_PRJNA20035_low_complextity_region_(dust)"
+ "type" : "FeatureTrack",
+ "category" : [
+ "Genome Structure",
+ "Repeats"
+ ]
},
{
- "description" : "ESTs and mRNAs from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each cDNA sequence. mRNAs are shown in light blue; ESTs in green.",
- "name" : "WormBase nematode mRNAs/ESTs (best)",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/WormBase nematode mRNAs_ESTs (best)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/WormBase nematode mRNAs_ESTs (best)/{refseq}/trackData.jsonz"
}
},
- "type" : "FeatureTrack",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA_BEST'?'lightblue':get(feature,'source')=='BLAT_Caen_EST_BEST'?'green':'black'",
- "type" : "SvgFeatureRenderer",
+ "height" : 4,
"labels" : {
"name" : "jexl:get(feature,'species') || get(feature,'id')"
},
- "height" : 4
+ "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA_BEST'?'lightblue':get(feature,'source')=='BLAT_Caen_EST_BEST'?'green':'black'",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "wormbase_nematode_mrnas/ests_(best)-c_brenneri_PRJNA20035-LinearBasicDisplay"
}
],
+ "name" : "WormBase nematode mRNAs/ESTs (best)",
"trackId" : "wormbase_nematode_mrnas/ests_(best)-c_brenneri_PRJNA20035",
+ "description" : "ESTs and mRNAs from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each cDNA sequence. mRNAs are shown in light blue; ESTs in green.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_brenneri_PRJNA20035"
],
@@ -4069,106 +3658,115 @@
]
},
{
- "description" : "This track shows the location and coordinates of contigs (mostly cosmids) submitted to GenBank/EMBL.",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Contig submissions/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "Contig submissions",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
+ "height" : 7,
"color1" : "sienna",
- "type" : "SvgFeatureRenderer",
- "height" : 7
+ "type" : "SvgFeatureRenderer"
},
"displayId" : "contig_submissions-c_brenneri_PRJNA20035-LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
- ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Contig submissions/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"category" : [
"Genome Structure",
"Assembly & Curation"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_brenneri_PRJNA20035"
+ ],
+ "description" : "This track shows the location and coordinates of contigs (mostly cosmids) submitted to GenBank/EMBL.",
+ "name" : "Contig submissions",
"trackId" : "c_brenneri_PRJNA20035_contig_submissions"
},
{
"name" : "C. elegans proteins",
+ "trackId" : "c_brenneri_PRJNA20035_C_elegans_proteins",
+ "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_brenneri_PRJNA20035"
+ ],
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/C. elegans proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "NCListAdapter"
},
- "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "trackId" : "c_brenneri_PRJNA20035_C_elegans_proteins",
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
- ],
"displays" : [
{
- "displayId" : "C_elegans_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "orange",
- "height" : 4
+ "height" : 4,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay"
+ "displayId" : "C_elegans_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay"
}
]
},
{
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Non-C. elegans Isoseq collection (best)/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Non-C. elegans Isoseq collection (best)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "name" : "Non-C. elegans Isoseq collection (best)",
- "description" : "IsoSeq from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each IsoSeqsequence.",
- "category" : [
- "Sequence Similarity",
- "Nucleotide"
- ],
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
- ],
- "trackId" : "non-c._elegans_isoseq_collection_(best)-c_brenneri_PRJNA20035",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "non-c._elegans_isoseq_collection_(best)-c_brenneri_PRJNA20035-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"color1" : "green",
"height" : 4
- },
- "displayId" : "non-c._elegans_isoseq_collection_(best)-c_brenneri_PRJNA20035-LinearBasicDisplay"
+ }
}
- ]
+ ],
+ "description" : "IsoSeq from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each IsoSeqsequence.",
+ "trackId" : "non-c._elegans_isoseq_collection_(best)-c_brenneri_PRJNA20035",
+ "name" : "Non-C. elegans Isoseq collection (best)",
+ "category" : [
+ "Sequence Similarity",
+ "Nucleotide"
+ ],
+ "assemblyNames" : [
+ "c_brenneri_PRJNA20035"
+ ],
+ "type" : "FeatureTrack"
},
{
"description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "C. brenneri proteins",
+ "trackId" : "c_brenneri_PRJNA20035_C_brenneri_proteins",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_brenneri_PRJNA20035"
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -4176,132 +3774,130 @@
"locationType" : "UriLocation"
}
},
- "name" : "C. brenneri proteins",
"displays" : [
{
- "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
+ "color1" : "orange",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "orange"
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "C_brenneri_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "C_brenneri_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ],
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "trackId" : "c_brenneri_PRJNA20035_C_brenneri_proteins"
+ ]
},
{
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "S. cerevisiae proteins",
"description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "S. cerevisiae proteins",
+ "trackId" : "c_brenneri_PRJNA20035_S_cerevisiae_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_brenneri_PRJNA20035"
],
- "trackId" : "c_brenneri_PRJNA20035_S_cerevisiae_proteins",
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
- "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "S_cerevisiae_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
+ "color1" : "orange",
+ "height" : 4,
"showLabels" : false
},
- "type" : "LinearBasicDisplay",
- "displayId" : "S_cerevisiae_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')",
+ "type" : "LinearBasicDisplay"
}
]
},
{
- "description" : "These boxes indicate alignments of short read sequences from all available RNASeq projects. The number of reads has been normalised by averaging over the number of libraries. The height of all boxes indicates the relative score of the feature.",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/RNASeq/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/RNASeq/{refseq}/trackData.jsonz"
+ }
},
- "type" : "FeatureTrack",
- "name" : "RNASeq",
"displays" : [
{
- "displayId" : "rnaseq-c_brenneri_PRJNA20035-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
- "mouseover" : "jexl:'Score: '+get(feature,'score')",
+ "displayId" : "rnaseq-c_brenneri_PRJNA20035-LinearBasicDisplay",
"renderer" : {
- "displayMode" : "collapse",
"showDescriptions" : false,
"height" : "jexl:get(feature,'score')>100?50:floor(get(feature,'score')/2)>4?floor(get(feature,'score')/2):4",
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "black"
- }
+ "color1" : "black",
+ "type" : "SvgFeatureRenderer",
+ "displayMode" : "collapse"
+ },
+ "mouseover" : "jexl:'Score: '+get(feature,'score')"
}
],
- "category" : [
- "Expression"
- ],
+ "name" : "RNASeq",
+ "trackId" : "c_brenneri_PRJNA20035_rnaseq",
+ "description" : "These boxes indicate alignments of short read sequences from all available RNASeq projects. The number of reads has been normalised by averaging over the number of libraries. The height of all boxes indicates the relative score of the feature.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_brenneri_PRJNA20035"
],
- "trackId" : "c_brenneri_PRJNA20035_rnaseq"
+ "category" : [
+ "Expression"
+ ]
},
{
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display.",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/RNASeq introns/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "RNASeq introns",
"displays" : [
{
"displayId" : "rnaseq_introns-c_brenneri_PRJNA20035-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'score')+' reads'",
"renderer" : {
"color1" : "green",
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
"height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)",
- "showDescriptions" : false
- }
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
+ },
+ "mouseover" : "jexl:get(feature,'score')+' reads'",
+ "type" : "LinearBasicDisplay"
}
],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/RNASeq introns/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"assemblyNames" : [
"c_brenneri_PRJNA20035"
],
+ "type" : "FeatureTrack",
"category" : [
"Expression"
],
- "trackId" : "c_brenneri_PRJNA20035_rnaseq_introns"
+ "trackId" : "c_brenneri_PRJNA20035_rnaseq_introns",
+ "name" : "RNASeq introns",
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display."
},
{
"description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
+ "trackId" : "c_brenneri_PRJNA20035_rnaseq_splice_junctions_(common)",
"name" : "RNASeq Splice Junctions (common)",
+ "category" : [
+ "Expression"
+ ],
+ "assemblyNames" : [
+ "c_brenneri_PRJNA20035"
+ ],
"type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
@@ -4312,67 +3908,70 @@
},
"displays" : [
{
- "displayId" : "rnaseq_splice_junctions_(common)-c_brenneri_PRJNA20035-LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
+ "showLabels" : false,
+ "showDescriptions" : false,
"color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))"
},
"mouseover" : "jexl:get(feature,'score')+' reads'",
+ "displayId" : "rnaseq_splice_junctions_(common)-c_brenneri_PRJNA20035-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
- ],
- "trackId" : "c_brenneri_PRJNA20035_rnaseq_splice_junctions_(common)",
- "category" : [
- "Expression"
- ],
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
]
},
{
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "rnaseq_splice_junctions_(rare)-c_brenneri_PRJNA20035-LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
"maxHeight" : 5000,
+ "type" : "SvgFeatureRenderer",
"color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
- "showLabels" : false,
"height" : "jexl:4",
- "type" : "SvgFeatureRenderer"
+ "showDescriptions" : false,
+ "showLabels" : false
},
- "mouseover" : "jexl:get(feature,'score')+' reads'",
- "type" : "LinearBasicDisplay",
- "displayId" : "rnaseq_splice_junctions_(rare)-c_brenneri_PRJNA20035-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'score')+' reads'"
}
],
+ "name" : "RNASeq Splice Junctions (rare)",
"trackId" : "c_brenneri_PRJNA20035_rnaseq_splice_junctions_(rare)",
- "category" : [
- "Expression"
- ],
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_brenneri_PRJNA20035"
],
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
- "name" : "RNASeq Splice Junctions (rare)",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- }
+ "category" : [
+ "Expression"
+ ]
},
{
+ "name" : "Microarray oligo probes",
"trackId" : "c_brenneri_PRJNA20035_microarray_oligo_probes",
- "category" : [
- "Reagents"
- ],
+ "description" : "This track contains Affymetrix GeneChip and Washington University GSC microarray probe sets.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_brenneri_PRJNA20035"
],
+ "category" : [
+ "Reagents"
+ ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Microarray oligo probes/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
"renderer" : {
@@ -4380,154 +3979,144 @@
"color1" : "black",
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "microarray_oligo_probes-c_brenneri_PRJNA20035-LinearBasicDisplay"
+ "displayId" : "microarray_oligo_probes-c_brenneri_PRJNA20035-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
- "name" : "Microarray oligo probes",
- "type" : "FeatureTrack",
+ }
+ },
+ {
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Microarray oligo probes/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/S. ratti proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
}
},
- "description" : "This track contains Affymetrix GeneChip and Washington University GSC microarray probe sets."
- },
- {
"displays" : [
{
- "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
+ "height" : 4,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "orange",
- "height" : 4
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "S_ratti_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "S_ratti_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
+ "trackId" : "c_brenneri_PRJNA20035_S_ratti_proteins",
+ "name" : "S. ratti proteins",
+ "description" : "Matches to WormBase S. ratti proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"assemblyNames" : [
"c_brenneri_PRJNA20035"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
- ],
- "trackId" : "c_brenneri_PRJNA20035_S_ratti_proteins",
- "description" : "Matches to WormBase S. ratti proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/S. ratti proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "name" : "S. ratti proteins"
+ ]
},
{
- "description" : "Red boxes indicate regions where there are more than 2 times as many forward sense RNASeq reads aligned to the genome as reverse sense reads. This asymmetrical signal has been found empirically to be a sensitive marker for the ends of transcripts. Green boxes indicate regions where there are more than 2 times as many reverse sense RNASeq reads aligned to the genome as forward sense reads. This asymmetrical signal has been found empirically to be sensitive marker for the ends of transcripts. The height of all boxes indicates the relative score of the feature.",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/RNASeq Asymmetries/{refseq}/trackData.jsonz"
- }
- },
+ "assemblyNames" : [
+ "c_brenneri_PRJNA20035"
+ ],
"type" : "FeatureTrack",
+ "category" : [
+ "Expression"
+ ],
+ "trackId" : "c_brenneri_PRJNA20035_rnaseq_asymmetries",
"name" : "RNASeq Asymmetries",
+ "description" : "Red boxes indicate regions where there are more than 2 times as many forward sense RNASeq reads aligned to the genome as reverse sense reads. This asymmetrical signal has been found empirically to be a sensitive marker for the ends of transcripts. Green boxes indicate regions where there are more than 2 times as many reverse sense RNASeq reads aligned to the genome as forward sense reads. This asymmetrical signal has been found empirically to be sensitive marker for the ends of transcripts. The height of all boxes indicates the relative score of the feature.",
"displays" : [
{
- "mouseover" : "jexl:'Score: '+get(feature,'score')",
+ "displayId" : "rnaseq_asymmetries-c_brenneri_PRJNA20035-LinearBasicDisplay",
"renderer" : {
- "height" : 24,
"displayMode" : "collapse",
- "color1" : "jexl:get(feature,'source')=='RNASeq_R_asymmetry'?'red': get(feature,'source')=='RNASeq_F_asymmetry'?'green':'black'",
+ "type" : "SvgFeatureRenderer",
+ "height" : 24,
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "color1" : "jexl:get(feature,'source')=='RNASeq_R_asymmetry'?'red': get(feature,'source')=='RNASeq_F_asymmetry'?'green':'black'"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "rnaseq_asymmetries-c_brenneri_PRJNA20035-LinearBasicDisplay"
+ "mouseover" : "jexl:'Score: '+get(feature,'score')",
+ "type" : "LinearBasicDisplay"
}
],
- "category" : [
- "Expression"
- ],
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
- ],
- "trackId" : "c_brenneri_PRJNA20035_rnaseq_asymmetries"
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/RNASeq Asymmetries/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "C_remanei_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
+ "color1" : "orange",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "orange"
- },
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
- "displayId" : "C_remanei_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay"
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
+ }
}
],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/C. remanei proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_brenneri_PRJNA20035"
],
- "trackId" : "c_brenneri_PRJNA20035_C_remanei_proteins",
"description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/C. remanei proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "C. remanei proteins"
+ "name" : "C. remanei proteins",
+ "trackId" : "c_brenneri_PRJNA20035_C_remanei_proteins"
},
{
- "description" : "Repetitive regions identified by RepeatMasker.",
"name" : "Repeat Region (RepeatMasker)",
+ "trackId" : "c_brenneri_PRJNA20035_repeat_region_(repeatmasker)",
+ "description" : "Repetitive regions identified by RepeatMasker.",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_brenneri_PRJNA20035"
+ ],
+ "category" : [
+ "Genome Structure",
+ "Repeats"
+ ],
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
},
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "repeat_region_(repeatmasker)-c_brenneri_PRJNA20035-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "showDescriptions" : false,
- "color1" : "bisque",
"type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "color1" : "bisque",
+ "showLabels" : false,
+ "height" : 4,
+ "showDescriptions" : false
},
- "displayId" : "repeat_region_(repeatmasker)-c_brenneri_PRJNA20035-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
- ],
- "trackId" : "c_brenneri_PRJNA20035_repeat_region_(repeatmasker)",
- "category" : [
- "Genome Structure",
- "Repeats"
- ],
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
]
},
{
@@ -4539,164 +4128,143 @@
"displayId" : "links_and_superlinks-c_brenneri_PRJNA20035-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "color1" : "black",
- "height" : 4
+ "height" : 4,
+ "color1" : "black"
},
"type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
- ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Links and Superlinks/{refseq}/trackData.jsonz"
+ }
+ },
"category" : [
"Genome Structure",
"Assembly & Curation"
],
- "trackId" : "c_brenneri_PRJNA20035_links_and_superlinks",
- "description" : "This track shows the location and coordinates of contigs created during the assembly of the C. elegans genome.",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_brenneri_PRJNA20035"
+ ],
+ "description" : "This track shows the location and coordinates of contigs created during the assembly of the C. elegans genome.",
+ "name" : "Links and Superlinks",
+ "trackId" : "c_brenneri_PRJNA20035_links_and_superlinks"
+ },
+ {
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/Links and Superlinks/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/P. pacificus proteins/{refseq}/trackData.jsonz"
}
},
- "name" : "Links and Superlinks"
- },
- {
- "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "P. pacificus proteins",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/P. pacificus proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
"displays" : [
{
- "mouseover" : "jexl:get(feature,'clone')",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "orange",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "height" : 4
+ "color1" : "orange",
+ "height" : 4,
+ "showLabels" : false
},
- "type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"displayId" : "P_pacificus_proteins-c_brenneri_PRJNA20035-LinearBasicDisplay"
}
],
"trackId" : "c_brenneri_PRJNA20035_P_pacificus_proteins",
+ "name" : "P. pacificus proteins",
+ "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "assemblyNames" : [
+ "c_brenneri_PRJNA20035"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
- ],
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
]
},
{
- "trackId" : "c_brenneri_PRJNA20035_TTCN_sequence_search",
+ "assemblyNames" : [
+ "c_brenneri_PRJNA20035"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
- ],
+ "trackId" : "c_brenneri_PRJNA20035_TTCN_sequence_search",
+ "name" : "Cas12e TTCN PAM sites",
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
"displays" : [
{
"displayId" : "TTCN_sequence_search_c_brenneri_PRJNA20035-LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "SlateBlue",
"showDescriptions" : false,
"height" : 4,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "SlateBlue"
+ "showLabels" : false
},
"type" : "LinearBasicDisplay"
}
],
- "name" : "Cas12e TTCN PAM sites",
- "type" : "FeatureTrack",
"adapter" : {
"search" : "TTC.",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
"gziLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
},
+ "type" : "BgzipFastaAdapter",
+ "fastaLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz"
+ },
"faiLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz.fai"
- },
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
}
- },
- "type" : "SequenceSearchAdapter"
- },
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time."
+ }
+ }
},
{
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
+ "assemblyNames" : [
+ "c_brenneri_PRJNA20035"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
+ "trackId" : "c_brenneri_PRJNA20035_TTN_sequence_search",
+ "name" : "Cas12a TTN PAM sites",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "TTN_sequence_search_c_brenneri_PRJNA20035-LinearBasicDisplay",
"renderer" : {
- "color1" : "Indigo",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
+ "showDescriptions" : false,
"height" : 4,
- "showDescriptions" : false
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "TTN_sequence_search_c_brenneri_PRJNA20035-LinearBasicDisplay"
+ "showLabels" : false,
+ "color1" : "Indigo",
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
- ],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "trackId" : "c_brenneri_PRJNA20035_TTN_sequence_search",
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
- "type" : "FeatureTrack",
"adapter" : {
"search" : "TT.",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz.gzi"
},
- "fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz"
- },
- "faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz.fai"
- },
- "type" : "BgzipFastaAdapter"
- },
- "type" : "SequenceSearchAdapter"
- },
- "name" : "Cas12a TTN PAM sites"
- },
- {
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
- "adapter" : {
- "type" : "SequenceSearchAdapter",
- "search" : "..G[AG][AG]T",
- "sequenceAdapter" : {
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
- },
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
@@ -4704,610 +4272,519 @@
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
- },
- "type" : "BgzipFastaAdapter"
+ }
}
- },
- "type" : "FeatureTrack",
- "name" : "SaCas9 NNGRRT PAM sites",
+ }
+ },
+ {
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "NNGRRT_sequence_search_c_brenneri_PRJNA20035-LinearBasicDisplay",
"renderer" : {
+ "showLabels" : false,
"height" : 4,
"showDescriptions" : false,
"color1" : "DarkViolet",
- "showLabels" : false,
"type" : "SvgFeatureRenderer"
- },
- "displayId" : "NNGRRT_sequence_search_c_brenneri_PRJNA20035-LinearBasicDisplay"
+ }
}
],
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
- ],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "trackId" : "c_brenneri_PRJNA20035_NNGRRT_sequence_search"
- },
- {
- "name" : "SpCas9 NGG PAM sites",
"adapter" : {
"sequenceAdapter" : {
"type" : "BgzipFastaAdapter",
"gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz.gzi"
+ },
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
"faiLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz.fai"
- },
- "fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz"
}
},
- "search" : ".GG",
- "type" : "SequenceSearchAdapter"
+ "type" : "SequenceSearchAdapter",
+ "search" : "..G[AG][AG]T"
},
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
"type" : "FeatureTrack",
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
- "trackId" : "c_brenneri_PRJNA20035_NGG_sequence_search",
"assemblyNames" : [
"c_brenneri_PRJNA20035"
],
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
+ "name" : "SaCas9 NNGRRT PAM sites",
+ "trackId" : "c_brenneri_PRJNA20035_NNGRRT_sequence_search"
+ },
+ {
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_brenneri_PRJNA20035"
+ ],
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
+ "name" : "SpCas9 NGG PAM sites",
+ "trackId" : "c_brenneri_PRJNA20035_NGG_sequence_search",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "NGG_sequence_search_c_brenneri_PRJNA20035-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "showDescriptions" : false,
- "color1" : "RebeccaPurple",
"type" : "SvgFeatureRenderer",
+ "color1" : "RebeccaPurple",
+ "showDescriptions" : false,
+ "height" : 4,
"showLabels" : false
},
- "displayId" : "NGG_sequence_search_c_brenneri_PRJNA20035-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "sequenceAdapter" : {
+ "faiLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz.fai"
+ },
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ }
+ },
+ "type" : "SequenceSearchAdapter",
+ "search" : ".GG"
+ }
},
{
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display.",
- "name" : "RNASeq introns",
+ "description" : "These are transposon spans reviewed by WormBase curators.",
+ "trackId" : "c_briggsae_PRJNA10731_transposons",
+ "name" : "Transposons",
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
+ "assemblyNames" : [
+ "c_briggsae_PRJNA10731"
+ ],
"type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/RNASeq introns/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Transposons/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
"displays" : [
{
- "mouseover" : "jexl:get(feature,'score')+' reads'",
"renderer" : {
- "showDescriptions" : false,
- "height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "green"
+ "color1" : "gray",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "rnaseq_introns-c_brenneri_PRJNA20035-LinearBasicDisplay"
+ "displayId" : "transposons-c_briggsae_PRJNA10731-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ],
- "trackId" : "c_brenneri_PRJNA20035_rnaseq_introns",
- "category" : [
- "Expression"
- ],
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
]
},
{
- "trackId" : "c_brenneri_PRJNA20035_rnaseq_splice_junctions_(common)",
- "category" : [
- "Expression"
- ],
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
- ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/genBlastG CDS predictions/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'score')+' reads'",
+ "displayId" : "genblastg_cds_predictions-c_briggsae_PRJNA10731-LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "color1" : "jexl:get(feature,'score')>1000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/1000))))+'00'+hex(round(255-(140*(get(feature,'score')/1000)))):'#00'+hex(round(255-(140*(get(feature,'score')/1000))))+hex(round(255-(140*(get(feature,'score')/1000))))",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "type" : "SvgFeatureRenderer",
+ "height" : 7
},
- "displayId" : "rnaseq_splice_junctions_(common)-c_brenneri_PRJNA20035-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "name" : "RNASeq Splice Junctions (common)",
+ "description" : "Data from 'genBlastG: using BLAST searches to build homologous gene models' (WBPaper00040677).",
+ "name" : "genBlastG CDS predictions",
+ "trackId" : "c_briggsae_PRJNA10731_genblastg_cds_predictions",
+ "category" : [
+ "Genes",
+ "Ab-initio predictions"
+ ],
"type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/RNASeq Splice Junctions (common)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads."
+ "assemblyNames" : [
+ "c_briggsae_PRJNA10731"
+ ]
},
{
- "name" : "RNASeq Splice Junctions (rare)",
+ "name" : "Genome sequence errors",
+ "trackId" : "c_briggsae_PRJNA10731_genome_sequence_errors",
+ "description" : "Positions within the reference genome sequence that have been identified as having a base call error. This error has not yet been corrected.",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_briggsae_PRJNA10731"
+ ],
+ "category" : [
+ "Genome Structure",
+ "Assembly & Curation"
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Genome sequence errors/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
}
},
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
- "trackId" : "c_brenneri_PRJNA20035_rnaseq_splice_junctions_(rare)",
- "assemblyNames" : [
- "c_brenneri_PRJNA20035"
- ],
- "category" : [
- "Expression"
- ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"displays" : [
{
- "mouseover" : "jexl:get(feature,'score')+' reads'",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : "jexl:4",
"type" : "SvgFeatureRenderer",
- "showDescriptions" : false,
- "showLabels" : false,
- "color1" : "jexl:get(feature,'score')>1000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/1000))))+'00'+hex(round(255-(140*(get(feature,'score')/1000)))):'#00'+hex(round(255-(140*(get(feature,'score')/1000))))+hex(round(255-(140*(get(feature,'score')/1000))))",
- "maxHeight" : 5000
+ "color1" : "red",
+ "height" : 6
},
- "type" : "LinearBasicDisplay",
- "displayId" : "rnaseq_splice_junctions_(rare)-c_brenneri_PRJNA20035-LinearBasicDisplay"
+ "displayId" : "genome_sequence_errors-c_briggsae_PRJNA10731-LinearBasicDisplay"
}
]
},
{
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "assemblyNames" : [
- "c_briggsae_PRJNA10731"
- ],
- "trackId" : "c_briggsae_PRJNA10731_transposons",
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Classical_alleles/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+'', WormBase: 'Variation Page'}"
},
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "classical_alleles-c_briggsae_PRJNA10731-LinearBasicDisplay",
"renderer" : {
- "color1" : "gray",
- "type" : "SvgFeatureRenderer"
+ "type" : "SvgFeatureRenderer",
+ "color1" : "jexl:get(feature,'vep_impact')=='HIGH'?'red':get(feature,'vep_impact')=='MODIFIER'?'purple':get(feature,'vep_impact')=='MODERATE'?'gold':get(feature,'vep_impact')=='LOW'?'cyan':'white'",
+ "showLabels" : false,
+ "outline" : "jexl:get(feature,'vep_impact')=='HIGH'?'red':get(feature,'vep_impact')=='MODIFIER'?'purple':get(feature,'vep_impact')=='MODERATE'?'gold':get(feature,'vep_impact')=='LOW'?'cyan':'black'",
+ "showDescriptions" : false
},
- "displayId" : "transposons-c_briggsae_PRJNA10731-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Transposons/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
+ "trackId" : "c_briggsae_PRJNA10731_classical_alleles",
+ "name" : "Classical Alleles",
+ "description" : "This track shows classical alleles comprised of insertions, deletions, substitutions and complex changes. These alleles were typically generated during forward genetic screens. Boxes represent deletions or substitutions; and white triangles represent insertions. Color signifies the severity of impact predicted by Ensembl's Variant Effect Predictor. 'HIGH' impacts are red, 'MEDIUM' are yellow, 'LOW' are cyan (light blue), and 'MODIFIER' are purple. This is the same color scheme as is used at the Alliance of Genome Resources.",
+ "assemblyNames" : [
+ "c_briggsae_PRJNA10731"
+ ],
"type" : "FeatureTrack",
- "name" : "Transposons",
- "description" : "These are transposon spans reviewed by WormBase curators."
+ "category" : [
+ "Alleles, Variations, RNAi"
+ ]
},
{
- "name" : "genBlastG CDS predictions",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/genBlastG CDS predictions/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "description" : "Data from 'genBlastG: using BLAST searches to build homologous gene models' (WBPaper00040677).",
- "trackId" : "c_briggsae_PRJNA10731_genblastg_cds_predictions",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
+ "type" : "FeatureTrack",
"category" : [
- "Genes",
- "Ab-initio predictions"
+ "Sequence Features",
+ "Translated Features"
],
+ "trackId" : "c_briggsae_PRJNA10731_protein_motifs",
+ "name" : "Protein motifs",
+ "description" : "This track shows the extent of predicted protein motifs. Note these spans correspond to amino acid coordinates interpolated onto the physical map. Included are signal peptide (signalp), coiled coil (ncoils) and transmembrane (tmhmm) domains, regions of low complexity (seg), and Pfam annotated motif homologies.",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"displays" : [
{
- "displayId" : "genblastg_cds_predictions-c_briggsae_PRJNA10731-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
+ "displayId" : "protein_motifs-c_briggsae_PRJNA10731-LinearBasicDisplay",
"renderer" : {
+ "color1" : "jexl:parent(feature)=='undefined'?'purple':get(parent(feature),'predictiontype')=='tmhmm'?'magenta':get(parent(feature),'predictiontype')=='seg'?'lightseagreen':get(parent(feature),'predictiontype')=='signalp'?'aquamarine':get(parent(feature),'predictiontype')=='ncoils'?'chartreuse':\nget(parent(feature),'predictiontype')=='pfam'?'lightsalmon':'purple'",
"height" : 7,
"type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay"
+ }
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Protein motifs/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
}
},
{
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "gene_models_(historical)-c_briggsae_PRJNA10731-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "color1" : "red",
- "height" : 6
- },
- "displayId" : "genome_sequence_errors-c_briggsae_PRJNA10731-LinearBasicDisplay"
+ "labels" : {
+ "description" : "jexl:get(feature,'type')"
+ },
+ "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'"
+ }
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Gene Models (historical)/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
},
- "trackId" : "c_briggsae_PRJNA10731_genome_sequence_errors",
- "category" : [
- "Genome Structure",
- "Assembly & Curation"
- ],
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
- "description" : "Positions within the reference genome sequence that have been identified as having a base call error. This error has not yet been corrected.",
- "name" : "Genome sequence errors",
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Genome sequence errors/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- }
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
+ "trackId" : "c_briggsae_PRJNA10731_gene_models_(historical)",
+ "name" : "Gene Models (historical)",
+ "description" : "Historical gene predictions."
},
{
"formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+'', WormBase: 'Variation Page'}"
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "curated_genes_(pseudogenes)-c_briggsae_PRJNA10731-LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "outline" : "jexl:get(feature,'vep_impact')=='HIGH'?'red':get(feature,'vep_impact')=='MODIFIER'?'purple':get(feature,'vep_impact')=='MODERATE'?'gold':get(feature,'vep_impact')=='LOW'?'cyan':'black'",
- "color1" : "jexl:get(feature,'vep_impact')=='HIGH'?'red':get(feature,'vep_impact')=='MODIFIER'?'purple':get(feature,'vep_impact')=='MODERATE'?'gold':get(feature,'vep_impact')=='LOW'?'cyan':'white'",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "displayId" : "classical_alleles-c_briggsae_PRJNA10731-LinearBasicDisplay"
+ "height" : 6,
+ "color1" : "gray",
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "assemblyNames" : [
- "c_briggsae_PRJNA10731"
- ],
- "category" : [
- "Alleles, Variations, RNAi"
- ],
- "trackId" : "c_briggsae_PRJNA10731_classical_alleles",
- "description" : "This track shows classical alleles comprised of insertions, deletions, substitutions and complex changes. These alleles were typically generated during forward genetic screens. Boxes represent deletions or substitutions; and white triangles represent insertions. Color signifies the severity of impact predicted by Ensembl's Variant Effect Predictor. 'HIGH' impacts are red, 'MEDIUM' are yellow, 'LOW' are cyan (light blue), and 'MODIFIER' are purple. This is the same color scheme as is used at the Alliance of Genome Resources.",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Classical_alleles/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Curated Genes (pseudogenes)/{refseq}/trackData.jsonz"
}
},
- "name" : "Classical Alleles"
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
+ "assemblyNames" : [
+ "c_briggsae_PRJNA10731"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "A subset of the full Curated Genes set limited to pseudogenes only. Pseudogenes of tRNA are lighter gray and pseudogenes of rRNA are darker gray than pseudogenes of protein coding genes.",
+ "trackId" : "c_briggsae_PRJNA10731_curated_genes_pseudogenes",
+ "name" : "Curated Genes (pseudogenes)"
},
{
- "description" : "This track shows the extent of predicted protein motifs. Note these spans correspond to amino acid coordinates interpolated onto the physical map. Included are signal peptide (signalp), coiled coil (ncoils) and transmembrane (tmhmm) domains, regions of low complexity (seg), and Pfam annotated motif homologies.",
- "name" : "Protein motifs",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Protein motifs/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "curated_genes_(protein_coding)-c_briggsae_PRJNA10731-LinearBasicDisplay",
"renderer" : {
- "height" : 7,
+ "maxHeight" : 5000,
"type" : "SvgFeatureRenderer",
- "color1" : "jexl:parent(feature)=='undefined'?'purple':get(parent(feature),'predictiontype')=='tmhmm'?'magenta':get(parent(feature),'predictiontype')=='seg'?'lightseagreen':get(parent(feature),'predictiontype')=='signalp'?'aquamarine':get(parent(feature),'predictiontype')=='ncoils'?'chartreuse':\nget(parent(feature),'predictiontype')=='pfam'?'lightsalmon':'purple'"
+ "color3" : "#965567",
+ "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'"
},
- "displayId" : "protein_motifs-c_briggsae_PRJNA10731-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
"formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
- "trackId" : "c_briggsae_PRJNA10731_protein_motifs",
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
+ "name" : "Curated Genes (protein coding)",
+ "trackId" : "c_briggsae_PRJNA10731_curated_genes_protein_coding",
"category" : [
- "Sequence Features",
- "Translated Features"
+ "Genes",
+ "Curated Genes"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
]
},
{
- "trackId" : "c_briggsae_PRJNA10731_gene_models_(historical)",
+ "trackId" : "c_briggsae_PRJNA10731_curated_genes",
+ "name" : "Curated Genes",
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
+ "assemblyNames" : [
+ "c_briggsae_PRJNA10731"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"Genes",
"Curated Genes"
],
- "assemblyNames" : [
- "c_briggsae_PRJNA10731"
- ],
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
- "type" : "SvgFeatureRenderer",
- "labels" : {
- "description" : "jexl:get(feature,'type')"
- }
- },
- "displayId" : "gene_models_(historical)-c_briggsae_PRJNA10731-LinearBasicDisplay"
- }
- ],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
- "name" : "Gene Models (historical)",
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Gene Models (historical)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Historical gene predictions."
- },
- {
- "description" : "A subset of the full Curated Genes set limited to pseudogenes only. Pseudogenes of tRNA are lighter gray and pseudogenes of rRNA are darker gray than pseudogenes of protein coding genes.",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Curated Genes (pseudogenes)/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Curated_Genes/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "name" : "Curated Genes (pseudogenes)",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
- "displays" : [
- {
- "displayId" : "curated_genes_(pseudogenes)-c_briggsae_PRJNA10731-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "gray"
- }
- }
- ],
- "assemblyNames" : [
- "c_briggsae_PRJNA10731"
- ],
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "trackId" : "c_briggsae_PRJNA10731_curated_genes_pseudogenes"
- },
- {
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "Curated Genes (protein coding)",
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
- "assemblyNames" : [
- "c_briggsae_PRJNA10731"
- ],
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "trackId" : "c_briggsae_PRJNA10731_curated_genes_protein_coding",
"formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ "feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
},
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "curated_genes-c_briggsae_PRJNA10731-LinearBasicDisplay",
"renderer" : {
- "color3" : "#965567",
"type" : "SvgFeatureRenderer",
"maxHeight" : 5000,
- "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'"
- },
- "displayId" : "curated_genes_(protein_coding)-c_briggsae_PRJNA10731-LinearBasicDisplay"
- }
- ]
- },
- {
- "name" : "Curated Genes",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Curated_Genes/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
- "trackId" : "c_briggsae_PRJNA10731_curated_genes",
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "assemblyNames" : [
- "c_briggsae_PRJNA10731"
- ],
- "displays" : [
- {
- "displayId" : "curated_genes-c_briggsae_PRJNA10731-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
"color3" : "#965567",
- "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
- "maxHeight" : 5000,
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
},
- "type" : "SvgFeatureRenderer"
+ "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'"
}
}
- ],
- "formatDetails" : {
- "feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
- }
+ ]
},
{
- "trackId" : "c_briggsae_PRJNA10731_polya_sites_and_signal_sequences",
- "category" : [
- "Sequence Features",
- "Signals & Motifs"
- ],
- "assemblyNames" : [
- "c_briggsae_PRJNA10731"
- ],
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
"labels" : {
"description" : "jexl:get(feature,'type') || get(feature,'description')"
},
- "type" : "SvgFeatureRenderer",
- "color1" : "purple"
+ "color1" : "purple",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "polya_sites_and_signal_sequences-c_briggsae_PRJNA10731-LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "name" : "PolyA sites and signal sequences",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/PolyA sites and signal sequences/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/PolyA sites and signal sequences/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
}
},
- "description" : "High-confidence polyadenylation signal sequences and sites calculated by an algorithm trained with verified sites from full-length mRNAs. Signals are indicated with a diamond; sites with a triangle."
- },
- {
- "trackId" : "c_briggsae_PRJNA10731_yacs_fosmids_cosmids",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
+ "type" : "FeatureTrack",
"category" : [
- "Reagents"
+ "Sequence Features",
+ "Signals & Motifs"
],
+ "trackId" : "c_briggsae_PRJNA10731_polya_sites_and_signal_sequences",
+ "name" : "PolyA sites and signal sequences",
+ "description" : "High-confidence polyadenylation signal sequences and sites calculated by an algorithm trained with verified sites from full-length mRNAs. Signals are indicated with a diamond; sites with a triangle."
+ },
+ {
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "yacs,_fosmids,_&_cosmids-c_briggsae_PRJNA10731-LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 3,
- "color1" : "black",
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "yacs,_fosmids,_&_cosmids-c_briggsae_PRJNA10731-LinearBasicDisplay"
+ "color1" : "black"
+ }
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
- "name" : "YACs, Fosmids, & Cosmids",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/YACs, Fosmids, & Cosmids/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
+ }
},
"type" : "FeatureTrack",
- "description" : "This track shows the locations of the cosmids, fosmids, and YACs used for the physical mapping and sequencing of the C. elegans genome. The clone termini do not necessarily correspond to the termini of submitted GenBank/EMBL entries. In some cases the exact termini of the clones is not known. For example, YACs were sequenced using PCR amplification across gaps in the cosmid maps. When a clone end is not known, it is shown as an arrow extending to the end of the display. Such data is to be treated with caution. The Vancouver fosmids can be ordered directly from GeneService."
- },
- {
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
"category" : [
- "Genes",
- "Curated Genes"
+ "Reagents"
],
+ "name" : "YACs, Fosmids, & Cosmids",
+ "trackId" : "c_briggsae_PRJNA10731_yacs_fosmids_cosmids",
+ "description" : "This track shows the locations of the cosmids, fosmids, and YACs used for the physical mapping and sequencing of the C. elegans genome. The clone termini do not necessarily correspond to the termini of submitted GenBank/EMBL entries. In some cases the exact termini of the clones is not known. For example, YACs were sequenced using PCR amplification across gaps in the cosmid maps. When a clone end is not known, it is shown as an arrow extending to the end of the display. Such data is to be treated with caution. The Vancouver fosmids can be ordered directly from GeneService."
+ },
+ {
+ "description" : "Non-coding curated gene models, including ncRNA, tRNA, miRNA, snRNA, snoRNA, piRNA, lincRNA and antisense RNA.",
+ "name" : "Curated Genes (noncoding)",
"trackId" : "c_briggsae_PRJNA10731_curated_genes_noncoding",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
- "displays" : [
- {
- "displayId" : "curated_genes_(noncoding)-c_briggsae_PRJNA10731-LinearBasicDisplay",
- "renderer" : {
- "height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "gray"
- },
- "type" : "LinearBasicDisplay"
- }
+ "category" : [
+ "Genes",
+ "Curated Genes"
],
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_briggsae_PRJNA10731"
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Curated Genes (noncoding)/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Curated Genes (noncoding)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
}
},
- "name" : "Curated Genes (noncoding)",
- "description" : "Non-coding curated gene models, including ncRNA, tRNA, miRNA, snRNA, snoRNA, piRNA, lincRNA and antisense RNA."
- },
- {
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "jexl:get(feature,'source')=='SL1'?'red':get(feature,'source')=='SL2'?'green':'black'",
- "labels" : {
- "description" : "jexl:get(feature,'source') || get(feature,'description')"
- },
+ "color1" : "gray",
+ "height" : 6,
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "trans-spliced_acceptor-c_briggsae_PRJNA10731-LinearBasicDisplay"
+ "displayId" : "curated_genes_(noncoding)-c_briggsae_PRJNA10731-LinearBasicDisplay"
}
],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ }
+ },
+ {
+ "description" : "This track contains SL1 and SL2 trans-spliced acceptors from a variety of sources: SL1 and SL2 trans-spliced acceptors published by Blumenthal et al, Nature (2002), Trans-Spliced Exon Coupled RNA End Determination (TEC-RED) Hwang et al, PNAS (2004), EST/mRNA sequence data, RNASeq read data from ENA. SL1 acceptors are show in red, SL2 in green. Direction of transcription is indicated by arrow direction.",
+ "trackId" : "c_briggsae_PRJNA10731_trans-spliced_acceptor",
+ "name" : "Trans-spliced acceptor",
"category" : [
"Sequence Features",
"Signals & Motifs"
@@ -5315,8 +4792,7 @@
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
- "trackId" : "c_briggsae_PRJNA10731_trans-spliced_acceptor",
- "description" : "This track contains SL1 and SL2 trans-spliced acceptors from a variety of sources: SL1 and SL2 trans-spliced acceptors published by Blumenthal et al, Nature (2002), Trans-Spliced Exon Coupled RNA End Determination (TEC-RED) Hwang et al, PNAS (2004), EST/mRNA sequence data, RNASeq read data from ENA. SL1 acceptors are show in red, SL2 in green. Direction of transcription is indicated by arrow direction.",
+ "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -5324,8 +4800,22 @@
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "name" : "Trans-spliced acceptor"
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "trans-spliced_acceptor-c_briggsae_PRJNA10731-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "labels" : {
+ "description" : "jexl:get(feature,'source') || get(feature,'description')"
+ },
+ "color1" : "jexl:get(feature,'source')=='SL1'?'red':get(feature,'source')=='SL2'?'green':'black'"
+ }
+ }
+ ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ }
},
{
"formatDetails" : {
@@ -5335,14 +4825,22 @@
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "outline" : "black",
- "color1" : "jexl:startsWith(get(feature,'source'),'BLAT_mRNA_')==true?'yellow':'gray'",
"type" : "SvgFeatureRenderer",
- "height" : 6
+ "color1" : "jexl:startsWith(get(feature,'source'),'BLAT_mRNA_')==true?'yellow':'gray'",
+ "height" : 6,
+ "outline" : "black"
},
"displayId" : "mrnas/ncrnas_(best)-c_briggsae_PRJNA10731-LinearBasicDisplay"
}
],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/mRNAs_ncRNAs (best)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
@@ -5350,19 +4848,15 @@
"Genes",
"Supporting Evidence"
],
+ "name" : "mRNAs/ncRNAs (best)",
"trackId" : "c_briggsae_PRJNA10731_mrnas/ncrnas_(best)",
- "description" : "Native (same species) full length cDNAs and ncRNAs aligned to the genome using BLAT. This track shows the best unique location for each cDNA.",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/mRNAs_ncRNAs (best)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "name" : "mRNAs/ncRNAs (best)"
+ "description" : "Native (same species) full length cDNAs and ncRNAs aligned to the genome using BLAT. This track shows the best unique location for each cDNA."
},
{
+ "name" : "Transposon Genes",
+ "trackId" : "c_briggsae_PRJNA10731_transposon_genes",
+ "description" : "These are transposon spans reviewed by WormBase curators.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
@@ -5370,77 +4864,73 @@
"Genes",
"Curated Genes"
],
- "trackId" : "c_briggsae_PRJNA10731_transposon_genes",
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Transposon Genes/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
"displays" : [
{
- "displayId" : "transposon_genes-c_briggsae_PRJNA10731-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "gray",
"labels" : {
"description" : "jexl:get(feature,'type')=='pseudogenic_transcript'?'transposon pseudogene':'transposon mRNA'"
- },
- "type" : "SvgFeatureRenderer",
- "height" : 6
+ }
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "transposon_genes-c_briggsae_PRJNA10731-LinearBasicDisplay"
}
- ],
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Transposon Genes/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "name" : "Transposon Genes",
- "description" : "These are transposon spans reviewed by WormBase curators."
+ ]
},
{
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Polymorphisms/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "Polymorphisms",
"description" : "This track shows single nucleotide polymorphisms (SNPs). In this track, the molecular nature of the polymorphism is indicated by its glyph: Boxes are deletions; triangles are insertions; point mutations and substitutions are diamonds. Color reflects the source strain: polymorphisms found in CB4858 (Pasadena) are shown in blue; those found in CB4856 (Hawaii) in yellow, and all others in white.",
- "assemblyNames" : [
- "c_briggsae_PRJNA10731"
- ],
+ "name" : "Polymorphisms",
+ "trackId" : "c_briggsae_PRJNA10731_polymorphisms",
"category" : [
"Alleles, Variations, RNAi"
],
- "trackId" : "c_briggsae_PRJNA10731_polymorphisms",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+'', WormBase: 'Variation Page'}"
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_briggsae_PRJNA10731"
+ ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Polymorphisms/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
},
"displays" : [
{
"displayId" : "polymorphisms-c_briggsae_PRJNA10731-LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'type')+': '+get(feature,'strain')",
"renderer" : {
"outline" : "jexl:get(feature,'strain')=='CB4858'||get(feature,'strain')=='AF16'?'blue':get(feature,'strain')=='CB4856'||get(feature,'strain')=='HK104'?'yellow':'black'",
"color1" : "jexl:get(feature,'strain')=='CB4858'||get(feature,'strain')=='AF16'?'blue':get(feature,'strain')=='CB4856'||get(feature,'strain')=='HK104'?'yellow':'white'",
- "maxHeight" : 5000,
- "type" : "SvgFeatureRenderer"
+ "type" : "SvgFeatureRenderer",
+ "maxHeight" : 5000
},
+ "mouseover" : "jexl:get(feature,'type')+': '+get(feature,'strain')",
"type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+'', WormBase: 'Variation Page'}"
+ }
},
{
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "darkgreen",
- "type" : "SvgFeatureRenderer"
+ "type" : "SvgFeatureRenderer",
+ "color1" : "darkgreen"
},
"displayId" : "dicistronic_mrnas-c_briggsae_PRJNA10731-LinearBasicDisplay"
}
@@ -5448,94 +4938,117 @@
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "trackId" : "c_briggsae_PRJNA10731_dicistronic_mrnas",
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Dicistronic mRNAs/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"category" : [
"Genes",
"Curated Genes"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
"description" : "Dicistronic mRNA operons - manually observed by curators",
"name" : "Dicistronic mRNAs",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Dicistronic mRNAs/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- }
+ "trackId" : "c_briggsae_PRJNA10731_dicistronic_mrnas"
},
{
- "description" : "This track shows single nucleotide polymorphisms (SNPs) that may generate a change of function. In this track, the molecular nature of the polymorphism is indicated by its glyph: Boxes are deletions or substitutions; triangles are insertions; point mutations are diamonds. Color signifies the severity of impact predicted by Ensembl's Variant Effect Predictor. 'HIGH' impacts are red, 'MEDIUM' are yellow, 'LOW' are cyan (light blue), and 'MODIFIER' are purple. This is the same color scheme as is used at the Alliance of Genome Resources.",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Change-of-function polymorphisms/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Change-of-function polymorphisms/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "name" : "Change of function polymorphisms",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+'', WormBase: 'Variation Page'}"
- },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "change_of_function_polymorphisms-c_briggsae_PRJNA10731-LinearBasicDisplay",
"renderer" : {
- "color1" : "jexl:get(feature,'vep_impact')=='HIGH'?'red':get(feature,'vep_impact')=='MODIFIER'?'purple':get(feature,'vep_impact')=='MODERATE'?'gold':get(feature,'vep_impact')=='LOW'?'cyan':'white'",
+ "type" : "SvgFeatureRenderer",
"maxHeight" : 5000,
"outline" : "jexl:get(feature,'vep_impact')=='HIGH'?'red':get(feature,'vep_impact')=='MODIFIER'?'purple':get(feature,'vep_impact')=='MODERATE'?'gold':get(feature,'vep_impact')=='LOW'?'cyan':'black'",
- "type" : "SvgFeatureRenderer"
+ "color1" : "jexl:get(feature,'vep_impact')=='HIGH'?'red':get(feature,'vep_impact')=='MODIFIER'?'purple':get(feature,'vep_impact')=='MODERATE'?'gold':get(feature,'vep_impact')=='LOW'?'cyan':'white'"
},
- "mouseover" : "jexl:get(feature,'name')+', '+get(feature,'consequence')",
- "type" : "LinearBasicDisplay",
- "displayId" : "change_of_function_polymorphisms-c_briggsae_PRJNA10731-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'name')+', '+get(feature,'consequence')"
}
],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+'', WormBase: 'Variation Page'}"
+ },
+ "description" : "This track shows single nucleotide polymorphisms (SNPs) that may generate a change of function. In this track, the molecular nature of the polymorphism is indicated by its glyph: Boxes are deletions or substitutions; triangles are insertions; point mutations are diamonds. Color signifies the severity of impact predicted by Ensembl's Variant Effect Predictor. 'HIGH' impacts are red, 'MEDIUM' are yellow, 'LOW' are cyan (light blue), and 'MODIFIER' are purple. This is the same color scheme as is used at the Alliance of Genome Resources.",
+ "name" : "Change of function polymorphisms",
+ "trackId" : "c_briggsae_PRJNA10731-change_of_function_polymorphisms",
"category" : [
"Alleles, Variations, RNAi"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
- ],
- "trackId" : "c_briggsae_PRJNA10731-change_of_function_polymorphisms"
+ ]
},
{
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/P. pacificus proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/P. pacificus proteins/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "P_pacificus_proteins-c_briggsae_PRJNA10731-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "orange",
+ "showLabels" : false,
+ "height" : 4
+ }
+ }
+ ],
+ "trackId" : "c_briggsae_PRJNA10731_P_pacificus_proteins",
"name" : "P. pacificus proteins",
"description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
- ],
- "trackId" : "c_briggsae_PRJNA10731_P_pacificus_proteins",
+ ]
+ },
+ {
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/H. sapiens proteins/{refseq}/trackData.jsonz"
+ }
+ },
"displays" : [
{
- "displayId" : "P_pacificus_proteins-c_briggsae_PRJNA10731-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "H_sapiens_proteins-c_briggsae_PRJNA10731-LinearBasicDisplay",
"renderer" : {
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
+ "height" : 4,
"color1" : "orange",
- "height" : 4
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "mouseover" : "jexl:get(feature,'clone')"
}
- ]
- },
- {
+ ],
+ "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_briggsae_PRJNA10731_H_sapiens_proteins",
+ "name" : "H. sapiens proteins",
"category" : [
"Sequence Similarity",
"Proteins"
@@ -5543,43 +5056,43 @@
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
- "trackId" : "c_briggsae_PRJNA10731_H_sapiens_proteins",
+ "type" : "FeatureTrack"
+ },
+ {
+ "assemblyNames" : [
+ "c_briggsae_PRJNA10731"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "trackId" : "c_briggsae_PRJNA10731_O_volvulus_proteins",
+ "name" : "O. volvulus proteins",
+ "description" : "Matches to WormBase O. volvulus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"displays" : [
{
"type" : "LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
"height" : 4,
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "orange"
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "H_sapiens_proteins-c_briggsae_PRJNA10731-LinearBasicDisplay"
+ "displayId" : "O_volvulus_proteins-c_briggsae_PRJNA10731-LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/H. sapiens proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "name" : "H. sapiens proteins",
- "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/O. volvulus proteins/{refseq}/trackData.jsonz"
+ }
+ }
},
{
- "name" : "O. volvulus proteins",
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/O. volvulus proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "description" : "Matches to WormBase O. volvulus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "trackId" : "c_briggsae_PRJNA10731_O_volvulus_proteins",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
@@ -5587,143 +5100,111 @@
"Sequence Similarity",
"Proteins"
],
+ "name" : "T. muris proteins",
+ "trackId" : "c_briggsae_PRJNA10731_T_muris_proteins",
+ "description" : "Matches to WormBase T. muris proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"displays" : [
{
- "displayId" : "O_volvulus_proteins-c_briggsae_PRJNA10731-LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
+ "showLabels" : false,
"height" : 4,
"color1" : "orange",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "type" : "SvgFeatureRenderer"
},
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "T_muris_proteins-c_briggsae_PRJNA10731-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/T. muris proteins/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_briggsae_PRJNA10731"
+ ],
+ "category" : [
+ "Genome Structure",
+ "Assembly & Curation"
+ ],
+ "name" : "Contig submissions",
+ "trackId" : "c_briggsae_PRJNA10731_contig_submissions",
+ "description" : "This track shows the location and coordinates of contigs (mostly cosmids) submitted to GenBank/EMBL.",
"displays" : [
{
"renderer" : {
- "height" : 4,
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "orange"
+ "height" : 7,
+ "color1" : "sienna"
},
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
- "displayId" : "T_muris_proteins-c_briggsae_PRJNA10731-LinearBasicDisplay"
+ "displayId" : "contig_submissions-c_briggsae_PRJNA10731-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_briggsae_PRJNA10731_T_muris_proteins",
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "c_briggsae_PRJNA10731"
- ],
- "description" : "Matches to WormBase T. muris proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "T. muris proteins",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/T. muris proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "type" : "FeatureTrack"
- },
- {
- "description" : "This track shows the location and coordinates of contigs (mostly cosmids) submitted to GenBank/EMBL.",
- "name" : "Contig submissions",
"adapter" : {
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Contig submissions/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
},
"type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "displays" : [
- {
- "renderer" : {
- "height" : 7,
- "type" : "SvgFeatureRenderer",
- "color1" : "sienna"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "contig_submissions-c_briggsae_PRJNA10731-LinearBasicDisplay"
- }
- ],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
- "trackId" : "c_briggsae_PRJNA10731_contig_submissions",
- "category" : [
- "Genome Structure",
- "Assembly & Curation"
- ],
- "assemblyNames" : [
- "c_briggsae_PRJNA10731"
- ]
+ }
},
{
- "trackId" : "c_briggsae_PRJNA10731_C_remanei_proteins",
- "assemblyNames" : [
- "c_briggsae_PRJNA10731"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
"displays" : [
{
"displayId" : "C_remanei_proteins-c_briggsae_PRJNA10731-LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
"color1" : "orange",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 4
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
},
+ "mouseover" : "jexl:get(feature,'clone')",
"type" : "LinearBasicDisplay"
}
],
- "name" : "C. remanei proteins",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/C. remanei proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/C. remanei proteins/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "assemblyNames" : [
+ "c_briggsae_PRJNA10731"
+ ],
"type" : "FeatureTrack",
- "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_briggsae_PRJNA10731_C_remanei_proteins",
+ "name" : "C. remanei proteins"
},
{
"displays" : [
{
- "type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "C_brenneri_proteins-c_briggsae_PRJNA10731-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
+ "color1" : "orange",
+ "height" : 4,
"showLabels" : false
},
- "displayId" : "C_brenneri_proteins-c_briggsae_PRJNA10731-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')",
+ "type" : "LinearBasicDisplay"
}
],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "c_briggsae_PRJNA10731"
- ],
- "trackId" : "c_briggsae_PRJNA10731_C_brenneri_proteins",
- "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"adapter" : {
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/C. brenneri proteins/{refseq}/trackData.jsonz",
@@ -5731,44 +5212,63 @@
},
"type" : "NCListAdapter"
},
+ "assemblyNames" : [
+ "c_briggsae_PRJNA10731"
+ ],
"type" : "FeatureTrack",
- "name" : "C. brenneri proteins"
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "trackId" : "c_briggsae_PRJNA10731_C_brenneri_proteins",
+ "name" : "C. brenneri proteins",
+ "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
},
{
- "displays" : [
- {
- "mouseover" : "jexl:'Score: '+get(feature,'score')",
- "renderer" : {
- "displayMode" : "collapse",
- "height" : 24,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "jexl:get(feature,'source')=='RNASeq_R_asymmetry'?'red': get(feature,'source')=='RNASeq_F_asymmetry'?'green':'black'"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "rnaseq_asymmetries-c_briggsae_PRJNA10731-LinearBasicDisplay"
- }
- ],
"trackId" : "c_briggsae_PRJNA10731_rnaseq_asymmetries",
+ "name" : "RNASeq Asymmetries",
+ "description" : "Red boxes indicate regions where there are more than 2 times as many forward sense RNASeq reads aligned to the genome as reverse sense reads. This asymmetrical signal has been found empirically to be a sensitive marker for the ends of transcripts. Green boxes indicate regions where there are more than 2 times as many reverse sense RNASeq reads aligned to the genome as forward sense reads. This asymmetrical signal has been found empirically to be sensitive marker for the ends of transcripts. The height of all boxes indicates the relative score of the feature.",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
+ "type" : "FeatureTrack",
"category" : [
"Expression"
],
- "description" : "Red boxes indicate regions where there are more than 2 times as many forward sense RNASeq reads aligned to the genome as reverse sense reads. This asymmetrical signal has been found empirically to be a sensitive marker for the ends of transcripts. Green boxes indicate regions where there are more than 2 times as many reverse sense RNASeq reads aligned to the genome as forward sense reads. This asymmetrical signal has been found empirically to be sensitive marker for the ends of transcripts. The height of all boxes indicates the relative score of the feature.",
- "name" : "RNASeq Asymmetries",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/RNASeq Asymmetries/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
+ "displays" : [
+ {
+ "renderer" : {
+ "color1" : "jexl:get(feature,'source')=='RNASeq_R_asymmetry'?'red': get(feature,'source')=='RNASeq_F_asymmetry'?'green':'black'",
+ "height" : 24,
+ "showLabels" : false,
+ "displayMode" : "collapse",
+ "type" : "SvgFeatureRenderer"
+ },
+ "mouseover" : "jexl:'Score: '+get(feature,'score')",
+ "displayId" : "rnaseq_asymmetries-c_briggsae_PRJNA10731-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- }
+ ]
},
{
+ "description" : "Native (same-species) Expressed Sequence Tags (ESTs), aligned to the genome using BLAT. This track shows the best unique location for each EST. The paired 5' and 3' ESTs from the same cDNA clone are connected by a dashed line and a colored light green. ESTs with no mate are yellow, and ESTs with a mate that is 'far away' are dark green.",
+ "name" : "ESTs",
+ "trackId" : "c_briggsae_PRJNA10731_ests",
+ "category" : [
+ "Genes",
+ "Supporting Evidence"
+ ],
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_briggsae_PRJNA10731"
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -5776,43 +5276,45 @@
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/ESTs (best)/{refseq}/trackData.jsonz"
}
},
- "name" : "ESTs",
- "description" : "Native (same-species) Expressed Sequence Tags (ESTs), aligned to the genome using BLAT. This track shows the best unique location for each EST. The paired 5' and 3' ESTs from the same cDNA clone are connected by a dashed line and a colored light green. ESTs with no mate are yellow, and ESTs with a mate that is 'far away' are dark green.",
- "assemblyNames" : [
- "c_briggsae_PRJNA10731"
- ],
- "category" : [
- "Genes",
- "Supporting Evidence"
- ],
- "trackId" : "c_briggsae_PRJNA10731_ests",
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
"maxHeight" : 5000,
- "color1" : "jexl:parent(feature)=='undefined'?'red':get(parent(feature),'has_mate')==1?'limegreen':get(parent(feature),'has_mate')==2?'green':get(parent(feature),'has_mate')==0?'gold':'black'",
- "type" : "SvgFeatureRenderer"
+ "type" : "SvgFeatureRenderer",
+ "color1" : "jexl:parent(feature)=='undefined'?'red':get(parent(feature),'has_mate')==1?'limegreen':get(parent(feature),'has_mate')==2?'green':get(parent(feature),'has_mate')==0?'gold':'black'"
},
- "displayId" : "ests-c_briggsae_PRJNA10731-LinearBasicDisplay"
+ "displayId" : "ests-c_briggsae_PRJNA10731-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
]
},
{
- "name" : "Nanopore matches",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Nanopore matches/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Nanopore matches/{refseq}/trackData.jsonz"
+ }
},
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "maxHeight" : 5000,
+ "type" : "SvgFeatureRenderer",
+ "height" : 4,
+ "showLabels" : false,
+ "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA'?'lightblue':'green'"
+ },
+ "displayId" : "nanopore_matches-c_briggsae_PRJNA10731-LinearBasicDisplay"
+ }
+ ],
"description" : "This Nanopore transcript data is from the paper 'The full-length transcriptome of C. elegans using direct RNA sequencing' Roach et al. https://doi.org/10.1101/598763. Where several transcripts are nearly identical, they are represented by a single transcript and the number of transcripts is recorded in the read coverage. Sequencing is from 3' to 5' and randomly terminates, so the 5' end of transcripts is often incomplete.",
"trackId" : "c_briggsae_PRJNA10731_nanopore_matches",
+ "name" : "Nanopore matches",
"category" : [
"Genes",
"Supporting Evidence"
@@ -5820,79 +5322,53 @@
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
+ "type" : "FeatureTrack"
+ },
+ {
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
- "displayId" : "nanopore_matches-c_briggsae_PRJNA10731-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
+ "displayId" : "repeat_region_(repeatmasker)-c_briggsae_PRJNA10731-LinearBasicDisplay",
"renderer" : {
- "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA'?'lightblue':'green'",
- "maxHeight" : 5000,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 4
- },
- "type" : "LinearBasicDisplay"
+ "height" : 4,
+ "showDescriptions" : false,
+ "color1" : "bisque",
+ "type" : "SvgFeatureRenderer"
+ }
}
- ]
- },
- {
+ ],
+ "trackId" : "c_briggsae_PRJNA10731_repeat_region_(repeatmasker)",
+ "name" : "Repeat Region (RepeatMasker)",
+ "description" : "Repetitive regions identified by RepeatMasker.",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
+ "type" : "FeatureTrack",
"category" : [
"Genome Structure",
"Repeats"
- ],
- "trackId" : "c_briggsae_PRJNA10731_repeat_region_(repeatmasker)",
- "displays" : [
- {
- "renderer" : {
- "color1" : "bisque",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 4,
- "showDescriptions" : false
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "repeat_region_(repeatmasker)-c_briggsae_PRJNA10731-LinearBasicDisplay"
- }
- ],
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz"
- }
- },
- "type" : "FeatureTrack",
- "name" : "Repeat Region (RepeatMasker)",
- "description" : "Repetitive regions identified by RepeatMasker."
+ ]
},
{
+ "name" : "Genbank submissions",
"trackId" : "c_briggsae_PRJNA10731_genbank_submissions",
- "category" : [
- "Genome Structure",
- "Assembly & Curation"
- ],
+ "description" : "The C. elegans genome was submitted to the GenBank and EMBL databases in in the form of a set of minimally-overlapping segments. This track shows the position of these accessioned entries.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'genbank')",
- "renderer" : {
- "height" : 4,
- "color1" : "sienna",
- "type" : "SvgFeatureRenderer"
- },
- "displayId" : "genbank_submissions-c_briggsae_PRJNA10731-LinearBasicDisplay"
- }
+ "category" : [
+ "Genome Structure",
+ "Assembly & Curation"
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
- "name" : "Genbank submissions",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -5900,164 +5376,175 @@
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Genbank submissions/{refseq}/trackData.jsonz"
}
},
- "description" : "The C. elegans genome was submitted to the GenBank and EMBL databases in in the form of a set of minimally-overlapping segments. This track shows the position of these accessioned entries."
- },
- {
"displays" : [
{
- "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "height" : 4,
+ "color1" : "sienna"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "S_ratti_proteins-c_briggsae_PRJNA10731-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'genbank')",
+ "displayId" : "genbank_submissions-c_briggsae_PRJNA10731-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ }
+ },
+ {
+ "description" : "Matches to WormBase S. ratti proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "S. ratti proteins",
"trackId" : "c_briggsae_PRJNA10731_S_ratti_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
- "description" : "Matches to WormBase S. ratti proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "S. ratti proteins",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/S. ratti proteins/{refseq}/trackData.jsonz"
}
- }
- },
- {
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/RNASeq introns/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
},
- "type" : "FeatureTrack",
- "name" : "RNASeq introns",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display.",
- "assemblyNames" : [
- "c_briggsae_PRJNA10731"
- ],
- "category" : [
- "Expression"
- ],
- "trackId" : "c_briggsae_PRJNA10731_rnaseq_introns",
"displays" : [
{
- "type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'score')+' reads'",
+ "displayId" : "S_ratti_proteins-c_briggsae_PRJNA10731-LinearBasicDisplay",
"renderer" : {
- "color1" : "green",
+ "height" : 4,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)",
- "showDescriptions" : false
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "rnaseq_introns-c_briggsae_PRJNA10731-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')",
+ "type" : "LinearBasicDisplay"
}
]
},
{
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/RNASeq introns/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
- "displayId" : "rnaseq_splice_junctions_(common)-c_briggsae_PRJNA10731-LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'score')+' reads'",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
- "showDescriptions" : false
+ "color1" : "green",
+ "height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)",
+ "showDescriptions" : false,
+ "showLabels" : false
},
- "type" : "LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'score')+' reads'",
+ "displayId" : "rnaseq_introns-c_briggsae_PRJNA10731-LinearBasicDisplay"
}
],
+ "name" : "RNASeq introns",
+ "trackId" : "c_briggsae_PRJNA10731_rnaseq_introns",
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_briggsae_PRJNA10731"
+ ],
+ "category" : [
+ "Expression"
+ ]
+ },
+ {
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
+ "name" : "RNASeq Splice Junctions (common)",
+ "trackId" : "c_briggsae_PRJNA10731_rnaseq_splice_junctions_(common)",
"category" : [
"Expression"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
- "trackId" : "c_briggsae_PRJNA10731_rnaseq_splice_junctions_(common)",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/RNASeq Splice Junctions (common)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "name" : "RNASeq Splice Junctions (common)"
- },
- {
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
- "name" : "RNASeq Splice Junctions (rare)",
"adapter" : {
"rootUrlTemplate" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/RNASeq Splice Junctions (common)/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "rnaseq_splice_junctions_(rare)-c_briggsae_PRJNA10731-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
+ "showLabels" : false,
+ "showDescriptions" : false
+ },
+ "mouseover" : "jexl:get(feature,'score')+' reads'",
+ "displayId" : "rnaseq_splice_junctions_(common)-c_briggsae_PRJNA10731-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ]
+ },
+ {
+ "displays" : [
+ {
"type" : "LinearBasicDisplay",
+ "displayId" : "rnaseq_splice_junctions_(rare)-c_briggsae_PRJNA10731-LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'score')+' reads'",
"renderer" : {
- "height" : "jexl:4",
- "type" : "SvgFeatureRenderer",
- "showDescriptions" : false,
"maxHeight" : 5000,
+ "type" : "SvgFeatureRenderer",
"color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
+ "height" : "jexl:4",
+ "showDescriptions" : false,
"showLabels" : false
}
}
],
- "trackId" : "c_briggsae_PRJNA10731_rnaseq_splice_junctions_(rare)",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"category" : [
"Expression"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
- ]
+ ],
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
+ "name" : "RNASeq Splice Junctions (rare)",
+ "trackId" : "c_briggsae_PRJNA10731_rnaseq_splice_junctions_(rare)"
},
{
- "description" : "Low-complexity regions identified by Dust.",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "name" : "Low complextity region (Dust)",
"displays" : [
{
+ "displayId" : "low_complextity_region_(dust)-c_briggsae_PRJNA10731-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "showDescriptions" : false,
"color1" : "bisque",
"showLabels" : false,
+ "height" : 4,
+ "showDescriptions" : false,
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "low_complextity_region_(dust)-c_briggsae_PRJNA10731-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"category" : [
"Genome Structure",
"Repeats"
@@ -6065,89 +5552,83 @@
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
- "trackId" : "c_briggsae_PRJNA10731_low_complextity_region_(dust)"
+ "type" : "FeatureTrack",
+ "description" : "Low-complexity regions identified by Dust.",
+ "trackId" : "c_briggsae_PRJNA10731_low_complextity_region_(dust)",
+ "name" : "Low complextity region (Dust)"
},
{
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Change-of-function alleles/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
- "displayId" : "change-of-function_alleles-c_briggsae_PRJNA10731-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
+ "maxHeight" : 5000,
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "jexl:get(feature,'vep_impact')=='HIGH'?'red':get(feature,'vep_impact')=='MODIFIER'?'purple':get(feature,'vep_impact')=='MODERATE'?'gold':get(feature,'vep_impact')=='LOW'?'cyan':'white'",
- "maxHeight" : 5000,
- "showDescriptions" : false
+ "showDescriptions" : false,
+ "showLabels" : false
},
- "mouseover" : "jexl:get(feature,'name')+', '+get(feature,'consequence')"
+ "mouseover" : "jexl:get(feature,'name')+', '+get(feature,'consequence')",
+ "displayId" : "change-of-function_alleles-c_briggsae_PRJNA10731-LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+'', WormBase: 'Variation Page'}"
},
"trackId" : "c_briggsae_PRJNA10731_change-of-function_alleles",
- "category" : [
- "Alleles, Variations, RNAi"
- ],
+ "name" : "Change-of-function alleles",
+ "description" : "This track shows alleles that generate a putative change-of-function. In this track, the type of mutation is indicated by its glyph: Boxes are deletions or substitutions. Triangles are insertions. Point mutations are diamonds. Color signifies the severity of impact predicted by Ensembl's Variant Effect Predictor. 'HIGH' impacts are red, 'MEDIUM' are yellow, 'LOW' are cyan (light blue), and 'MODIFIER' are purple. This is the same color scheme as is used at the Alliance of Genome Resources.",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
- "description" : "This track shows alleles that generate a putative change-of-function. In this track, the type of mutation is indicated by its glyph: Boxes are deletions or substitutions. Triangles are insertions. Point mutations are diamonds. Color signifies the severity of impact predicted by Ensembl's Variant Effect Predictor. 'HIGH' impacts are red, 'MEDIUM' are yellow, 'LOW' are cyan (light blue), and 'MODIFIER' are purple. This is the same color scheme as is used at the Alliance of Genome Resources.",
- "name" : "Change-of-function alleles",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Change-of-function alleles/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack"
+ "type" : "FeatureTrack",
+ "category" : [
+ "Alleles, Variations, RNAi"
+ ]
},
{
- "name" : "WormBase nematode mRNAs/ESTs (best)",
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA_BEST'?'lightblue':get(feature,'source')=='BLAT_Caen_EST_BEST'?'green':'black'",
+ "labels" : {
+ "name" : "jexl:get(feature,'species') || get(feature,'id')"
+ },
+ "height" : 4
+ },
+ "displayId" : "wormbase_nematode_mrnas/ests_(best)-c_briggsae_PRJNA10731-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/WormBase nematode mRNAs_ESTs (best)/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "description" : "ESTs and mRNAs from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each cDNA sequence. mRNAs are shown in light blue; ESTs in green.",
- "trackId" : "wormbase_nematode_mrnas/ests_(best)-c_briggsae_PRJNA10731",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Nucleotide"
],
- "displays" : [
- {
- "renderer" : {
- "height" : 4,
- "labels" : {
- "name" : "jexl:get(feature,'species') || get(feature,'id')"
- },
- "type" : "SvgFeatureRenderer",
- "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA_BEST'?'lightblue':get(feature,'source')=='BLAT_Caen_EST_BEST'?'green':'black'"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "wormbase_nematode_mrnas/ests_(best)-c_briggsae_PRJNA10731-LinearBasicDisplay"
- }
- ]
+ "trackId" : "wormbase_nematode_mrnas/ests_(best)-c_briggsae_PRJNA10731",
+ "name" : "WormBase nematode mRNAs/ESTs (best)",
+ "description" : "ESTs and mRNAs from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each cDNA sequence. mRNAs are shown in light blue; ESTs in green."
},
{
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Non-C. elegans Isoseq collection (best)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
"type" : "FeatureTrack",
- "name" : "Non-C. elegans Isoseq collection (best)",
- "description" : "IsoSeq from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each IsoSeqsequence.",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
@@ -6155,162 +5636,181 @@
"Sequence Similarity",
"Nucleotide"
],
+ "name" : "Non-C. elegans Isoseq collection (best)",
"trackId" : "non-c._elegans_isoseq_collection_(best)-c_briggsae_PRJNA10731",
+ "description" : "IsoSeq from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each IsoSeqsequence.",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "green",
"type" : "SvgFeatureRenderer",
+ "color1" : "green",
"height" : 4
},
"displayId" : "non-c._elegans_isoseq_collection_(best)-c_briggsae_PRJNA10731-LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Non-C. elegans Isoseq collection (best)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
- "trackId" : "c_briggsae_PRJNA10731_C_briggsae_proteins",
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "c_briggsae_PRJNA10731"
- ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/C. briggsae proteins/{refseq}/trackData.jsonz"
+ }
+ },
"displays" : [
{
- "displayId" : "C_briggsae_proteins-c_briggsae_PRJNA10731-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
"type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "orange",
- "height" : 4
+ "height" : 4,
+ "color1" : "orange"
},
- "mouseover" : "jexl:get(feature,'clone')"
+ "displayId" : "C_briggsae_proteins-c_briggsae_PRJNA10731-LinearBasicDisplay"
}
],
+ "trackId" : "c_briggsae_PRJNA10731_C_briggsae_proteins",
"name" : "C. briggsae proteins",
+ "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "assemblyNames" : [
+ "c_briggsae_PRJNA10731"
+ ],
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/C. briggsae proteins/{refseq}/trackData.jsonz"
- }
- },
- "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ]
},
{
- "description" : "BAC end-reads aligned to Assembly CB25 ultracontigs using BLAT. Best matches indicated in white, those with reduced but still significant nucleotide identity in gray.",
- "name" : "BAC end reads",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/BAC end reads/{refseq}/trackData.jsonz"
- }
- },
"displays" : [
{
+ "displayId" : "bac_end_reads-c_briggsae_PRJNA10731-LinearBasicDisplay",
"renderer" : {
- "outline" : "black",
"color1" : "white",
- "type" : "SvgFeatureRenderer",
- "height" : 6
+ "height" : 6,
+ "outline" : "black",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "bac_end_reads-c_briggsae_PRJNA10731-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_briggsae_PRJNA10731_bac_end_reads",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/BAC end reads/{refseq}/trackData.jsonz"
+ }
+ },
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
"category" : [
"Assembly"
- ]
+ ],
+ "name" : "BAC end reads",
+ "trackId" : "c_briggsae_PRJNA10731_bac_end_reads",
+ "description" : "BAC end-reads aligned to Assembly CB25 ultracontigs using BLAT. Best matches indicated in white, those with reduced but still significant nucleotide identity in gray."
},
{
+ "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_briggsae_PRJNA10731_C_japonica_proteins",
+ "name" : "C. japonica proteins",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "assemblyNames" : [
+ "c_briggsae_PRJNA10731"
+ ],
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/C. japonica proteins/{refseq}/trackData.jsonz"
+ }
+ },
"displays" : [
{
"displayId" : "C_japonica_proteins-c_briggsae_PRJNA10731-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
"height" : 4,
+ "showLabels" : false,
"color1" : "orange",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')",
"type" : "LinearBasicDisplay"
}
- ],
- "assemblyNames" : [
- "c_briggsae_PRJNA10731"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "trackId" : "c_briggsae_PRJNA10731_C_japonica_proteins",
- "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ ]
+ },
+ {
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/C. japonica proteins/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/C. elegans proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "name" : "C. japonica proteins"
- },
- {
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "C_elegans_proteins-c_briggsae_PRJNA10731-LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
"showLabels" : false,
- "height" : 4
+ "height" : 4,
+ "color1" : "orange"
},
- "type" : "LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')"
}
],
+ "name" : "C. elegans proteins",
"trackId" : "c_briggsae_PRJNA10731_C_elegans_proteins",
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
+ "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
- "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "C. elegans proteins",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/C. elegans proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- }
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ]
},
{
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Tandem and Inverted Repeats/{refseq}/trackData.jsonz"
+ }
+ },
"displays" : [
{
- "displayId" : "tandem_and_inverted_repeats-c_briggsae_PRJNA10731-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "showDescriptions" : false,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "bisque",
- "showDescriptions" : false
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "tandem_and_inverted_repeats-c_briggsae_PRJNA10731-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
+ "description" : "Exact tandem and inverted repetitive elements.",
+ "trackId" : "c_briggsae_PRJNA10731_tandem_and_inverted_repeats",
+ "name" : "Tandem and Inverted Repeats",
"category" : [
"Genome Structure",
"Repeats"
@@ -6318,107 +5818,75 @@
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
- "trackId" : "c_briggsae_PRJNA10731_tandem_and_inverted_repeats",
- "description" : "Exact tandem and inverted repetitive elements.",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Tandem and Inverted Repeats/{refseq}/trackData.jsonz"
- }
- },
- "name" : "Tandem and Inverted Repeats"
+ "type" : "FeatureTrack"
},
{
+ "displays" : [
+ {
+ "displayId" : "S_cerevisiae_proteins-c_briggsae_PRJNA10731-LinearBasicDisplay",
+ "renderer" : {
+ "showLabels" : false,
+ "height" : 4,
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
+ },
+ "mouseover" : "jexl:get(feature,'clone')",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "NCListAdapter"
},
+ "assemblyNames" : [
+ "c_briggsae_PRJNA10731"
+ ],
"type" : "FeatureTrack",
- "name" : "S. cerevisiae proteins",
- "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "assemblyNames" : [
- "c_briggsae_PRJNA10731"
- ],
"trackId" : "c_briggsae_PRJNA10731_S_cerevisiae_proteins",
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
- "renderer" : {
- "height" : 4,
- "color1" : "orange",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "displayId" : "S_cerevisiae_proteins-c_briggsae_PRJNA10731-LinearBasicDisplay"
- }
- ]
+ "name" : "S. cerevisiae proteins",
+ "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
},
{
+ "description" : "This track contains Affymetrix GeneChip and Washington University GSC microarray probe sets.",
"trackId" : "c_briggsae_PRJNA10731_microarray_oligo_probes",
+ "name" : "Microarray oligo probes",
"category" : [
"Reagents"
],
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Microarray oligo probes/{refseq}/trackData.jsonz"
+ }
+ },
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 4,
- "color1" : "black",
- "type" : "SvgFeatureRenderer"
+ "color1" : "black"
},
"displayId" : "microarray_oligo_probes-c_briggsae_PRJNA10731-LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
- "name" : "Microarray oligo probes",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Microarray oligo probes/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "This track contains Affymetrix GeneChip and Washington University GSC microarray probe sets."
+ }
},
{
- "trackId" : "c_briggsae_PRJNA10731_trinity-assembled_rnaseq",
- "assemblyNames" : [
- "c_briggsae_PRJNA10731"
- ],
- "category" : [
- "Genes",
- "Supporting Evidence"
- ],
- "displays" : [
- {
- "displayId" : "trinity-assembled_rnaseq-c_briggsae_PRJNA10731-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "mediumpurple",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 5
- }
- }
- ],
- "name" : "Trinity-assembled RNAseq",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -6426,24 +5894,35 @@
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Trinity-assembled RNAseq/{refseq}/trackData.jsonz"
}
},
- "description" : "Native (same species) RNAseq data was assembled with Trinity and then aligned to the genome with BLAT"
- },
- {
"displays" : [
{
- "displayId" : "tec-red_tags-c_briggsae_PRJNA10731-LinearBasicDisplay",
+ "displayId" : "trinity-assembled_rnaseq-c_briggsae_PRJNA10731-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "red",
- "height" : 5
+ "showLabels" : false,
+ "height" : 5,
+ "color1" : "mediumpurple",
+ "type" : "SvgFeatureRenderer"
},
"type" : "LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
+ "name" : "Trinity-assembled RNAseq",
+ "trackId" : "c_briggsae_PRJNA10731_trinity-assembled_rnaseq",
+ "description" : "Native (same species) RNAseq data was assembled with Trinity and then aligned to the genome with BLAT",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_briggsae_PRJNA10731"
+ ],
+ "category" : [
+ "Genes",
+ "Supporting Evidence"
+ ]
+ },
+ {
+ "name" : "TEC-RED tags",
"trackId" : "c_briggsae_PRJNA10731_tec-red_tags",
+ "description" : "Trans-spliced Exon Coupled RNA End Determination (TEC-RED) tags. TEC-RED uses a method similar to SAGE to identify expressed genes and characterize the 5' end of transcripts.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
@@ -6451,153 +5930,176 @@
"Genes",
"Supporting Evidence"
],
- "description" : "Trans-spliced Exon Coupled RNA End Determination (TEC-RED) tags. TEC-RED uses a method similar to SAGE to identify expressed genes and characterize the 5' end of transcripts.",
- "name" : "TEC-RED tags",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/TEC-RED tags/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/TEC-RED tags/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack"
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "red",
+ "height" : 5
+ },
+ "displayId" : "tec-red_tags-c_briggsae_PRJNA10731-LinearBasicDisplay"
+ }
+ ]
},
{
- "assemblyNames" : [
- "c_briggsae_PRJNA10731"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "trackId" : "c_briggsae_PRJNA10731_B_malayi_proteins",
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/B. malayi proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
"displayId" : "B_malayi_proteins-c_briggsae_PRJNA10731-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
"type" : "SvgFeatureRenderer",
+ "height" : 4,
"showLabels" : false,
"color1" : "orange"
},
- "mouseover" : "jexl:get(feature,'clone')"
+ "type" : "LinearBasicDisplay"
}
],
+ "description" : "Matches to WormBase B. malayi proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_briggsae_PRJNA10731_B_malayi_proteins",
+ "name" : "B. malayi proteins",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "assemblyNames" : [
+ "c_briggsae_PRJNA10731"
+ ],
+ "type" : "FeatureTrack"
+ },
+ {
"adapter" : {
"rootUrlTemplate" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/B. malayi proteins/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/RNASeq/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "name" : "B. malayi proteins",
- "description" : "Matches to WormBase B. malayi proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
- },
- {
"displays" : [
{
+ "mouseover" : "jexl:'Score: '+get(feature,'score')",
"renderer" : {
- "height" : "jexl:get(feature,'score')>100?50:floor(get(feature,'score')/2)>4?floor(get(feature,'score')/2):4",
- "showDescriptions" : false,
"displayMode" : "collapse",
+ "type" : "SvgFeatureRenderer",
"color1" : "black",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "showDescriptions" : false,
+ "height" : "jexl:get(feature,'score')>100?50:floor(get(feature,'score')/2)>4?floor(get(feature,'score')/2):4",
+ "showLabels" : false
},
- "mouseover" : "jexl:'Score: '+get(feature,'score')",
- "type" : "LinearBasicDisplay",
- "displayId" : "rnaseq-c_briggsae_PRJNA10731-LinearBasicDisplay"
+ "displayId" : "rnaseq-c_briggsae_PRJNA10731-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
+ "trackId" : "c_briggsae_PRJNA10731_rnaseq",
+ "name" : "RNASeq",
+ "description" : "These boxes indicate alignments of short read sequences from all available RNASeq projects. The number of reads has been normalised by averaging over the number of libraries. The height of all boxes indicates the relative score of the feature.",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
+ "type" : "FeatureTrack",
"category" : [
"Expression"
- ],
- "trackId" : "c_briggsae_PRJNA10731_rnaseq",
- "description" : "These boxes indicate alignments of short read sequences from all available RNASeq projects. The number of reads has been normalised by averaging over the number of libraries. The height of all boxes indicates the relative score of the feature.",
+ ]
+ },
+ {
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/RNASeq/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz"
}
},
- "type" : "FeatureTrack",
- "name" : "RNASeq"
- },
- {
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
"color1" : "orange",
- "height" : 4
+ "height" : 4,
+ "showLabels" : false
},
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
"displayId" : "D_melanogaster_proteins-c_briggsae_PRJNA10731-LinearBasicDisplay"
}
],
+ "trackId" : "c_briggsae_PRJNA10731_D_melanogaster_proteins",
+ "name" : "D. melanogaster proteins",
+ "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
- ],
- "trackId" : "c_briggsae_PRJNA10731_D_melanogaster_proteins",
- "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "D. melanogaster proteins"
+ ]
},
{
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Links and Superlinks/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "Links and Superlinks",
"description" : "This track shows the location and coordinates of contigs created during the assembly of the C. elegans genome.",
+ "name" : "Links and Superlinks",
+ "trackId" : "c_briggsae_PRJNA10731_links_and_superlinks",
"category" : [
"Genome Structure",
"Assembly & Curation"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
- "trackId" : "c_briggsae_PRJNA10731_links_and_superlinks",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Links and Superlinks/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
},
"displays" : [
{
- "displayId" : "links_and_superlinks-c_briggsae_PRJNA10731-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"color1" : "black",
- "height" : 4
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "links_and_superlinks-c_briggsae_PRJNA10731-LinearBasicDisplay"
}
- ]
+ ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ }
},
{
- "name" : "Other UniProt proteins",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "other_uniprot_proteins-c_briggsae_PRJNA10731-LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "orange",
+ "height" : 4,
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
+ }
+ }
+ ],
"adapter" : {
"rootUrlTemplate" : {
"locationType" : "UriLocation",
@@ -6605,343 +6107,233 @@
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "trackId" : "c_briggsae_PRJNA10731_other_uniprot_proteins",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "showDescriptions" : false,
- "height" : 4,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "orange"
- },
- "displayId" : "other_uniprot_proteins-c_briggsae_PRJNA10731-LinearBasicDisplay"
- }
- ]
+ "trackId" : "c_briggsae_PRJNA10731_other_uniprot_proteins",
+ "name" : "Other UniProt proteins",
+ "description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation)."
},
{
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/Operons/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "Operons",
- "description" : "this is a published set of operons from WBPaper00041271.",
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "assemblyNames" : [
- "c_briggsae_PRJNA10731"
- ],
- "trackId" : "c_briggsae_PRJNA10731_operons",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
+ "type" : "NCListAdapter"
},
"displays" : [
{
- "displayId" : "operons-c_briggsae_PRJNA10731-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "operons-c_briggsae_PRJNA10731-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "green"
+ "color1" : "green",
+ "type" : "SvgFeatureRenderer"
}
}
- ]
- },
- {
+ ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
+ "name" : "Operons",
+ "trackId" : "c_briggsae_PRJNA10731_operons",
+ "description" : "this is a published set of operons from WBPaper00041271.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ]
+ },
+ {
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
+ "assemblyNames" : [
+ "c_briggsae_PRJNA10731"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
"trackId" : "c_briggsae_PRJNA10731_TTCN_sequence_search",
+ "name" : "Cas12e TTCN PAM sites",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "TTCN_sequence_search_c_briggsae_PRJNA10731-LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
"height" : 4,
- "type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
"showLabels" : false,
- "color1" : "SlateBlue"
- },
- "type" : "LinearBasicDisplay"
+ "color1" : "SlateBlue",
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "SequenceSearchAdapter",
"search" : "TTC.",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
"type" : "BgzipFastaAdapter",
"gziLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_briggsae.PRJNA10731.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
},
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_briggsae.PRJNA10731.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
+ },
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_briggsae.PRJNA10731.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
- },
- "fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_briggsae.PRJNA10731.WS284.genomic.fa.gz"
}
}
- },
- "name" : "Cas12e TTCN PAM sites",
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time."
+ }
},
{
- "displays" : [
- {
- "displayId" : "TTN_sequence_search_c_briggsae_PRJNA10731-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "Indigo",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "height" : 4,
- "showDescriptions" : false
- }
- }
+ "name" : "Cas12a TTN PAM sites",
+ "trackId" : "c_briggsae_PRJNA10731_TTN_sequence_search",
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_briggsae_PRJNA10731"
],
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "assemblyNames" : [
- "c_briggsae_PRJNA10731"
- ],
- "trackId" : "c_briggsae_PRJNA10731_TTN_sequence_search",
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
- "type" : "FeatureTrack",
"adapter" : {
"search" : "TT.",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_briggsae.PRJNA10731.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
- },
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_briggsae.PRJNA10731.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
- },
"gziLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_briggsae.PRJNA10731.WS284.genomic.fa.gz.gzi"
},
- "type" : "BgzipFastaAdapter"
- },
- "type" : "SequenceSearchAdapter"
- },
- "name" : "Cas12a TTN PAM sites"
- },
- {
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "SequenceSearchAdapter",
- "sequenceAdapter" : {
"type" : "BgzipFastaAdapter",
- "gziLocation" : {
+ "fastaLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_briggsae.PRJNA10731.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_briggsae.PRJNA10731.WS284.genomic.fa.gz"
},
"faiLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_briggsae.PRJNA10731.WS284.genomic.fa.gz.fai"
- },
- "fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_briggsae.PRJNA10731.WS284.genomic.fa.gz"
}
- },
- "search" : "..G[AG][AG]T"
+ }
},
- "name" : "SaCas9 NNGRRT PAM sites",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "DarkViolet",
+ "height" : 4,
"showDescriptions" : false,
- "height" : 4
+ "color1" : "Indigo",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "NNGRRT_sequence_search_c_briggsae_PRJNA10731-LinearBasicDisplay"
+ "displayId" : "TTN_sequence_search_c_briggsae_PRJNA10731-LinearBasicDisplay"
}
- ],
- "assemblyNames" : [
- "c_briggsae_PRJNA10731"
- ],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "trackId" : "c_briggsae_PRJNA10731_NNGRRT_sequence_search"
+ ]
},
{
- "assemblyNames" : [
- "c_briggsae_PRJNA10731"
- ],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "trackId" : "c_briggsae_PRJNA10731_NGG_sequence_search",
- "displays" : [
- {
- "displayId" : "NGG_sequence_search_c_briggsae_PRJNA10731-LinearBasicDisplay",
- "renderer" : {
- "color1" : "RebeccaPurple",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 4,
- "showDescriptions" : false
- },
- "type" : "LinearBasicDisplay"
- }
- ],
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_briggsae.PRJNA10731.WS284.genomic.fa.gz.fai",
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_briggsae.PRJNA10731.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
},
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_briggsae.PRJNA10731.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
- "gziLocation" : {
+ "faiLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_briggsae.PRJNA10731.WS284.genomic.fa.gz.gzi"
- },
- "type" : "BgzipFastaAdapter"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_briggsae.PRJNA10731.WS284.genomic.fa.gz.fai"
+ }
},
- "search" : ".GG"
- },
- "name" : "SpCas9 NGG PAM sites",
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time."
- },
- {
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display.",
- "name" : "RNASeq introns",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/RNASeq introns/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
+ "type" : "SequenceSearchAdapter",
+ "search" : "..G[AG][AG]T"
},
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "rnaseq_introns-c_briggsae_PRJNA10731-LinearBasicDisplay",
+ "displayId" : "NNGRRT_sequence_search_c_briggsae_PRJNA10731-LinearBasicDisplay",
"renderer" : {
- "height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)",
+ "color1" : "DarkViolet",
"showDescriptions" : false,
- "color1" : "green",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "height" : 4,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'score')+' reads'",
"type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_briggsae_PRJNA10731_rnaseq_introns",
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
+ "name" : "SaCas9 NNGRRT PAM sites",
+ "trackId" : "c_briggsae_PRJNA10731_NNGRRT_sequence_search",
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
- ],
- "category" : [
- "Expression"
]
},
{
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
"adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/RNASeq Splice Junctions (common)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "search" : ".GG",
+ "sequenceAdapter" : {
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_briggsae.PRJNA10731.WS284.genomic.fa.gz.gzi"
+ },
+ "fastaLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_briggsae.PRJNA10731.WS284.genomic.fa.gz"
+ },
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_briggsae.PRJNA10731.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
+ }
},
- "type" : "NCListAdapter"
+ "type" : "SequenceSearchAdapter"
},
- "type" : "FeatureTrack",
- "name" : "RNASeq Splice Junctions (common)",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "NGG_sequence_search_c_briggsae_PRJNA10731-LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "color1" : "jexl:get(feature,'score')>1000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/1000))))+'00'+hex(round(255-(140*(get(feature,'score')/1000)))):'#00'+hex(round(255-(140*(get(feature,'score')/1000))))+hex(round(255-(140*(get(feature,'score')/1000))))",
"type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "mouseover" : "jexl:get(feature,'score')+' reads'",
- "displayId" : "rnaseq_splice_junctions_(common)-c_briggsae_PRJNA10731-LinearBasicDisplay"
+ "color1" : "RebeccaPurple",
+ "showLabels" : false,
+ "height" : 4,
+ "showDescriptions" : false
+ }
}
],
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
+ "name" : "SpCas9 NGG PAM sites",
+ "trackId" : "c_briggsae_PRJNA10731_NGG_sequence_search",
"category" : [
- "Expression"
- ],
- "assemblyNames" : [
- "c_briggsae_PRJNA10731"
+ "Externally Sourced Resources",
+ "CRISPR predictions"
],
- "trackId" : "c_briggsae_PRJNA10731_rnaseq_splice_junctions_(common)"
- },
- {
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
"type" : "FeatureTrack",
- "name" : "RNASeq Splice Junctions (rare)",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
- "category" : [
- "Expression"
- ],
"assemblyNames" : [
"c_briggsae_PRJNA10731"
- ],
- "trackId" : "c_briggsae_PRJNA10731_rnaseq_splice_junctions_(rare)",
- "displays" : [
- {
- "displayId" : "rnaseq_splice_junctions_(rare)-c_briggsae_PRJNA10731-LinearBasicDisplay",
- "renderer" : {
- "color1" : "jexl:get(feature,'score')>1000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/1000))))+'00'+hex(round(255-(140*(get(feature,'score')/1000)))):'#00'+hex(round(255-(140*(get(feature,'score')/1000))))+hex(round(255-(140*(get(feature,'score')/1000))))",
- "maxHeight" : 5000,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "height" : "jexl:4",
- "showDescriptions" : false
- },
- "mouseover" : "jexl:get(feature,'score')+' reads'",
- "type" : "LinearBasicDisplay"
- }
]
},
{
+ "type" : "VariantTrack",
"assemblyNames" : [
"c_briggsae_PRJNA10731"
],
@@ -6949,80 +6341,68 @@
"Externally Sourced Resources",
"Other"
],
+ "name" : "C. briggsae variation",
"trackId" : "c_briggsae_PRJNA10731_variation",
+ "description" : "This track shows C. briggsae SNPs from the Cutter Lab (University of Toronto). Here they performed high-coverage whole-genome sequencing of 37 wild isolates of the nematode C. briggsae; SNP calling was done by GATK UnifiedGenotyper. After filtering a total of 2,700,664 sites across all strains were identified, of which 439,139 SNPs had high-quality allele calls in every strain. (WBPaper00046558) Thomas CG et al. (2015) Genome Res 'Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis.'",
"displays" : [
{
"type" : "LinearVariantDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "green"
+ "color1" : "green",
+ "type" : "SvgFeatureRenderer"
},
"displayId" : "c_briggsae_PRJNA10731_variation-LinearVariantDisplay"
},
{
- "type" : "ChordVariantDisplay",
- "displayId" : "c_briggsae_PRJNA10731_variation-ChordVariantDisplay"
+ "displayId" : "c_briggsae_PRJNA10731_variation-ChordVariantDisplay",
+ "type" : "ChordVariantDisplay"
}
],
"adapter" : {
+ "type" : "VcfTabixAdapter",
"index" : {
"location" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/jbrowse/data/c_briggsae_PRJNA10731/c.briggsae_snps.vcf.gz.tbi"
}
},
- "type" : "VcfTabixAdapter",
"vcfGzLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/jbrowse/data/c_briggsae_PRJNA10731/c.briggsae_snps.vcf.gz",
"locationType" : "UriLocation"
}
- },
- "type" : "VariantTrack",
- "name" : "C. briggsae variation",
- "description" : "This track shows C. briggsae SNPs from the Cutter Lab (University of Toronto). Here they performed high-coverage whole-genome sequencing of 37 wild isolates of the nematode C. briggsae; SNP calling was done by GATK UnifiedGenotyper. After filtering a total of 2,700,664 sites across all strains were identified, of which 439,139 SNPs had high-quality allele calls in every strain. (WBPaper00046558) Thomas CG et al. (2015) Genome Res 'Full-genome evolutionary histories of selfing, splitting, and selection in Caenorhabditis.'"
+ }
},
{
- "trackId" : "c_elegans_PRJEB28388_n2_genes_(minimap)",
"category" : [
"Genes",
"Supporting Evidence"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJEB28388"
],
+ "description" : "Regions present in the VC2010 assembly that are not in the N2 assembly.",
+ "name" : "N2 Genes (minimap)",
+ "trackId" : "c_elegans_PRJEB28388_n2_genes_(minimap)",
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 5,
- "type" : "SvgFeatureRenderer"
+ "type" : "SvgFeatureRenderer",
+ "height" : 5
},
- "displayId" : "c_elegans_PRJEB28388_n2_genes_(minimap)-LinearBasicDisplay"
+ "displayId" : "c_elegans_PRJEB28388_n2_genes_(minimap)-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "name" : "N2 Genes (minimap)",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/N2 Genes (minimap)/{refseq}/trackData.jsonz"
- }
- },
- "description" : "Regions present in the VC2010 assembly that are not in the N2 assembly."
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/N2 Genes (minimap)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
- "name" : "Curated Genes (noncoding)",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/Curated Genes (noncoding)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "description" : "Non-coding curated gene models, including ncRNA, tRNA, miRNA, snRNA, snoRNA, piRNA, lincRNA and antisense RNA.",
- "trackId" : "c_elegans_PRJEB28388_curated_genes_noncoding",
"category" : [
"Genes",
"Curated Genes"
@@ -7030,12 +6410,16 @@
"assemblyNames" : [
"c_elegans_PRJEB28388"
],
+ "type" : "FeatureTrack",
+ "description" : "Non-coding curated gene models, including ncRNA, tRNA, miRNA, snRNA, snoRNA, piRNA, lincRNA and antisense RNA.",
+ "trackId" : "c_elegans_PRJEB28388_curated_genes_noncoding",
+ "name" : "Curated Genes (noncoding)",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "gray",
"type" : "SvgFeatureRenderer",
+ "color1" : "gray",
"height" : 6
},
"displayId" : "curated_genes_(noncoding)-c_elegans_PRJEB28388-LinearBasicDisplay"
@@ -7043,297 +6427,370 @@
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/Curated Genes (noncoding)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
}
},
{
+ "trackId" : "c_elegans_PRJEB28388_curated_genes",
+ "name" : "Curated Genes",
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
+ "assemblyNames" : [
+ "c_elegans_PRJEB28388"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/Curated_Genes/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"formatDetails" : {
"feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
},
"displays" : [
{
- "displayId" : "curated_genes-c_elegans_PRJEB28388-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
+ "maxHeight" : 5000,
"type" : "SvgFeatureRenderer",
+ "color3" : "#965567",
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
},
- "maxHeight" : 5000,
- "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
- "color3" : "#965567"
- }
+ "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'"
+ },
+ "displayId" : "curated_genes-c_elegans_PRJEB28388-LinearBasicDisplay"
}
+ ]
+ },
+ {
+ "name" : "Curated Genes (pseudogenes)",
+ "trackId" : "c_elegans_PRJEB28388_curated_genes_pseudogenes",
+ "description" : "A subset of the full Curated Genes set limited to pseudogenes only. Pseudogenes of tRNA are lighter gray and pseudogenes of rRNA are darker gray than pseudogenes of protein coding genes.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJEB28388"
],
"category" : [
"Genes",
"Curated Genes"
],
- "assemblyNames" : [
- "c_elegans_PRJEB28388"
- ],
- "trackId" : "c_elegans_PRJEB28388_curated_genes",
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/Curated_Genes/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/Curated Genes (pseudogenes)/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "name" : "Curated Genes"
- },
- {
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "assemblyNames" : [
- "c_elegans_PRJEB28388"
- ],
- "trackId" : "c_elegans_PRJEB28388_curated_genes_pseudogenes",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
"displays" : [
{
- "displayId" : "curated_genes_(pseudogenes)-c_elegans_PRJEB28388-LinearBasicDisplay",
"renderer" : {
- "color1" : "gray",
"type" : "SvgFeatureRenderer",
+ "color1" : "gray",
"height" : 6
},
+ "displayId" : "curated_genes_(pseudogenes)-c_elegans_PRJEB28388-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/Curated Genes (pseudogenes)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "Curated Genes (pseudogenes)",
- "description" : "A subset of the full Curated Genes set limited to pseudogenes only. Pseudogenes of tRNA are lighter gray and pseudogenes of rRNA are darker gray than pseudogenes of protein coding genes."
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ }
},
{
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
- "name" : "Curated Genes (protein coding)",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
+ }
},
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "curated_genes_(protein_coding)-c_elegans_PRJEB28388-LinearBasicDisplay",
"renderer" : {
- "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
"maxHeight" : 5000,
"type" : "SvgFeatureRenderer",
- "color3" : "#965567"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "curated_genes_(protein_coding)-c_elegans_PRJEB28388-LinearBasicDisplay"
+ "color3" : "#965567",
+ "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'"
+ }
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
+ "name" : "Curated Genes (protein coding)",
"trackId" : "c_elegans_PRJEB28388_curated_genes_protein_coding",
- "assemblyNames" : [
- "c_elegans_PRJEB28388"
- ],
"category" : [
"Genes",
"Curated Genes"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJEB28388"
]
},
{
- "description" : "These are transposon spans reviewed by WormBase curators.",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/Transposon Genes/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJEB28388"
+ ],
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
"name" : "Transposon Genes",
+ "trackId" : "c_elegans_PRJEB28388_transposon_genes",
+ "description" : "These are transposon spans reviewed by WormBase curators.",
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "transposon_genes-c_elegans_PRJEB28388-LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 6,
"color1" : "gray",
"labels" : {
"description" : "jexl:get(feature,'type')=='pseudogenic_transcript'?'transposon pseudogene':'transposon mRNA'"
- },
- "type" : "SvgFeatureRenderer"
- },
- "displayId" : "transposon_genes-c_elegans_PRJEB28388-LinearBasicDisplay"
+ }
+ }
}
],
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "assemblyNames" : [
- "c_elegans_PRJEB28388"
- ],
- "trackId" : "c_elegans_PRJEB28388_transposon_genes"
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/Transposon Genes/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
- "displayId" : "D_melanogaster_proteins-c_elegans_PRJEB28388-LinearBasicDisplay",
"renderer" : {
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
+ "color1" : "orange",
"showLabels" : false,
"height" : 4
},
"mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "D_melanogaster_proteins-c_elegans_PRJEB28388-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
+ "name" : "D. melanogaster proteins",
"trackId" : "c_elegans_PRJEB28388_D_melanogaster_proteins",
+ "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJEB28388"
],
"category" : [
"Sequence Similarity",
"Proteins"
+ ]
+ },
+ {
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "P_pacificus_proteins-c_elegans_PRJEB28388-LinearBasicDisplay",
+ "renderer" : {
+ "height" : 4,
+ "showLabels" : false,
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
+ },
+ "mouseover" : "jexl:get(feature,'clone')"
+ }
],
- "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "D. melanogaster proteins",
"adapter" : {
"rootUrlTemplate" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/P. pacificus proteins/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack"
- },
- {
- "trackId" : "c_elegans_PRJEB28388_P_pacificus_proteins",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
"assemblyNames" : [
"c_elegans_PRJEB28388"
],
+ "type" : "FeatureTrack",
+ "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_elegans_PRJEB28388_P_pacificus_proteins",
+ "name" : "P. pacificus proteins"
+ },
+ {
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJEB28388"
+ ],
+ "description" : "Matches to WormBase O. volvulus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "O. volvulus proteins",
+ "trackId" : "c_elegans_PRJEB28388_O_volvulus_proteins",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "O_volvulus_proteins-c_elegans_PRJEB28388-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
"color1" : "orange",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "mouseover" : "jexl:get(feature,'clone')",
- "displayId" : "P_pacificus_proteins-c_elegans_PRJEB28388-LinearBasicDisplay"
+ "height" : 4,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "name" : "P. pacificus proteins",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/P. pacificus proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/O. volvulus proteins/{refseq}/trackData.jsonz"
+ }
+ }
+ },
+ {
+ "trackId" : "c_elegans_PRJEB28388_regions_not_lifted_over_from_n2",
+ "name" : "Regions not lifted over from N2",
+ "assemblyNames" : [
+ "c_elegans_PRJEB28388"
+ ],
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/Regions not lifted over from N2/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "c_elegans_PRJEB28388_regions_not_lifted_over_from_n2-LinearBasicDisplay"
+ }
+ ]
},
{
- "description" : "Matches to WormBase O. volvulus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "O. volvulus proteins",
+ "name" : "C. brenneri proteins",
+ "trackId" : "c_elegans_PRJEB28388_C_brenneri_proteins",
+ "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJEB28388"
+ ],
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/O. volvulus proteins/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/C. brenneri proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
"displays" : [
{
- "displayId" : "O_volvulus_proteins-c_elegans_PRJEB28388-LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
+ "type" : "LinearBasicDisplay",
+ "displayId" : "C_brenneri_proteins-c_elegans_PRJEB28388-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "orange",
- "height" : 4
+ "height" : 4,
+ "showLabels" : false
},
- "type" : "LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')"
}
+ ]
+ },
+ {
+ "assemblyNames" : [
+ "c_elegans_PRJEB28388"
],
- "trackId" : "c_elegans_PRJEB28388_O_volvulus_proteins",
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "assemblyNames" : [
- "c_elegans_PRJEB28388"
- ]
- },
- {
+ "trackId" : "c_elegans_PRJEB28388_S_ratti_proteins",
+ "name" : "S. ratti proteins",
+ "description" : "Matches to WormBase S. ratti proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"displays" : [
{
- "type" : "LinearBasicDisplay",
- "displayId" : "c_elegans_PRJEB28388_regions_not_lifted_over_from_n2-LinearBasicDisplay"
+ "displayId" : "S_ratti_proteins-c_elegans_PRJEB28388-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
+ "renderer" : {
+ "height" : 4,
+ "showLabels" : false,
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJEB28388"
- ],
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/Regions not lifted over from N2/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "trackId" : "c_elegans_PRJEB28388_regions_not_lifted_over_from_n2",
- "name" : "Regions not lifted over from N2"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/S. ratti proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
- "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "C. brenneri proteins",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/C. brenneri proteins/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/C. remanei proteins/{refseq}/trackData.jsonz"
}
},
"displays" : [
{
- "displayId" : "C_brenneri_proteins-c_elegans_PRJEB28388-LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
+ "type" : "LinearBasicDisplay",
+ "displayId" : "C_remanei_proteins-c_elegans_PRJEB28388-LinearBasicDisplay",
"renderer" : {
"color1" : "orange",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 4
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')"
}
],
- "trackId" : "c_elegans_PRJEB28388_C_brenneri_proteins",
+ "name" : "C. remanei proteins",
+ "trackId" : "c_elegans_PRJEB28388_C_remanei_proteins",
+ "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJEB28388"
],
@@ -7343,83 +6800,92 @@
]
},
{
+ "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "S. cerevisiae proteins",
+ "trackId" : "c_elegans_PRJEB28388_S_cerevisiae_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJEB28388"
],
- "trackId" : "c_elegans_PRJEB28388_S_ratti_proteins",
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
+ "height" : 4,
"color1" : "orange",
- "height" : 4
+ "type" : "SvgFeatureRenderer"
},
"mouseover" : "jexl:get(feature,'clone')",
- "displayId" : "S_ratti_proteins-c_elegans_PRJEB28388-LinearBasicDisplay"
- }
- ],
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/S. ratti proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "displayId" : "S_cerevisiae_proteins-c_elegans_PRJEB28388-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- },
- "type" : "FeatureTrack",
- "name" : "S. ratti proteins",
- "description" : "Matches to WormBase S. ratti proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ ]
},
{
- "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/C. remanei proteins/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "name" : "C. remanei proteins",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "low_complextity_region_(dust)-c_elegans_PRJEB28388-LinearBasicDisplay",
"renderer" : {
+ "showLabels" : false,
"height" : 4,
- "color1" : "orange",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "showDescriptions" : false,
+ "color1" : "bisque",
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')",
- "displayId" : "C_remanei_proteins-c_elegans_PRJEB28388-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
+ "name" : "Low complextity region (Dust)",
+ "trackId" : "c_elegans_PRJEB28388_low_complextity_region_(dust)",
+ "description" : "Low-complexity regions identified by Dust.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJEB28388"
],
- "trackId" : "c_elegans_PRJEB28388_C_remanei_proteins"
+ "category" : [
+ "Genome Structure",
+ "Repeats"
+ ]
},
{
- "name" : "S. cerevisiae proteins",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "B_malayi_proteins-c_elegans_PRJEB28388-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
+ "renderer" : {
+ "showLabels" : false,
+ "height" : 4,
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
+ }
+ }
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/B. malayi proteins/{refseq}/trackData.jsonz"
}
},
- "type" : "FeatureTrack",
- "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "trackId" : "c_elegans_PRJEB28388_S_cerevisiae_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
@@ -7427,311 +6893,238 @@
"assemblyNames" : [
"c_elegans_PRJEB28388"
],
- "displays" : [
- {
- "displayId" : "S_cerevisiae_proteins-c_elegans_PRJEB28388-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
- "renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "orange",
- "height" : 4
- }
- }
- ]
+ "type" : "FeatureTrack",
+ "description" : "Matches to WormBase B. malayi proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_elegans_PRJEB28388_B_malayi_proteins",
+ "name" : "B. malayi proteins"
},
{
- "name" : "Low complextity region (Dust)",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/C. elegans proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ }
},
- "description" : "Low-complexity regions identified by Dust.",
- "trackId" : "c_elegans_PRJEB28388_low_complextity_region_(dust)",
- "category" : [
- "Genome Structure",
- "Repeats"
- ],
- "assemblyNames" : [
- "c_elegans_PRJEB28388"
- ],
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "C_elegans_proteins-c_elegans_PRJEB28388-LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 4,
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "bisque"
+ "color1" : "orange",
+ "height" : 4,
+ "showLabels" : false
},
- "displayId" : "low_complextity_region_(dust)-c_elegans_PRJEB28388-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')",
+ "type" : "LinearBasicDisplay"
}
+ ],
+ "trackId" : "c_elegans_PRJEB28388_C_elegans_proteins",
+ "name" : "C. elegans proteins",
+ "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "assemblyNames" : [
+ "c_elegans_PRJEB28388"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
]
},
{
- "name" : "B. malayi proteins",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/B. malayi proteins/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/C. briggsae proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "description" : "Matches to WormBase B. malayi proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "trackId" : "c_elegans_PRJEB28388_B_malayi_proteins",
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "c_elegans_PRJEB28388"
- ],
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "C_briggsae_proteins-c_elegans_PRJEB28388-LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
"color1" : "orange",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
- },
- "displayId" : "B_malayi_proteins-c_elegans_PRJEB28388-LinearBasicDisplay"
- }
- ]
- },
- {
- "displays" : [
- {
- "displayId" : "C_elegans_proteins-c_elegans_PRJEB28388-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
"height" : 4,
- "color1" : "orange",
- "showLabels" : false,
"type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')"
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJEB28388_C_elegans_proteins",
+ "name" : "C. briggsae proteins",
+ "trackId" : "c_elegans_PRJEB28388_C_briggsae_proteins",
+ "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJEB28388"
],
"category" : [
"Sequence Similarity",
"Proteins"
- ],
- "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "C. elegans proteins",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/C. elegans proteins/{refseq}/trackData.jsonz"
- }
- }
+ ]
},
{
- "trackId" : "c_elegans_PRJEB28388_C_briggsae_proteins",
+ "trackId" : "c_elegans_PRJEB28388_C_japonica_proteins",
+ "name" : "C. japonica proteins",
+ "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"assemblyNames" : [
"c_elegans_PRJEB28388"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "displays" : [
- {
- "renderer" : {
- "height" : 4,
- "color1" : "orange",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
- },
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
- "displayId" : "C_briggsae_proteins-c_elegans_PRJEB28388-LinearBasicDisplay"
- }
- ],
- "name" : "C. briggsae proteins",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/C. briggsae proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
- },
- {
- "name" : "C. japonica proteins",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/C. japonica proteins/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/C. japonica proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "trackId" : "c_elegans_PRJEB28388_C_japonica_proteins",
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "c_elegans_PRJEB28388"
- ],
"displays" : [
{
- "displayId" : "C_japonica_proteins-c_elegans_PRJEB28388-LinearBasicDisplay",
"renderer" : {
+ "color1" : "orange",
"height" : 4,
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "orange"
+ "type" : "SvgFeatureRenderer"
},
"mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "C_japonica_proteins-c_elegans_PRJEB28388-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
]
},
{
- "displays" : [
- {
- "renderer" : {
- "height" : 4,
- "showDescriptions" : false,
- "color1" : "orange",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "other_uniprot_proteins-c_elegans_PRJEB28388-LinearBasicDisplay"
- }
- ],
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJEB28388"
],
- "trackId" : "c_elegans_PRJEB28388_other_uniprot_proteins",
"description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "Other UniProt proteins",
+ "trackId" : "c_elegans_PRJEB28388_other_uniprot_proteins",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "other_uniprot_proteins-c_elegans_PRJEB28388-LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "orange",
+ "height" : 4,
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
+ }
+ }
+ ],
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/Other UniProt proteins/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/Other UniProt proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "Other UniProt proteins"
+ }
},
{
- "description" : "Matches to WormBase T. muris proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"name" : "T. muris proteins",
+ "trackId" : "c_elegans_PRJEB28388_T_muris_proteins",
+ "description" : "Matches to WormBase T. muris proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJEB28388"
+ ],
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/T. muris proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/T. muris proteins/{refseq}/trackData.jsonz"
+ }
},
- "type" : "FeatureTrack",
"displays" : [
{
+ "displayId" : "T_muris_proteins-c_elegans_PRJEB28388-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
+ "height" : 4,
"color1" : "orange",
- "height" : 4
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
- "displayId" : "T_muris_proteins-c_elegans_PRJEB28388-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
+ ]
+ },
+ {
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
],
- "trackId" : "c_elegans_PRJEB28388_T_muris_proteins",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJEB28388"
],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ]
- },
- {
"description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/H. sapiens proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
"name" : "H. sapiens proteins",
+ "trackId" : "c_elegans_PRJEB28388_H_sapiens_proteins",
"displays" : [
{
"type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "H_sapiens_proteins-c_elegans_PRJEB28388-LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 4,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "orange"
},
- "displayId" : "H_sapiens_proteins-c_elegans_PRJEB28388-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')"
}
],
- "assemblyNames" : [
- "c_elegans_PRJEB28388"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "trackId" : "c_elegans_PRJEB28388_H_sapiens_proteins"
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/tracks/H. sapiens proteins/{refseq}/trackData.jsonz"
+ }
+ }
},
{
- "assemblyNames" : [
- "c_elegans_PRJEB28388"
- ],
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJEB28388"
+ ],
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
+ "name" : "Cas12e TTCN PAM sites",
"trackId" : "c_elegans_PRJEB28388_TTCN_sequence_search",
"displays" : [
{
- "displayId" : "TTCN_sequence_search_c_elegans_PRJEB28388-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "TTCN_sequence_search_c_elegans_PRJEB28388-LinearBasicDisplay",
"renderer" : {
"color1" : "SlateBlue",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"height" : 4,
- "showDescriptions" : false
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
}
}
],
"adapter" : {
- "type" : "SequenceSearchAdapter",
"search" : "TTC.",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
"fastaLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJEB28388.WS284.genomic.fa.gz"
@@ -7743,17 +7136,24 @@
"gziLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJEB28388.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BgzipFastaAdapter"
}
- },
- "type" : "FeatureTrack",
- "name" : "Cas12e TTCN PAM sites",
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time."
+ }
},
{
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
+ "name" : "Cas12a TTN PAM sites",
+ "trackId" : "c_elegans_PRJEB28388_TTN_sequence_search",
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJEB28388"
+ ],
"adapter" : {
- "type" : "SequenceSearchAdapter",
- "search" : "TT.",
"sequenceAdapter" : {
"type" : "BgzipFastaAdapter",
"gziLocation" : {
@@ -7765,50 +7165,76 @@
"locationType" : "UriLocation"
},
"fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJEB28388.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJEB28388.WS284.genomic.fa.gz"
}
- }
+ },
+ "type" : "SequenceSearchAdapter",
+ "search" : "TT."
},
- "type" : "FeatureTrack",
- "name" : "Cas12a TTN PAM sites",
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "assemblyNames" : [
- "c_elegans_PRJEB28388"
- ],
- "trackId" : "c_elegans_PRJEB28388_TTN_sequence_search",
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "color1" : "Indigo",
+ "showLabels" : false,
"showDescriptions" : false,
"height" : 4,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "Indigo"
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "TTN_sequence_search_c_elegans_PRJEB28388-LinearBasicDisplay"
+ "displayId" : "TTN_sequence_search_c_elegans_PRJEB28388-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
]
},
{
+ "adapter" : {
+ "search" : "..G[AG][AG]T",
+ "sequenceAdapter" : {
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJEB28388.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BgzipFastaAdapter",
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJEB28388.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
+ },
+ "fastaLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJEB28388.WS284.genomic.fa.gz"
+ }
+ },
+ "type" : "SequenceSearchAdapter"
+ },
"displays" : [
{
- "displayId" : "NNGRRT_sequence_search_c_elegans_PRJEB28388-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "NNGRRT_sequence_search_c_elegans_PRJEB28388-LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "DarkViolet",
+ "showLabels" : false,
"showDescriptions" : false,
- "height" : 4
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
}
}
],
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
+ "name" : "SaCas9 NNGRRT PAM sites",
+ "trackId" : "c_elegans_PRJEB28388_NNGRRT_sequence_search",
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJEB28388"
+ ]
+ },
+ {
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
+ "trackId" : "c_elegans_PRJEB28388_NGG_sequence_search",
+ "name" : "SpCas9 NGG PAM sites",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
@@ -7816,119 +7242,99 @@
"assemblyNames" : [
"c_elegans_PRJEB28388"
],
- "trackId" : "c_elegans_PRJEB28388_NNGRRT_sequence_search",
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
"type" : "FeatureTrack",
"adapter" : {
+ "search" : ".GG",
"type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJEB28388.WS284.genomic.fa.gz.gzi",
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJEB28388.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJEB28388.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJEB28388.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
- }
- },
- "search" : "..G[AG][AG]T"
- },
- "name" : "SaCas9 NNGRRT PAM sites"
- },
- {
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
- "name" : "SpCas9 NGG PAM sites",
- "adapter" : {
- "type" : "SequenceSearchAdapter",
- "sequenceAdapter" : {
"type" : "BgzipFastaAdapter",
"gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJEB28388.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
- },
- "fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJEB28388.WS284.genomic.fa.gz"
- },
- "faiLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJEB28388.WS284.genomic.fa.gz.fai"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJEB28388.WS284.genomic.fa.gz.gzi"
}
- },
- "search" : ".GG"
+ }
},
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "NGG_sequence_search_c_elegans_PRJEB28388-LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
+ "color1" : "RebeccaPurple",
"height" : 4,
- "type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
"showLabels" : false,
- "color1" : "RebeccaPurple"
+ "type" : "SvgFeatureRenderer"
},
+ "displayId" : "NGG_sequence_search_c_elegans_PRJEB28388-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
- ],
- "trackId" : "c_elegans_PRJEB28388_NGG_sequence_search",
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "assemblyNames" : [
- "c_elegans_PRJEB28388"
]
},
{
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Binding regions/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Binding regions/{refseq}/trackData.jsonz"
}
},
- "type" : "FeatureTrack",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
+ "displays" : [
+ {
+ "renderer" : {
+ "color1" : "green",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "binding_regions-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"name" : "Binding regions",
+ "trackId" : "c_elegans_PRJNA13758_binding_regions",
"description" : "Regions within which there may be one or more binding sites of a non-TF, non-Histone molecule.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"Sequence Features",
"Binding Sites & Regions"
- ],
- "trackId" : "c_elegans_PRJNA13758_binding_regions",
+ ]
+ },
+ {
"formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
"displays" : [
{
"renderer" : {
- "color1" : "green",
+ "height" : 6,
+ "labels" : {
+ "description" : "jexl:get(feature,'type')=='pseudogenic_transcript'?'transposon pseudogene':'transposon mRNA'"
+ },
+ "color1" : "gray",
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "binding_regions-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "displayId" : "transposon_genes-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ]
- },
- {
- "type" : "FeatureTrack",
+ ],
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Transposon Genes/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "NCListAdapter"
},
- "name" : "Transposon Genes",
- "description" : "These are transposon spans reviewed by WormBase curators.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -7936,43 +7342,14 @@
"Genes",
"Curated Genes"
],
+ "name" : "Transposon Genes",
"trackId" : "c_elegans_PRJNA13758_transposon_genes",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
- "displays" : [
- {
- "displayId" : "transposon_genes-c_elegans_PRJNA13758-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "gray",
- "labels" : {
- "description" : "jexl:get(feature,'type')=='pseudogenic_transcript'?'transposon pseudogene':'transposon mRNA'"
- },
- "type" : "SvgFeatureRenderer",
- "height" : 6
- }
- }
- ]
+ "description" : "These are transposon spans reviewed by WormBase curators."
},
{
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "labels" : {
- "description" : "jexl:get(feature,'source') || get(feature,'description')"
- },
- "color1" : "jexl:get(feature,'source')=='SL1'?'red':get(feature,'source')=='SL2'?'green':'black'"
- },
- "displayId" : "trans-spliced_acceptor-c_elegans_PRJNA13758-LinearBasicDisplay"
- }
- ],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
+ "description" : "This track contains SL1 and SL2 trans-spliced acceptors from a variety of sources: SL1 and SL2 trans-spliced acceptors published by Blumenthal et al, Nature (2002), Trans-Spliced Exon Coupled RNA End Determination (TEC-RED) Hwang et al, PNAS (2004), EST/mRNA sequence data, RNASeq read data from ENA. SL1 acceptors are show in red, SL2 in green. Direction of transcription is indicated by arrow direction.",
"trackId" : "c_elegans_PRJNA13758_trans-spliced_acceptor",
+ "name" : "Trans-spliced acceptor",
"category" : [
"Sequence Features",
"Signals & Motifs"
@@ -7980,52 +7357,70 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : "This track contains SL1 and SL2 trans-spliced acceptors from a variety of sources: SL1 and SL2 trans-spliced acceptors published by Blumenthal et al, Nature (2002), Trans-Spliced Exon Coupled RNA End Determination (TEC-RED) Hwang et al, PNAS (2004), EST/mRNA sequence data, RNASeq read data from ENA. SL1 acceptors are show in red, SL2 in green. Direction of transcription is indicated by arrow direction.",
- "name" : "Trans-spliced acceptor",
"type" : "FeatureTrack",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Trans-spliced acceptor/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Trans-spliced acceptor/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "jexl:get(feature,'source')=='SL1'?'red':get(feature,'source')=='SL2'?'green':'black'",
+ "labels" : {
+ "description" : "jexl:get(feature,'source') || get(feature,'description')"
+ }
+ },
+ "displayId" : "trans-spliced_acceptor-c_elegans_PRJNA13758-LinearBasicDisplay"
}
- }
+ ]
},
{
- "description" : "A subset of the full Curated Genes set limited to pseudogenes only. Pseudogenes of tRNA are lighter gray and pseudogenes of rRNA are darker gray than pseudogenes of protein coding genes.",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Curated Genes (pseudogenes)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "name" : "Curated Genes (pseudogenes)",
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
"displays" : [
{
"displayId" : "curated_genes_(pseudogenes)-c_elegans_PRJNA13758-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "gray",
- "height" : 6
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Curated Genes (pseudogenes)/{refseq}/trackData.jsonz"
+ }
+ },
"category" : [
"Genes",
"Curated Genes"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "A subset of the full Curated Genes set limited to pseudogenes only. Pseudogenes of tRNA are lighter gray and pseudogenes of rRNA are darker gray than pseudogenes of protein coding genes.",
+ "name" : "Curated Genes (pseudogenes)",
"trackId" : "c_elegans_PRJNA13758_curated_genes_pseudogenes"
},
{
+ "name" : "Regulatory regions",
+ "trackId" : "c_elegans_PRJNA13758_regulatory_regions",
+ "description" : "Assorted or unspecified regulatory elements with experimental evidence.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -8033,20 +7428,6 @@
"Sequence Features",
"Binding Sites & Regions"
],
- "trackId" : "c_elegans_PRJNA13758_regulatory_regions",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
- "displays" : [
- {
- "displayId" : "regulatory_regions-c_elegans_PRJNA13758-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "green"
- }
- }
- ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -8054,90 +7435,94 @@
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "name" : "Regulatory regions",
- "description" : "Assorted or unspecified regulatory elements with experimental evidence."
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
+ "displays" : [
+ {
+ "renderer" : {
+ "color1" : "green",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "regulatory_regions-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
- "description" : "This track shows the extent of predicted protein motifs. Note these spans correspond to amino acid coordinates interpolated onto the physical map. Included are signal peptide (signalp), coiled coil (ncoils) and transmembrane (tmhmm) domains, regions of low complexity (seg), and Pfam annotated motif homologies.",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Protein motifs/{refseq}/trackData.jsonz"
- }
- },
- "name" : "Protein motifs",
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "protein_motifs-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
- "color1" : "jexl:parent(feature)=='undefined'?'purple':get(parent(feature),'predictiontype')=='tmhmm'?'magenta':get(parent(feature),'predictiontype')=='seg'?'lightseagreen':get(parent(feature),'predictiontype')=='signalp'?'aquamarine':get(parent(feature),'predictiontype')=='ncoils'?'chartreuse':\nget(parent(feature),'predictiontype')=='pfam'?'lightsalmon':'purple'",
"type" : "SvgFeatureRenderer",
+ "color1" : "jexl:parent(feature)=='undefined'?'purple':get(parent(feature),'predictiontype')=='tmhmm'?'magenta':get(parent(feature),'predictiontype')=='seg'?'lightseagreen':get(parent(feature),'predictiontype')=='signalp'?'aquamarine':get(parent(feature),'predictiontype')=='ncoils'?'chartreuse':\nget(parent(feature),'predictiontype')=='pfam'?'lightsalmon':'purple'",
"height" : 7
- },
- "type" : "LinearBasicDisplay"
+ }
}
],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Protein motifs/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Features",
"Translated Features"
],
- "trackId" : "c_elegans_PRJNA13758_protein_motifs"
+ "trackId" : "c_elegans_PRJNA13758_protein_motifs",
+ "name" : "Protein motifs",
+ "description" : "This track shows the extent of predicted protein motifs. Note these spans correspond to amino acid coordinates interpolated onto the physical map. Included are signal peptide (signalp), coiled coil (ncoils) and transmembrane (tmhmm) domains, regions of low complexity (seg), and Pfam annotated motif homologies."
},
{
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "Sequence Features",
+ "Signals & Motifs"
+ ],
+ "name" : "DNaseI hypersensitive site",
+ "trackId" : "c_elegans_PRJNA13758_dnasei_hypersensitive_site",
+ "description" : "DNase I hypersensitive sites from the 2009 paper by Shi et al.",
"displays" : [
{
- "displayId" : "dnasei_hypersensitive_site-c_elegans_PRJNA13758-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"color1" : "green"
- }
+ },
+ "displayId" : "dnasei_hypersensitive_site-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "trackId" : "c_elegans_PRJNA13758_dnasei_hypersensitive_site",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "Sequence Features",
- "Signals & Motifs"
- ],
- "description" : "DNase I hypersensitive sites from the 2009 paper by Shi et al.",
- "name" : "DNaseI hypersensitive site",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/DNaseI hypersensitive site/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/DNaseI hypersensitive site/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
- },
- "type" : "FeatureTrack"
+ }
},
{
- "description" : "Regions within which there is experimental evidence for a promoter.",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Promoter regions/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "name" : "Promoter regions",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ }
},
"displays" : [
{
@@ -8149,172 +7534,178 @@
"type" : "LinearBasicDisplay"
}
],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
+ "trackId" : "c_elegans_PRJNA13758_promoter_regions",
+ "name" : "Promoter regions",
+ "description" : "Regions within which there is experimental evidence for a promoter.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Features",
"Binding Sites & Regions"
- ],
- "trackId" : "c_elegans_PRJNA13758_promoter_regions"
+ ]
},
{
- "name" : "Balancers",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Balancers/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "description" : "This track shows the approximate location of balancers.",
- "trackId" : "c_elegans_PRJNA13758-balancers",
"category" : [
"Alleles, Variations, RNAi"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "This track shows the approximate location of balancers.",
+ "name" : "Balancers",
+ "trackId" : "c_elegans_PRJNA13758-balancers",
"displays" : [
{
- "mouseover" : "jexl:get(feature,'balancer')+': '+get(feature,'note')",
+ "displayId" : "balancers-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
+ "color1" : "black",
"labels" : {
"description" : "jexl:get(feature,'balancer_type') || get(feature,'description')"
},
- "type" : "SvgFeatureRenderer",
- "color1" : "black"
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "balancers-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'balancer')+': '+get(feature,'note')",
+ "type" : "LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Balancers/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
}
},
{
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "transcription_end_site-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "outline" : "black",
- "color1" : "white"
- },
- "displayId" : "transcription_end_site-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "color1" : "white",
+ "outline" : "black"
+ }
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "trackId" : "c_elegans_PRJNA13758_transcription_end_site",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Transcription end site/{refseq}/trackData.jsonz"
+ }
+ },
"category" : [
"Sequence Features",
"Signals & Motifs"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"description" : "Transcription_end_site defined by analysis of RNASeq short read datasets (example Hillier et al.)",
- "name" : "Transcription end site",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Transcription end site/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack"
+ "trackId" : "c_elegans_PRJNA13758_transcription_end_site",
+ "name" : "Transcription end site"
},
{
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/mRNAs_ncRNAs (best)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "mRNAs/ncRNAs (best)",
- "description" : "Native (same species) full length cDNAs and ncRNAs aligned to the genome using BLAT. This track shows the best unique location for each cDNA.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"Genes",
"Supporting Evidence"
],
"trackId" : "c_elegans_PRJNA13758_mrnas/ncrnas_(best)",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
+ "name" : "mRNAs/ncRNAs (best)",
+ "description" : "Native (same species) full length cDNAs and ncRNAs aligned to the genome using BLAT. This track shows the best unique location for each cDNA.",
"displays" : [
{
- "displayId" : "mrnas/ncrnas_(best)-c_elegans_PRJNA13758-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 6,
"outline" : "black",
- "color1" : "jexl:startsWith(get(feature,'source'),'BLAT_mRNA_')==true?'yellow':'gray'",
- "type" : "SvgFeatureRenderer"
- }
+ "color1" : "jexl:startsWith(get(feature,'source'),'BLAT_mRNA_')==true?'yellow':'gray'"
+ },
+ "displayId" : "mrnas/ncrnas_(best)-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/mRNAs_ncRNAs (best)/{refseq}/trackData.jsonz"
+ }
+ }
},
{
"description" : "Positions within the reference genome sequence that have been identified as having a base call error. This error has not yet been corrected.",
+ "name" : "Genome sequence errors",
+ "trackId" : "c_elegans_PRJNA13758_genome_sequence_errors",
+ "category" : [
+ "Genome Structure",
+ "Assembly & Curation"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Genome sequence errors/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "name" : "Genome sequence errors",
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "genome_sequence_errors-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
- "color1" : "red",
"type" : "SvgFeatureRenderer",
- "height" : 6
- },
- "type" : "LinearBasicDisplay"
+ "height" : 6,
+ "color1" : "red"
+ }
}
- ],
- "category" : [
- "Genome Structure",
- "Assembly & Curation"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_genome_sequence_errors"
+ ]
},
{
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/RNAi experiments (primary targets)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
+ "trackId" : "c_elegans_PRJNA13758_rnai_experiments_(primary_targets)",
"name" : "RNAi experiments (primary targets)",
"description" : "This track represents RNAi probes that have been aligned to the genome using a combination of BLAST and BLAT programs and have sequence identity to the target location of at least 95% over a stretch of at least 100 nt. Probes that satisfy these criteria are almost certain to produce RNAi effect on overlapping genes and the corresponding locations are usually the primary genomic targets of an RNAi experiment. Note that it is possible for a probe to have multiple primary targets within the genome. Click on the RNAi element to get more information about the experiment.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"Alleles, Variations, RNAi"
],
- "trackId" : "c_elegans_PRJNA13758_rnai_experiments_(primary_targets)",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/RNAi experiments (primary targets)/{refseq}/trackData.jsonz"
+ }
+ },
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
@@ -8330,39 +7721,46 @@
]
},
{
- "name" : "Histone binding sites",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Histone binding sites/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Histone binding sites/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "description" : "Regions within which there is experimental evidence for one or more binding sites of a histone.",
- "trackId" : "c_elegans_PRJNA13758_histone_binding_sites",
- "category" : [
- "Sequence Features",
- "Binding Sites & Regions"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"color1" : "green"
},
- "type" : "LinearBasicDisplay",
"displayId" : "histone_binding_sites-c_elegans_PRJNA13758-LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- }
+ },
+ "description" : "Regions within which there is experimental evidence for one or more binding sites of a histone.",
+ "trackId" : "c_elegans_PRJNA13758_histone_binding_sites",
+ "name" : "Histone binding sites",
+ "category" : [
+ "Sequence Features",
+ "Binding Sites & Regions"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack"
},
{
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Classical_alleles/{refseq}/trackData.jsonz"
+ }
+ },
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+'', WormBase: 'Variation Page'}"
},
@@ -8370,104 +7768,101 @@
{
"displayId" : "classical_alleles-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"showDescriptions" : false,
"outline" : "jexl:get(feature,'vep_impact')=='HIGH'?'red':get(feature,'vep_impact')=='MODIFIER'?'purple':get(feature,'vep_impact')=='MODERATE'?'gold':get(feature,'vep_impact')=='LOW'?'cyan':'black'",
- "color1" : "jexl:get(feature,'vep_impact')=='HIGH'?'red':get(feature,'vep_impact')=='MODIFIER'?'purple':get(feature,'vep_impact')=='MODERATE'?'gold':get(feature,'vep_impact')=='LOW'?'cyan':'white'",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "showLabels" : false,
+ "color1" : "jexl:get(feature,'vep_impact')=='HIGH'?'red':get(feature,'vep_impact')=='MODIFIER'?'purple':get(feature,'vep_impact')=='MODERATE'?'gold':get(feature,'vep_impact')=='LOW'?'cyan':'white'"
},
"type" : "LinearBasicDisplay"
}
],
+ "description" : "This track shows classical alleles comprised of insertions, deletions, substitutions and complex changes. These alleles were typically generated during forward genetic screens. Boxes represent deletions or substitutions; and white triangles represent insertions. Color signifies the severity of impact predicted by Ensembl's Variant Effect Predictor. 'HIGH' impacts are red, 'MEDIUM' are yellow, 'LOW' are cyan (light blue), and 'MODIFIER' are purple. This is the same color scheme as is used at the Alliance of Genome Resources.",
+ "name" : "Classical Alleles",
+ "trackId" : "c_elegans_PRJNA13758_classical_alleles",
+ "category" : [
+ "Alleles, Variations, RNAi"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ]
+ },
+ {
+ "trackId" : "c_elegans_PRJNA13758_transposon_insert_sites",
+ "name" : "Transposon insert sites",
+ "description" : "This track shows transposon insertion sites engineered by Laurent Segalat and others: 'Towards a genome-wide collection of transposon insertions', International C. elegans Meeting 1999 Yellow triangles are Mos-derived transposon insertions; red trangles are NemaGENETAG consortium insertion sites; blue triangles are Tc* derived transposon insertions.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"Alleles, Variations, RNAi"
],
- "trackId" : "c_elegans_PRJNA13758_classical_alleles",
- "description" : "This track shows classical alleles comprised of insertions, deletions, substitutions and complex changes. These alleles were typically generated during forward genetic screens. Boxes represent deletions or substitutions; and white triangles represent insertions. Color signifies the severity of impact predicted by Ensembl's Variant Effect Predictor. 'HIGH' impacts are red, 'MEDIUM' are yellow, 'LOW' are cyan (light blue), and 'MODIFIER' are purple. This is the same color scheme as is used at the Alliance of Genome Resources.",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Classical_alleles/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Transposon insert sites/{refseq}/trackData.jsonz"
}
},
- "name" : "Classical Alleles"
- },
- {
- "trackId" : "c_elegans_PRJNA13758_transposon_insert_sites",
- "category" : [
- "Alleles, Variations, RNAi"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "jexl:get(feature,'source')=='Mos_insertion_allele'?'yellow':get(feature,'source')=='NemaGENETAG_consortium'?'red':'blue'",
"type" : "SvgFeatureRenderer",
+ "color1" : "jexl:get(feature,'source')=='Mos_insertion_allele'?'yellow':get(feature,'source')=='NemaGENETAG_consortium'?'red':'blue'",
"height" : 8
},
- "displayId" : "transposon_insert_sites-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "displayId" : "transposon_insert_sites-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
- "name" : "Transposon insert sites",
- "type" : "FeatureTrack",
+ ]
+ },
+ {
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Transposon insert sites/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Segmental duplication/{refseq}/trackData.jsonz"
}
},
- "description" : "This track shows transposon insertion sites engineered by Laurent Segalat and others: 'Towards a genome-wide collection of transposon insertions', International C. elegans Meeting 1999 Yellow triangles are Mos-derived transposon insertions; red trangles are NemaGENETAG consortium insertion sites; blue triangles are Tc* derived transposon insertions."
- },
- {
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "Genome Structure",
- "Genome Structure"
- ],
- "trackId" : "c_elegans_PRJNA13758_segmental_duplication",
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
"displays" : [
{
- "displayId" : "segmental_duplication-c_elegans_PRJNA13758-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "outline" : "black",
"color1" : "white",
+ "outline" : "black",
"height" : 6
- }
+ },
+ "displayId" : "segmental_duplication-c_elegans_PRJNA13758-LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Segmental duplication/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
+ "trackId" : "c_elegans_PRJNA13758_segmental_duplication",
"name" : "Segmental duplication",
- "description" : "Polymorphic segmental duplication as defined by the tool OrthoCluster. This feature represents one sequence from a pair of duplicons in the N2 genome."
+ "description" : "Polymorphic segmental duplication as defined by the tool OrthoCluster. This feature represents one sequence from a pair of duplicons in the N2 genome.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Genome Structure",
+ "Genome Structure"
+ ]
},
{
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "gene_models_(historical)-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
"color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
@@ -8475,68 +7870,79 @@
"description" : "jexl:get(feature,'type')"
},
"type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay"
+ }
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Gene Models (historical)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
},
- "trackId" : "c_elegans_PRJNA13758_gene_models_(historical)",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"Genes",
"Curated Genes"
],
- "description" : "Historical gene predictions.",
- "name" : "Gene Models (historical)",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Gene Models (historical)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- }
+ "description" : "Historical gene predictions.",
+ "trackId" : "c_elegans_PRJNA13758_gene_models_(historical)",
+ "name" : "Gene Models (historical)"
},
{
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Binding sites (predicted)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
"type" : "FeatureTrack",
- "name" : "Binding sites (predicted)",
- "description" : "This track shows curated and predicted binding sites for microRNAs. Binding sites (indicated in green) are extracted from the cisRed database of computationally derived potential bind targets. miRanda predictions -- indicated in red -- are the predicted target sequences for microRNA genes, provided by Anton Enright's group using the miRanda program. PicTar predictions -- indicated in blue -- are the predicted target sequences for microRNA genes from Lall et al; A genome-wide map of conserved microRNA targets in C. elegans. Curr Biol. 2006 Mar 7;16(5):460-71.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"Sequence Features",
"Binding Sites & Regions"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "Binding sites (predicted)",
"trackId" : "c_elegans_PRJNA13758_binding_sites_predicted",
+ "description" : "This track shows curated and predicted binding sites for microRNAs. Binding sites (indicated in green) are extracted from the cisRed database of computationally derived potential bind targets. miRanda predictions -- indicated in red -- are the predicted target sequences for microRNA genes, provided by Anton Enright's group using the miRanda program. PicTar predictions -- indicated in blue -- are the predicted target sequences for microRNA genes from Lall et al; A genome-wide map of conserved microRNA targets in C. elegans. Curr Biol. 2006 Mar 7;16(5):460-71.",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "jexl:get(feature,'source')=='PicTar'?'blue':get(feature,'source')=='miRanda'?'red':'green'",
+ "type" : "SvgFeatureRenderer",
+ "maxHeight" : 5000
+ },
+ "displayId" : "binding_sites_(predicted)-c_elegans_PRJNA13758-LinearBasicDisplay"
+ }
+ ],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Binding sites (predicted)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ }
+ },
+ {
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+'', WormBase: 'Variation Page'}"
+ },
"displays" : [
{
- "displayId" : "binding_sites_(predicted)-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'type')+': '+get(feature,'strain')",
"renderer" : {
- "color1" : "jexl:get(feature,'source')=='PicTar'?'blue':get(feature,'source')=='miRanda'?'red':'green'",
+ "color1" : "jexl:get(feature,'strain')=='CB4858'||get(feature,'strain')=='AF16'?'blue':get(feature,'strain')=='CB4856'||get(feature,'strain')=='HK104'?'yellow':'white'",
+ "outline" : "jexl:get(feature,'strain')=='CB4858'||get(feature,'strain')=='AF16'?'blue':get(feature,'strain')=='CB4856'||get(feature,'strain')=='HK104'?'yellow':'black'",
"maxHeight" : 5000,
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "polymorphisms-c_elegans_PRJNA13758-LinearBasicDisplay"
}
- ]
- },
- {
- "type" : "FeatureTrack",
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -8544,44 +7950,40 @@
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Polymorphisms/{refseq}/trackData.jsonz"
}
},
- "name" : "Polymorphisms",
- "description" : "This track shows single nucleotide polymorphisms (SNPs). In this track, the molecular nature of the polymorphism is indicated by its glyph: Boxes are deletions; triangles are insertions; point mutations and substitutions are diamonds. Color reflects the source strain: polymorphisms found in CB4858 (Pasadena) are shown in blue; those found in CB4856 (Hawaii) in yellow, and all others in white.",
"category" : [
"Alleles, Variations, RNAi"
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "description" : "This track shows single nucleotide polymorphisms (SNPs). In this track, the molecular nature of the polymorphism is indicated by its glyph: Boxes are deletions; triangles are insertions; point mutations and substitutions are diamonds. Color reflects the source strain: polymorphisms found in CB4858 (Pasadena) are shown in blue; those found in CB4856 (Hawaii) in yellow, and all others in white.",
"trackId" : "c_elegans_PRJNA13758_polymorphisms",
+ "name" : "Polymorphisms"
+ },
+ {
"formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+'', WormBase: 'Variation Page'}"
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
"displays" : [
{
- "mouseover" : "jexl:get(feature,'type')+': '+get(feature,'strain')",
"renderer" : {
- "color1" : "jexl:get(feature,'strain')=='CB4858'||get(feature,'strain')=='AF16'?'blue':get(feature,'strain')=='CB4856'||get(feature,'strain')=='HK104'?'yellow':'white'",
- "outline" : "jexl:get(feature,'strain')=='CB4858'||get(feature,'strain')=='AF16'?'blue':get(feature,'strain')=='CB4856'||get(feature,'strain')=='HK104'?'yellow':'black'",
- "maxHeight" : 5000,
- "type" : "SvgFeatureRenderer"
+ "type" : "SvgFeatureRenderer",
+ "color1" : "gray",
+ "height" : 6
},
- "type" : "LinearBasicDisplay",
- "displayId" : "polymorphisms-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "displayId" : "alper_lincrna_(predicted)-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ]
- },
- {
- "name" : "Alper lincRNA (predicted)",
- "type" : "FeatureTrack",
+ ],
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Alper lincRNA (predicted)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Alper lincRNA (predicted)/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "description" : "Predicted lincRNAs. See WBPaper0005624 for more information.",
- "trackId" : "c_elegans_PRJNA13758_alper_lincrna_(predicted)",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -8589,73 +7991,68 @@
"Genes",
"Ab-initio predictions"
],
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "gray"
- },
- "displayId" : "alper_lincrna_(predicted)-c_elegans_PRJNA13758-LinearBasicDisplay"
- }
- ],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- }
+ "name" : "Alper lincRNA (predicted)",
+ "trackId" : "c_elegans_PRJNA13758_alper_lincrna_(predicted)",
+ "description" : "Predicted lincRNAs. See WBPaper0005624 for more information."
},
{
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "purple",
- "type" : "SvgFeatureRenderer",
- "labels" : {
- "description" : "jexl:get(feature,'type') || get(feature,'description')"
- }
- },
- "displayId" : "polya_sites_and_signal_sequences-c_elegans_PRJNA13758-LinearBasicDisplay"
- }
- ],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
"trackId" : "c_elegans_PRJNA13758_polya_sites_and_signal_sequences",
+ "name" : "PolyA sites and signal sequences",
+ "description" : "High-confidence polyadenylation signal sequences and sites calculated by an algorithm trained with verified sites from full-length mRNAs. Signals are indicated with a diamond; sites with a triangle.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Features",
"Signals & Motifs"
],
- "description" : "High-confidence polyadenylation signal sequences and sites calculated by an algorithm trained with verified sites from full-length mRNAs. Signals are indicated with a diamond; sites with a triangle.",
- "name" : "PolyA sites and signal sequences",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/PolyA sites and signal sequences/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/PolyA sites and signal sequences/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "labels" : {
+ "description" : "jexl:get(feature,'type') || get(feature,'description')"
+ },
+ "color1" : "purple"
+ },
+ "displayId" : "polya_sites_and_signal_sequences-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- }
+ ]
},
{
"displays" : [
{
- "displayId" : "curated_genes_(noncoding)-c_elegans_PRJNA13758-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "curated_genes_(noncoding)-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "gray",
- "height" : 6
+ "type" : "SvgFeatureRenderer"
}
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
- "trackId" : "c_elegans_PRJNA13758_curated_genes_noncoding",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Curated Genes (noncoding)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"category" : [
"Genes",
"Curated Genes"
@@ -8663,209 +8060,193 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : "Non-coding curated gene models, including ncRNA, tRNA, miRNA, snRNA, snoRNA, piRNA, lincRNA and antisense RNA.",
- "name" : "Curated Genes (noncoding)",
"type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Curated Genes (noncoding)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- }
+ "description" : "Non-coding curated gene models, including ncRNA, tRNA, miRNA, snRNA, snoRNA, piRNA, lincRNA and antisense RNA.",
+ "trackId" : "c_elegans_PRJNA13758_curated_genes_noncoding",
+ "name" : "Curated Genes (noncoding)"
},
{
- "description" : "These are transposon spans reviewed by WormBase curators.",
- "name" : "Transposons",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Transposons/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
"displays" : [
{
+ "displayId" : "transposons-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "gray"
+ "color1" : "gray",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "transposons-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
- "trackId" : "c_elegans_PRJNA13758_transposons",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Transposons/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"Genes",
"Curated Genes"
- ]
+ ],
+ "trackId" : "c_elegans_PRJNA13758_transposons",
+ "name" : "Transposons",
+ "description" : "These are transposon spans reviewed by WormBase curators."
},
{
- "description" : "Regions within which there is experimental evidence of one or more binding sites of a transcription factor.",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Transcription factor binding regions/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Transcription factor binding regions/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
},
- "name" : "Transcription factor binding regions",
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "height" : 5,
- "showLabels" : false,
+ "maxHeight" : 5000,
+ "color1" : "green",
"labels" : {
"name" : "jexl:!!get(feature,'tf_name')==true ? get(feature,'name') + ' (' + get(feature,'tf_name') +')' : get(feature,'name')"
},
- "color1" : "green",
- "maxHeight" : 5000,
- "showDescriptions" : false
+ "height" : 5,
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "transcription_factor_binding_regions-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "displayId" : "transcription_factor_binding_regions-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
+ "description" : "Regions within which there is experimental evidence of one or more binding sites of a transcription factor.",
+ "name" : "Transcription factor binding regions",
+ "trackId" : "c_elegans_PRJNA13758_transcription_factor_binding_regions",
"category" : [
"Sequence Features",
"Binding Sites & Regions"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_transcription_factor_binding_regions"
+ ]
},
{
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
- "displays" : [
- {
- "displayId" : "genome_sequence_corrections-c_elegans_PRJNA13758-LinearBasicDisplay",
- "renderer" : {
- "height" : 6,
- "color1" : "green",
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay"
- }
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"Genome Structure",
"Assembly & Curation"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"trackId" : "c_elegans_PRJNA13758_genome_sequence_corrections",
+ "name" : "Genome sequence corrections",
"description" : "Positions within the reference genome sequence that were previously identified as having a base call error. This error has now been corrected.",
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "genome_sequence_corrections-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "height" : 6,
+ "color1" : "green"
+ }
+ }
+ ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Genome sequence corrections/{refseq}/trackData.jsonz"
- }
- },
- "name" : "Genome sequence corrections"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
- "name" : "Change of function polymorphisms",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Change-of-function polymorphisms/{refseq}/trackData.jsonz"
- }
- },
- "type" : "FeatureTrack",
"description" : "This track shows single nucleotide polymorphisms (SNPs) that may generate a change of function. In this track, the molecular nature of the polymorphism is indicated by its glyph: Boxes are deletions or substitutions; triangles are insertions; point mutations are diamonds. Color signifies the severity of impact predicted by Ensembl's Variant Effect Predictor. 'HIGH' impacts are red, 'MEDIUM' are yellow, 'LOW' are cyan (light blue), and 'MODIFIER' are purple. This is the same color scheme as is used at the Alliance of Genome Resources.",
"trackId" : "c_elegans_PRJNA13758-change_of_function_polymorphisms",
+ "name" : "Change of function polymorphisms",
"category" : [
"Alleles, Variations, RNAi"
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Change-of-function polymorphisms/{refseq}/trackData.jsonz"
+ }
+ },
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+'', WormBase: 'Variation Page'}"
+ },
"displays" : [
{
- "displayId" : "change_of_function_polymorphisms-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'name')+', '+get(feature,'consequence')",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"color1" : "jexl:get(feature,'vep_impact')=='HIGH'?'red':get(feature,'vep_impact')=='MODIFIER'?'purple':get(feature,'vep_impact')=='MODERATE'?'gold':get(feature,'vep_impact')=='LOW'?'cyan':'white'",
+ "outline" : "jexl:get(feature,'vep_impact')=='HIGH'?'red':get(feature,'vep_impact')=='MODIFIER'?'purple':get(feature,'vep_impact')=='MODERATE'?'gold':get(feature,'vep_impact')=='LOW'?'cyan':'black'",
"maxHeight" : 5000,
- "outline" : "jexl:get(feature,'vep_impact')=='HIGH'?'red':get(feature,'vep_impact')=='MODIFIER'?'purple':get(feature,'vep_impact')=='MODERATE'?'gold':get(feature,'vep_impact')=='LOW'?'cyan':'black'"
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "change_of_function_polymorphisms-c_elegans_PRJNA13758-LinearBasicDisplay"
}
- ],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+'', WormBase: 'Variation Page'}"
- }
+ ]
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "trackId" : "c_elegans_PRJNA13758_curated_genes_protein_coding",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz"
+ }
+ },
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
"displays" : [
{
- "displayId" : "curated_genes_(protein_coding)-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"maxHeight" : 5000,
- "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
- "color3" : "#965567"
+ "color3" : "#965567",
+ "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "curated_genes_(protein_coding)-c_elegans_PRJNA13758-LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
+ "trackId" : "c_elegans_PRJNA13758_curated_genes_protein_coding",
"name" : "Curated Genes (protein coding)",
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track."
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack"
},
{
- "description" : "Dicistronic mRNA operons - manually observed by curators",
- "name" : "Dicistronic mRNAs",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Dicistronic mRNAs/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "dicistronic_mrnas-c_elegans_PRJNA13758-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "dicistronic_mrnas-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
"color1" : "darkgreen",
"type" : "SvgFeatureRenderer"
@@ -8875,84 +8256,94 @@
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "trackId" : "c_elegans_PRJNA13758_dicistronic_mrnas",
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Dicistronic mRNAs/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"Genes",
"Curated Genes"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ]
+ "name" : "Dicistronic mRNAs",
+ "trackId" : "c_elegans_PRJNA13758_dicistronic_mrnas",
+ "description" : "Dicistronic mRNA operons - manually observed by curators"
},
{
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+'', WormBase: 'Variation Page'}"
- },
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'name')+', '+get(feature,'strain')",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"labels" : {
"description" : "jexl:get(feature,'type') || get(feature,'description')"
},
+ "color1" : "jexl:get(feature,'vep_impact')=='HIGH'?'red':get(feature,'vep_impact')=='MODIFIER'?'purple':get(feature,'vep_impact')=='MODERATE'?'gold':get(feature,'vep_impact')=='LOW'?'cyan':'white'",
"outline" : "jexl:get(feature,'vep_impact')=='HIGH'?'red':get(feature,'vep_impact')=='MODIFIER'?'purple':get(feature,'vep_impact')=='MODERATE'?'gold':get(feature,'vep_impact')=='LOW'?'cyan':'black'",
- "color1" : "jexl:get(feature,'vep_impact')=='HIGH'?'red':get(feature,'vep_impact')=='MODIFIER'?'purple':get(feature,'vep_impact')=='MODERATE'?'gold':get(feature,'vep_impact')=='LOW'?'cyan':'white'"
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'name')+', '+get(feature,'strain')",
- "displayId" : "high-throughput_alleles-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "displayId" : "high-throughput_alleles-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "Alleles, Variations, RNAi"
- ],
- "trackId" : "c_elegans_PRJNA13758_high-throughput_alleles",
- "description" : "These are alleles generated through high-throughput, genome-wide projects. Million Mutation Project alleles are placed in a separate track. Color signifies the severity of impact predicted by Ensembl's Variant Effect Predictor. 'HIGH' impacts are red, 'MEDIUM' are yellow, 'LOW' are cyan (light blue), and 'MODIFIER' are purple. This is the same color scheme as is used at the Alliance of Genome Resources.",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+'', WormBase: 'Variation Page'}"
+ },
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/High-throughput alleles/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/High-throughput alleles/{refseq}/trackData.jsonz"
+ }
},
- "type" : "FeatureTrack",
- "name" : "High-throughput alleles"
- },
- {
- "trackId" : "c_elegans_PRJNA13758_rnai_experiments_(secondary_targets)",
"category" : [
"Alleles, Variations, RNAi"
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "description" : "These are alleles generated through high-throughput, genome-wide projects. Million Mutation Project alleles are placed in a separate track. Color signifies the severity of impact predicted by Ensembl's Variant Effect Predictor. 'HIGH' impacts are red, 'MEDIUM' are yellow, 'LOW' are cyan (light blue), and 'MODIFIER' are purple. This is the same color scheme as is used at the Alliance of Genome Resources.",
+ "trackId" : "c_elegans_PRJNA13758_high-throughput_alleles",
+ "name" : "High-throughput alleles"
+ },
+ {
"displays" : [
{
- "displayId" : "rnai_experiments_(secondary_targets)-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 4,
- "color1" : "red",
- "type" : "SvgFeatureRenderer"
+ "color1" : "red"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "rnai_experiments_(secondary_targets)-c_elegans_PRJNA13758-LinearBasicDisplay"
}
],
- "name" : "RNAi experiments (secondary targets)",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/RNAi experiments (secondary targets)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/RNAi experiments (secondary targets)/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
},
+ "category" : [
+ "Alleles, Variations, RNAi"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
- "description" : "This track represents RNAi probes that have been aligned to the genome using BLAST program and have sequence identity to the target location from 80 to 94.99% over a stretch of at least 200 nt. Probes that satisfy these criteria may or may not produce RNAi effect on overlapping genes and the corresponding locations represent possible secondary (unintended) genomic targets of an RNAi experiment. Click on the RNAi element to get more information about the experiment."
+ "description" : "This track represents RNAi probes that have been aligned to the genome using BLAST program and have sequence identity to the target location from 80 to 94.99% over a stretch of at least 200 nt. Probes that satisfy these criteria may or may not produce RNAi effect on overlapping genes and the corresponding locations represent possible secondary (unintended) genomic targets of an RNAi experiment. Click on the RNAi element to get more information about the experiment.",
+ "trackId" : "c_elegans_PRJNA13758_rnai_experiments_(secondary_targets)",
+ "name" : "RNAi experiments (secondary targets)"
},
{
- "trackId" : "c_elegans_PRJNA13758_binding_sites_curated",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -8960,217 +8351,207 @@
"Sequence Features",
"Binding Sites & Regions"
],
+ "name" : "Binding sites (curated)",
+ "trackId" : "c_elegans_PRJNA13758_binding_sites_curated",
+ "description" : "Sites where there is experimental evidence of a non-TF, non-Histone molecule binding.",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"displays" : [
{
+ "displayId" : "binding_sites_(curated)-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "green"
+ "color1" : "green",
+ "type" : "SvgFeatureRenderer"
},
+ "type" : "LinearBasicDisplay"
+ }
+ ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Binding sites (curated)/{refseq}/trackData.jsonz"
+ }
+ }
+ },
+ {
+ "displays" : [
+ {
"type" : "LinearBasicDisplay",
- "displayId" : "binding_sites_(curated)-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "displayId" : "curated_genes-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "renderer" : {
+ "color3" : "#965567",
+ "type" : "SvgFeatureRenderer",
+ "maxHeight" : 5000,
+ "labels" : {
+ "name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
+ },
+ "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'"
+ }
}
],
"formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ "feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
},
- "name" : "Binding sites (curated)",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Binding sites (curated)/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Curated_Genes/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "description" : "Sites where there is experimental evidence of a non-TF, non-Histone molecule binding."
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
+ "name" : "Curated Genes",
+ "trackId" : "c_elegans_PRJNA13758_curated_genes"
},
{
- "type" : "FeatureTrack",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
+ "displays" : [
+ {
+ "displayId" : "transcription_factor_binding_sites-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "green",
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Curated_Genes/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Transcription factor binding sites/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
}
},
- "name" : "Curated Genes",
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
- "Genes",
- "Curated Genes"
+ "Sequence Features",
+ "Binding Sites & Regions"
],
- "trackId" : "c_elegans_PRJNA13758_curated_genes",
- "formatDetails" : {
- "feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
- },
- "displays" : [
- {
- "displayId" : "curated_genes-c_elegans_PRJNA13758-LinearBasicDisplay",
- "renderer" : {
- "color3" : "#965567",
- "maxHeight" : 5000,
- "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
- "type" : "SvgFeatureRenderer",
- "labels" : {
- "name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
- }
- },
- "type" : "LinearBasicDisplay"
- }
- ]
+ "trackId" : "c_elegans_PRJNA13758_transcription_factor_binding_sites",
+ "name" : "Transcription factor binding sites",
+ "description" : "Sites where there is experimental evidence of a transcription factor binding site."
},
{
- "description" : "Sites where there is experimental evidence of a transcription factor binding site.",
- "name" : "Transcription factor binding sites",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Transcription factor binding sites/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/YACs, Fosmids, & Cosmids/{refseq}/trackData.jsonz"
}
},
- "displays" : [
- {
- "renderer" : {
- "color1" : "green",
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "transcription_factor_binding_sites-c_elegans_PRJNA13758-LinearBasicDisplay"
- }
- ],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "trackId" : "c_elegans_PRJNA13758_transcription_factor_binding_sites",
- "category" : [
- "Sequence Features",
- "Binding Sites & Regions"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ]
- },
- {
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 3,
"type" : "SvgFeatureRenderer",
+ "height" : 3,
"color1" : "black"
},
"displayId" : "yacs,_fosmids,_&_cosmids-c_elegans_PRJNA13758-LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
"trackId" : "c_elegans_PRJNA13758_yacs_fosmids_cosmids",
+ "name" : "YACs, Fosmids, & Cosmids",
+ "description" : "This track shows the locations of the cosmids, fosmids, and YACs used for the physical mapping and sequencing of the C. elegans genome. The clone termini do not necessarily correspond to the termini of submitted GenBank/EMBL entries. In some cases the exact termini of the clones is not known. For example, YACs were sequenced using PCR amplification across gaps in the cosmid maps. When a clone end is not known, it is shown as an arrow extending to the end of the display. Such data is to be treated with caution. The Vancouver fosmids can be ordered directly from GeneService.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"Reagents"
- ],
- "description" : "This track shows the locations of the cosmids, fosmids, and YACs used for the physical mapping and sequencing of the C. elegans genome. The clone termini do not necessarily correspond to the termini of submitted GenBank/EMBL entries. In some cases the exact termini of the clones is not known. For example, YACs were sequenced using PCR amplification across gaps in the cosmid maps. When a clone end is not known, it is shown as an arrow extending to the end of the display. Such data is to be treated with caution. The Vancouver fosmids can be ordered directly from GeneService.",
- "name" : "YACs, Fosmids, & Cosmids",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/YACs, Fosmids, & Cosmids/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack"
+ ]
},
{
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"description" : "These are historical operon predictions.",
+ "trackId" : "c_elegans_PRJNA13758_deprecated_operons",
"name" : "Deprecated operons",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Deprecated operons/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "deprecated_operons-c_elegans_PRJNA13758-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "deprecated_operons-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "lightgreen"
+ "color1" : "lightgreen",
+ "type" : "SvgFeatureRenderer"
}
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
- "trackId" : "c_elegans_PRJNA13758_deprecated_operons",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "Genes",
- "Curated Genes"
- ]
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Deprecated operons/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_landmarks",
+ "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "landmarks-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'id')"
- },
- "type" : "SvgFeatureRenderer"
+ }
},
"mouseover" : "jexl:get(feature,'locus')",
+ "displayId" : "landmarks-c_elegans_PRJNA13758-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Landmarks/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Landmarks/{refseq}/trackData.jsonz"
+ }
},
- "type" : "FeatureTrack",
- "name" : "Landmarks"
+ "name" : "Landmarks",
+ "trackId" : "c_elegans_PRJNA13758_landmarks"
},
{
+ "trackId" : "c_elegans_PRJNA13758_low_complextity_region_(dust)",
+ "name" : "Low complextity region (Dust)",
+ "description" : "Low-complexity regions identified by Dust.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"Genome Structure",
"Repeats"
],
- "trackId" : "c_elegans_PRJNA13758_low_complextity_region_(dust)",
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "height" : 4,
- "showDescriptions" : false,
- "color1" : "bisque",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
- },
- "displayId" : "low_complextity_region_(dust)-c_elegans_PRJNA13758-LinearBasicDisplay"
- }
- ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -9178,22 +8559,22 @@
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "name" : "Low complextity region (Dust)",
- "description" : "Low-complexity regions identified by Dust."
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "low_complextity_region_(dust)-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "bisque",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 4
+ }
+ }
+ ]
},
{
- "name" : "P. pacificus proteins",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/P. pacificus proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
"type" : "FeatureTrack",
- "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "trackId" : "c_elegans_PRJNA13758_P_pacificus_proteins",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -9201,209 +8582,210 @@
"Sequence Similarity",
"Proteins"
],
+ "name" : "P. pacificus proteins",
+ "trackId" : "c_elegans_PRJNA13758_P_pacificus_proteins",
+ "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "P_pacificus_proteins-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "orange"
- },
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
- "displayId" : "P_pacificus_proteins-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "height" : 4,
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
+ }
}
- ]
+ ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/P. pacificus proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/RNASeq introns/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ }
},
- "type" : "FeatureTrack",
- "name" : "RNASeq introns",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display.",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "Expression"
- ],
- "trackId" : "c_elegans_PRJNA13758_rnaseq_introns",
"displays" : [
{
- "displayId" : "rnaseq_introns-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
- "height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)",
- "showDescriptions" : false,
- "color1" : "green",
"type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)",
+ "color1" : "green"
},
"mouseover" : "jexl:get(feature,'score')+' reads'",
+ "displayId" : "rnaseq_introns-c_elegans_PRJNA13758-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
+ ],
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display.",
+ "name" : "RNASeq introns",
+ "trackId" : "c_elegans_PRJNA13758_rnaseq_introns",
+ "category" : [
+ "Expression"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
]
},
{
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/RNASeq Splice Junctions (common)/{refseq}/trackData.jsonz"
+ }
+ },
"displays" : [
{
"displayId" : "rnaseq_splice_junctions_(common)-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'score')+' reads'",
"renderer" : {
- "color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "showDescriptions" : false
+ "color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
+ "showDescriptions" : false,
+ "showLabels" : false
},
- "mouseover" : "jexl:get(feature,'score')+' reads'",
"type" : "LinearBasicDisplay"
}
],
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
+ "name" : "RNASeq Splice Junctions (common)",
+ "trackId" : "c_elegans_PRJNA13758_rnaseq_splice_junctions_(common)",
"category" : [
"Expression"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_rnaseq_splice_junctions_(common)",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/RNASeq Splice Junctions (common)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "name" : "RNASeq Splice Junctions (common)"
+ ]
},
{
"displays" : [
{
- "displayId" : "rnaseq_splice_junctions_(rare)-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'score')+' reads'",
"renderer" : {
- "height" : "jexl:4",
"type" : "SvgFeatureRenderer",
+ "color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
"showDescriptions" : false,
+ "height" : "jexl:4",
"showLabels" : false,
- "maxHeight" : 5000,
- "color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))"
+ "maxHeight" : 5000
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "rnaseq_splice_junctions_(rare)-c_elegans_PRJNA13758-LinearBasicDisplay"
}
],
- "category" : [
- "Expression"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_rnaseq_splice_junctions_(rare)",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ }
},
+ "category" : [
+ "Expression"
+ ],
"type" : "FeatureTrack",
- "name" : "RNASeq Splice Junctions (rare)"
- },
- {
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
+ "name" : "RNASeq Splice Junctions (rare)",
+ "trackId" : "c_elegans_PRJNA13758_rnaseq_splice_junctions_(rare)"
+ },
+ {
+ "description" : "Matches to WormBase S. ratti proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "S. ratti proteins",
+ "trackId" : "c_elegans_PRJNA13758_S_ratti_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "trackId" : "c_elegans_PRJNA13758_S_ratti_proteins",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/S. ratti proteins/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
- "displayId" : "S_ratti_proteins-c_elegans_PRJNA13758-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "S_ratti_proteins-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
- "showLabels" : false
- }
+ "height" : 4,
+ "showLabels" : false,
+ "color1" : "orange"
+ },
+ "mouseover" : "jexl:get(feature,'clone')"
}
- ],
+ ]
+ },
+ {
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/S. ratti proteins/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/G4 Motif/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "name" : "S. ratti proteins",
- "description" : "Matches to WormBase S. ratti proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
- },
- {
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/G4 Motif/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "g4_motif-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "magenta",
+ "height" : 7,
+ "type" : "SvgFeatureRenderer"
+ }
+ }
+ ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "name" : "G4 Motif",
"description" : "This track shows the extent of G4 DNA signature. G4 motif is 'Intrinsically mutagenic motif, probably because it can form secondary structures during DNA replication'. Data are from Kruisselbrink E et al. (2008) Curr Biol 'Mutagenic Capacity of Endogenous G4 DNA Underlies Genome Instability in ....'.",
+ "name" : "G4 Motif",
+ "trackId" : "c_elegans_PRJNA13758_g4_motif",
"category" : [
"Sequence Features",
"Signals & Motifs"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_g4_motif",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "height" : 7,
- "type" : "SvgFeatureRenderer",
- "color1" : "magenta"
- },
- "displayId" : "g4_motif-c_elegans_PRJNA13758-LinearBasicDisplay"
- }
]
},
{
"displays" : [
{
- "mouseover" : "jexl:get(feature,'clone')",
+ "type" : "LinearBasicDisplay",
+ "displayId" : "C_japonica_proteins-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "orange"
+ "color1" : "orange",
+ "showLabels" : false,
+ "height" : 4
},
- "type" : "LinearBasicDisplay",
- "displayId" : "C_japonica_proteins-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "trackId" : "c_elegans_PRJNA13758_C_japonica_proteins",
- "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -9411,11 +8793,19 @@
"locationType" : "UriLocation"
}
},
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
+ "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_elegans_PRJNA13758_C_japonica_proteins",
"name" : "C. japonica proteins"
},
{
- "trackId" : "c_elegans_PRJNA13758_c._elegans_osts",
"category" : [
"Genes",
"Supporting Evidence"
@@ -9423,170 +8813,174 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "description" : "ORFeome project (http://worfdb.dfci.harvard.edu/) sequence reads. The ORFeome project designs primer assays for spliced C. elegans mRNAs and then performs sequence reads on rtPCR material, producing 'OSTs.' This track shows ORFeome project OSTs aligned to the genome using BLAT. This track shows the best unique location for each OST.",
+ "trackId" : "c_elegans_PRJNA13758_c._elegans_osts",
+ "name" : "C. elegans OSTs",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "c._elegans_osts-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
- "height" : 5,
"type" : "SvgFeatureRenderer",
+ "height" : 5,
"color1" : "cyan"
- },
- "type" : "LinearBasicDisplay"
+ }
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "name" : "C. elegans OSTs",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/C. elegans OSTs/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/C. elegans OSTs/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
- },
- "description" : "ORFeome project (http://worfdb.dfci.harvard.edu/) sequence reads. The ORFeome project designs primer assays for spliced C. elegans mRNAs and then performs sequence reads on rtPCR material, producing 'OSTs.' This track shows ORFeome project OSTs aligned to the genome using BLAT. This track shows the best unique location for each OST."
+ }
},
{
- "name" : "Microarray oligo probes",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Microarray oligo probes/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Microarray oligo probes/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "description" : "This track contains Affymetrix GeneChip and Washington University GSC microarray probe sets.",
- "trackId" : "c_elegans_PRJNA13758_microarray_oligo_probes",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "Reagents"
- ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"displays" : [
{
- "displayId" : "microarray_oligo_probes-c_elegans_PRJNA13758-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "microarray_oligo_probes-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"color1" : "black",
- "height" : 4
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
}
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- }
- },
- {
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "This track contains Affymetrix GeneChip and Washington University GSC microarray probe sets.",
+ "name" : "Microarray oligo probes",
+ "trackId" : "c_elegans_PRJNA13758_microarray_oligo_probes",
"category" : [
- "Sequence Features",
- "Binding Sites & Regions"
+ "Reagents"
],
- "trackId" : "c_elegans_PRJNA13758_enhancers",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ]
+ },
+ {
"displays" : [
{
- "displayId" : "enhancers-c_elegans_PRJNA13758-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "green",
"type" : "SvgFeatureRenderer"
- }
+ },
+ "displayId" : "enhancers-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Enhancers/{refseq}/trackData.jsonz"
- }
+ },
+ "type" : "NCListAdapter"
},
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
+ "category" : [
+ "Sequence Features",
+ "Binding Sites & Regions"
+ ],
+ "trackId" : "c_elegans_PRJNA13758_enhancers",
"name" : "Enhancers"
},
{
"description" : "Matches to WormBase O. volvulus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_elegans_PRJNA13758_O_volvulus_proteins",
+ "name" : "O. volvulus proteins",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/O. volvulus proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ }
},
- "type" : "FeatureTrack",
- "name" : "O. volvulus proteins",
"displays" : [
{
+ "displayId" : "O_volvulus_proteins-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
- "color1" : "orange",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 4
+ "height" : 4,
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
},
"mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
- "displayId" : "O_volvulus_proteins-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "trackId" : "c_elegans_PRJNA13758_O_volvulus_proteins"
+ ]
},
{
- "trackId" : "c_elegans_PRJNA13758_B_malayi_proteins",
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
- "displayId" : "B_malayi_proteins-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
"type" : "SvgFeatureRenderer",
+ "height" : 4,
"showLabels" : false,
"color1" : "orange"
},
"mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "B_malayi_proteins-c_elegans_PRJNA13758-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
- "name" : "B. malayi proteins",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/B. malayi proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "NCListAdapter"
},
"type" : "FeatureTrack",
- "description" : "Matches to WormBase B. malayi proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
- },
- {
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "name" : "B. malayi proteins",
+ "trackId" : "c_elegans_PRJNA13758_B_malayi_proteins",
+ "description" : "Matches to WormBase B. malayi proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ },
+ {
"category" : [
"Genes",
"Supporting Evidence"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "The submitted RACE data come from cloning and sequencing of 5' and 3' C.elegans RACE PCR products. The experiments were done using RNA isolated from 'mix stage' wild-type N2 worms. SL1 and SL2 were used as 5' universal primers for 5'RACE experiments. The 'RST's' (i.e., RACE Sequence Tags), are 5' reads from cloned RACE products (sequenced as minipools). Sequences are vector trimmed then quality trimmed (SL sequences are not removed from 5' RST's). In quality trimming, the first sliding window of 20 nt long with an average quality score higher than 15 marks the start of good quality sequences. Likewise, the first sliding window of 20 nt with average quality score lower than 15 marks the end of good quality sequences. Each RST is identified as being 5' or 3'(indicated as 5-RST or 3-RST) followed by a unique trace ID (e.g., >CCSB_5-RST_373657). 1,355 5' and 1589 3' RSTs are included in this submission. Data provided by Kourosh Salehi-Ashtiani, Vidal Lab. For information on the project, please see the (http://worfdb.dfci.harvard.edu/index.php?page=race) Race Project Page at (http://worfdb.dfci.harvard.edu/) WorfDB.",
+ "name" : "C.elegans RSTs",
"trackId" : "c_elegans_PRJNA13758_c.elegans_rsts",
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
@@ -9594,61 +8988,67 @@
"displays" : [
{
"displayId" : "c.elegans_rsts-c_elegans_PRJNA13758-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"color1" : "jexl:startsWith(get(feature,'Target'),'RST5')==true?'green':'red'",
"height" : 5
- }
+ },
+ "type" : "LinearBasicDisplay"
}
],
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/C.elegans RSTs/{refseq}/trackData.jsonz"
- }
- },
- "type" : "FeatureTrack",
- "name" : "C.elegans RSTs",
- "description" : "The submitted RACE data come from cloning and sequencing of 5' and 3' C.elegans RACE PCR products. The experiments were done using RNA isolated from 'mix stage' wild-type N2 worms. SL1 and SL2 were used as 5' universal primers for 5'RACE experiments. The 'RST's' (i.e., RACE Sequence Tags), are 5' reads from cloned RACE products (sequenced as minipools). Sequences are vector trimmed then quality trimmed (SL sequences are not removed from 5' RST's). In quality trimming, the first sliding window of 20 nt long with an average quality score higher than 15 marks the start of good quality sequences. Likewise, the first sliding window of 20 nt with average quality score lower than 15 marks the end of good quality sequences. Each RST is identified as being 5' or 3'(indicated as 5-RST or 3-RST) followed by a unique trace ID (e.g., >CCSB_5-RST_373657). 1,355 5' and 1589 3' RSTs are included in this submission. Data provided by Kourosh Salehi-Ashtiani, Vidal Lab. For information on the project, please see the (http://worfdb.dfci.harvard.edu/index.php?page=race) Race Project Page at (http://worfdb.dfci.harvard.edu/) WorfDB."
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/C.elegans RSTs/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Prediction: mSplicer-ORF/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
+ "trackId" : "c_elegans_PRJNA13758_prediction:_msplicer_orf",
"name" : "Prediction: mSplicer-ORF",
"description" : "mSplicer predict the splice forms for a given start and end of a transcript. (Note that it is not yet a full-featured gene-finder.) There are two versions: 1. 'mSplicer' which splices general pre-mRNA (including UTR or coding regions) without assuming the existence of a reading frame (requires transcription start and stop). 2. 'mSplicer-ORF' is optimized for coding regions and requires the knowledge of the translation start and stop. These predictions were generated against regions annotated in WS160. More details can be found at http://www.fml.mpg.de/raetsch/projects/msplicer",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"Genes",
"Ab-initio predictions"
],
- "trackId" : "c_elegans_PRJNA13758_prediction:_msplicer_orf",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Prediction: mSplicer-ORF/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
},
"displays" : [
{
- "displayId" : "prediction:_msplicer_orf-c_elegans_PRJNA13758-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "prediction:_msplicer_orf-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
"color1" : "palevioletred",
"type" : "SvgFeatureRenderer"
}
}
- ]
+ ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ }
},
{
"description" : "This Nanopore transcript data is from the paper 'The full-length transcriptome of C. elegans using direct RNA sequencing' Roach et al. https://doi.org/10.1101/598763. Where several transcripts are nearly identical, they are represented by a single transcript and the number of transcripts is recorded in the read coverage. Sequencing is from 3' to 5' and randomly terminates, so the 5' end of transcripts is often incomplete.",
"name" : "Nanopore matches",
+ "trackId" : "c_elegans_PRJNA13758_nanopore_matches",
+ "category" : [
+ "Genes",
+ "Supporting Evidence"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -9656,130 +9056,140 @@
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Nanopore matches/{refseq}/trackData.jsonz"
}
},
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "nanopore_matches-c_elegans_PRJNA13758-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
+ "height" : 4,
+ "showLabels" : false,
"color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA'?'lightblue':'green'",
"maxHeight" : 5000,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 4
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "nanopore_matches-c_elegans_PRJNA13758-LinearBasicDisplay"
}
- ],
- "trackId" : "c_elegans_PRJNA13758_nanopore_matches",
- "category" : [
- "Genes",
- "Supporting Evidence"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
]
},
{
- "description" : "This track indicates the location of primer pairs that were generated to confirm the existence of indels but the exact size and context of the alteration was not determined. The span feature identifies the broad region where the variation exists. Click on the element to obtain additional information.",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Variation PCR products/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Variation PCR products/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "name" : "Variation PCR products",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
"displays" : [
{
- "displayId" : "variation_pcr_products-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
"height" : 8,
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "variation_pcr_products-c_elegans_PRJNA13758-LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
+ "description" : "This track indicates the location of primer pairs that were generated to confirm the existence of indels but the exact size and context of the alteration was not determined. The span feature identifies the broad region where the variation exists. Click on the element to obtain additional information.",
+ "trackId" : "c_elegans_PRJNA13758_variation_pcr_products",
+ "name" : "Variation PCR products",
"category" : [
"Alleles, Variations, RNAi"
],
- "trackId" : "c_elegans_PRJNA13758_variation_pcr_products"
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack"
},
{
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "Genome Structure",
+ "Repeats"
+ ],
+ "name" : "Tandem and Inverted Repeats",
+ "trackId" : "c_elegans_PRJNA13758_tandem_and_inverted_repeats",
+ "description" : "Exact tandem and inverted repetitive elements.",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "tandem_and_inverted_repeats-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
"color1" : "bisque",
- "showDescriptions" : false
- },
- "displayId" : "tandem_and_inverted_repeats-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "showDescriptions" : false,
+ "showLabels" : false
+ }
}
],
- "category" : [
- "Genome Structure",
- "Repeats"
- ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Tandem and Inverted Repeats/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ }
+ },
+ {
+ "name" : "Genbank submissions",
+ "trackId" : "c_elegans_PRJNA13758_genbank_submissions",
+ "description" : "The C. elegans genome was submitted to the GenBank and EMBL databases in in the form of a set of minimally-overlapping segments. This track shows the position of these accessioned entries.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_tandem_and_inverted_repeats",
- "description" : "Exact tandem and inverted repetitive elements.",
- "type" : "FeatureTrack",
+ "category" : [
+ "Genome Structure",
+ "Assembly & Curation"
+ ],
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Tandem and Inverted Repeats/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Genbank submissions/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "NCListAdapter"
},
- "name" : "Tandem and Inverted Repeats"
- },
- {
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "genbank_submissions-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
"height" : 4,
"color1" : "sienna",
"type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'genbank')",
- "type" : "LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'genbank')"
}
],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ }
+ },
+ {
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "trackId" : "c_elegans_PRJNA13758_genbank_submissions",
- "category" : [
- "Genome Structure",
- "Assembly & Curation"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
+ "displays" : [
+ {
+ "displayId" : "prediction:_msplicer_transcript-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "palevioletred"
+ },
+ "type" : "LinearBasicDisplay"
+ }
],
- "description" : "The C. elegans genome was submitted to the GenBank and EMBL databases in in the form of a set of minimally-overlapping segments. This track shows the position of these accessioned entries.",
- "name" : "Genbank submissions",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Genbank submissions/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Prediction: mSplicer/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
}
- }
- },
- {
- "trackId" : "c_elegans_PRJNA13758_prediction:_msplicer_transcript",
+ },
"category" : [
"Genes",
"Ab-initio predictions"
@@ -9787,208 +9197,213 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "description" : "mSplicer predict the splice forms for a given start and end of a transcript. (Note that it is not yet a full-featured gene-finder.) There are two versions: 1. 'mSplicer' which splices general pre-mRNA (including UTR or coding regions) without assuming the existence of a reading frame (requires transcription start and stop). 2. 'mSplicer-ORF' is optimized for coding regions and requires the knowledge of the translation start and stop. These predictions were generated against regions annotated in WS160. More details can be found at http://www.fml.mpg.de/raetsch/projects/msplicer",
+ "trackId" : "c_elegans_PRJNA13758_prediction:_msplicer_transcript",
+ "name" : "Prediction: mSplicer"
+ },
+ {
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "palevioletred",
- "type" : "SvgFeatureRenderer"
+ "type" : "SvgFeatureRenderer",
+ "outline" : "jexl:get(feature,'vep_impact')=='HIGH'?'red':get(feature,'vep_impact')=='MODIFIER'?'purple':get(feature,'vep_impact')=='MODERATE'?'gold':get(feature,'vep_impact')=='LOW'?'cyan':'black'",
+ "color1" : "jexl:get(feature,'vep_impact')=='HIGH'?'red':get(feature,'vep_impact')=='MODIFIER'?'purple':get(feature,'vep_impact')=='MODERATE'?'gold':get(feature,'vep_impact')=='LOW'?'cyan':'white'",
+ "labels" : {
+ "name" : "jexl:get(feature,'other_name')=='undefined'?get(feature,'public_name'):get(feature,'public_name')+' '+get(feature,'other_name')"
+ }
},
- "displayId" : "prediction:_msplicer_transcript-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "displayId" : "million_mutation_project-c_elegans_PRJNA13758-LinearBasicDisplay"
}
],
"formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+'', WormBase: 'Variation Page'}"
},
- "name" : "Prediction: mSplicer",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Prediction: mSplicer/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Million Mutation Project/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
"type" : "FeatureTrack",
- "description" : "mSplicer predict the splice forms for a given start and end of a transcript. (Note that it is not yet a full-featured gene-finder.) There are two versions: 1. 'mSplicer' which splices general pre-mRNA (including UTR or coding regions) without assuming the existence of a reading frame (requires transcription start and stop). 2. 'mSplicer-ORF' is optimized for coding regions and requires the knowledge of the translation start and stop. These predictions were generated against regions annotated in WS160. More details can be found at http://www.fml.mpg.de/raetsch/projects/msplicer"
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "Alleles, Variations, RNAi"
+ ],
+ "name" : "Million Mutation Project",
+ "trackId" : "c_elegans_PRJNA13758_million_mutation_project",
+ "description" : "This track shows SNPs from the The Million Mutation Project (Waterston/Moerman). Color signifies the severity of impact predicted by Ensembl's Variant Effect Predictor. 'HIGH' impacts are red, 'MEDIUM' are yellow, 'LOW' are cyan (light blue), and 'MODIFIER' are purple. This is the same color scheme as is used at the Alliance of Genome Resources."
},
{
- "trackId" : "c_elegans_PRJNA13758_million_mutation_project",
+ "description" : "Native (same-species) Expressed Sequence Tags (ESTs), aligned to the genome using BLAT. This track shows the best unique location for each EST. The paired 5' and 3' ESTs from the same cDNA clone are connected by a dashed line and a colored light green. ESTs with no mate are yellow, and ESTs with a mate that is 'far away' are dark green.",
+ "name" : "ESTs",
+ "trackId" : "c_elegans_PRJNA13758_ests",
"category" : [
- "Alleles, Variations, RNAi"
+ "Genes",
+ "Supporting Evidence"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "displays" : [
- {
- "displayId" : "million_mutation_project-c_elegans_PRJNA13758-LinearBasicDisplay",
- "renderer" : {
- "labels" : {
- "name" : "jexl:get(feature,'other_name')=='undefined'?get(feature,'public_name'):get(feature,'public_name')+' '+get(feature,'other_name')"
- },
- "type" : "SvgFeatureRenderer",
- "outline" : "jexl:get(feature,'vep_impact')=='HIGH'?'red':get(feature,'vep_impact')=='MODIFIER'?'purple':get(feature,'vep_impact')=='MODERATE'?'gold':get(feature,'vep_impact')=='LOW'?'cyan':'black'",
- "color1" : "jexl:get(feature,'vep_impact')=='HIGH'?'red':get(feature,'vep_impact')=='MODIFIER'?'purple':get(feature,'vep_impact')=='MODERATE'?'gold':get(feature,'vep_impact')=='LOW'?'cyan':'white'"
- },
- "type" : "LinearBasicDisplay"
- }
- ],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+'', WormBase: 'Variation Page'}"
- },
- "name" : "Million Mutation Project",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Million Mutation Project/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/ESTs (best)/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "description" : "This track shows SNPs from the The Million Mutation Project (Waterston/Moerman). Color signifies the severity of impact predicted by Ensembl's Variant Effect Predictor. 'HIGH' impacts are red, 'MEDIUM' are yellow, 'LOW' are cyan (light blue), and 'MODIFIER' are purple. This is the same color scheme as is used at the Alliance of Genome Resources."
- },
- {
"displays" : [
{
- "displayId" : "ests-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "maxHeight" : 5000,
"color1" : "jexl:parent(feature)=='undefined'?'red':get(parent(feature),'has_mate')==1?'limegreen':get(parent(feature),'has_mate')==2?'green':get(parent(feature),'has_mate')==0?'gold':'black'",
+ "maxHeight" : 5000,
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "ests-c_elegans_PRJNA13758-LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
- "trackId" : "c_elegans_PRJNA13758_ests",
- "category" : [
- "Genes",
- "Supporting Evidence"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : "Native (same-species) Expressed Sequence Tags (ESTs), aligned to the genome using BLAT. This track shows the best unique location for each EST. The paired 5' and 3' ESTs from the same cDNA clone are connected by a dashed line and a colored light green. ESTs with no mate are yellow, and ESTs with a mate that is 'far away' are dark green.",
- "name" : "ESTs",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/ESTs (best)/{refseq}/trackData.jsonz"
- }
- },
- "type" : "FeatureTrack"
+ }
},
{
+ "name" : "Other UniProt proteins",
+ "trackId" : "c_elegans_PRJNA13758_other_uniprot_proteins",
"description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Other UniProt proteins/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Other UniProt proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "name" : "Other UniProt proteins",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "orange",
+ "height" : 4,
"showDescriptions" : false,
- "height" : 4
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "other_uniprot_proteins-c_elegans_PRJNA13758-LinearBasicDisplay"
}
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
+ ]
+ },
+ {
+ "name" : "Prediction: Twinscan",
+ "trackId" : "c_elegans_PRJNA13758_prediction:_twinscan",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_other_uniprot_proteins"
- },
- {
+ "category" : [
+ "Genes",
+ "Ab-initio predictions"
+ ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Prediction: Twinscan/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"displays" : [
{
- "displayId" : "prediction:_twinscan-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "palevioletred",
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "prediction:_twinscan-c_elegans_PRJNA13758-LinearBasicDisplay"
}
- ],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
- "trackId" : "c_elegans_PRJNA13758_prediction:_twinscan",
+ ]
+ },
+ {
+ "description" : "Native (same species) RNAseq data was assembled with Trinity and then aligned to the genome with BLAT",
+ "trackId" : "c_elegans_PRJNA13758_trinity-assembled_rnaseq",
+ "name" : "Trinity-assembled RNAseq",
"category" : [
"Genes",
- "Ab-initio predictions"
+ "Supporting Evidence"
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "name" : "Prediction: Twinscan",
+ "type" : "FeatureTrack",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Prediction: Twinscan/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Trinity-assembled RNAseq/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ }
},
- "type" : "FeatureTrack"
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "mediumpurple",
+ "height" : 5,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "trinity-assembled_rnaseq-c_elegans_PRJNA13758-LinearBasicDisplay"
+ }
+ ]
},
{
- "trackId" : "c_elegans_PRJNA13758_trinity-assembled_rnaseq",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"Genes",
- "Supporting Evidence"
+ "Ab-initio predictions"
],
+ "trackId" : "c_elegans_PRJNA13758_prediction:_rnaz",
+ "name" : "Prediction: RNAz non-coding RNA genes",
+ "description" : "RNAz-derived ncRNAs were predicted using the RNAz algorithm. Please select the RNA for more details.",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "prediction:_rnaz-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
- "height" : 5,
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "mediumpurple"
- },
- "displayId" : "trinity-assembled_rnaseq-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "color1" : "palevioletred"
+ }
}
],
- "name" : "Trinity-assembled RNAseq",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Trinity-assembled RNAseq/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/RNAz non-coding RNA genes/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Native (same species) RNAseq data was assembled with Trinity and then aligned to the genome with BLAT"
+ }
},
{
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/RNAz non-coding RNA genes/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
"type" : "FeatureTrack",
- "name" : "Prediction: RNAz non-coding RNA genes",
- "description" : "RNAz-derived ncRNAs were predicted using the RNAz algorithm. Please select the RNA for more details.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -9996,200 +9411,167 @@
"Genes",
"Ab-initio predictions"
],
- "trackId" : "c_elegans_PRJNA13758_prediction:_rnaz",
+ "name" : "Prediction: GeneFinder",
+ "trackId" : "c_elegans_PRJNA13758_prediction:_genefinder",
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
"displays" : [
{
- "displayId" : "prediction:_rnaz-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
- "color1" : "palevioletred",
- "type" : "SvgFeatureRenderer"
+ "type" : "SvgFeatureRenderer",
+ "color1" : "palevioletred"
},
+ "displayId" : "prediction:_genefinder-c_elegans_PRJNA13758-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Prediction: GeneFinder/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Links and Superlinks/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
- "displayId" : "prediction:_genefinder-c_elegans_PRJNA13758-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "palevioletred",
- "type" : "SvgFeatureRenderer"
- }
+ "type" : "SvgFeatureRenderer",
+ "height" : 4,
+ "color1" : "black"
+ },
+ "displayId" : "links_and_superlinks-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "trackId" : "c_elegans_PRJNA13758_prediction:_genefinder",
+ "name" : "Links and Superlinks",
+ "trackId" : "c_elegans_PRJNA13758_links_and_superlinks",
+ "description" : "This track shows the location and coordinates of contigs created during the assembly of the C. elegans genome.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
- "Genes",
- "Ab-initio predictions"
- ],
- "name" : "Prediction: GeneFinder",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Prediction: GeneFinder/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- }
+ "Genome Structure",
+ "Assembly & Curation"
+ ]
},
{
+ "trackId" : "c_elegans_PRJNA13758_contig_submissions",
+ "name" : "Contig submissions",
+ "description" : "This track shows the location and coordinates of contigs (mostly cosmids) submitted to GenBank/EMBL.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"Genome Structure",
"Assembly & Curation"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_links_and_superlinks",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Contig submissions/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
},
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "contig_submissions-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
"type" : "SvgFeatureRenderer",
- "color1" : "black"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "links_and_superlinks-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "color1" : "sienna",
+ "height" : 7
+ }
}
],
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Links and Superlinks/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "Links and Superlinks",
- "description" : "This track shows the location and coordinates of contigs created during the assembly of the C. elegans genome."
- },
- {
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
+ }
+ },
+ {
"displays" : [
{
- "displayId" : "contig_submissions-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
+ "displayId" : "S_cerevisiae_proteins-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
- "height" : 7,
"type" : "SvgFeatureRenderer",
- "color1" : "sienna"
+ "height" : 4,
+ "showLabels" : false,
+ "color1" : "orange"
},
- "type" : "LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')"
}
],
- "category" : [
- "Genome Structure",
- "Assembly & Curation"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_contig_submissions",
- "description" : "This track shows the location and coordinates of contigs (mostly cosmids) submitted to GenBank/EMBL.",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Contig submissions/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "Contig submissions"
- },
- {
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "name" : "S. cerevisiae proteins",
- "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
],
"trackId" : "c_elegans_PRJNA13758_S_cerevisiae_proteins",
- "displays" : [
- {
- "displayId" : "S_cerevisiae_proteins-c_elegans_PRJNA13758-LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
- "renderer" : {
- "height" : 4,
- "color1" : "orange",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay"
- }
- ]
+ "name" : "S. cerevisiae proteins",
+ "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
},
{
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Genes",
+ "Ab-initio predictions"
+ ],
+ "trackId" : "c_elegans_PRJNA13758_prediction:_mgene",
+ "name" : "Prediction: mGene",
"displays" : [
{
- "displayId" : "prediction:_mgene-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "palevioletred"
+ "color1" : "palevioletred",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "prediction:_mgene-c_elegans_PRJNA13758-LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "trackId" : "c_elegans_PRJNA13758_prediction:_mgene",
- "category" : [
- "Genes",
- "Ab-initio predictions"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "name" : "Prediction: mGene",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Prediction: mGene/{refseq}/trackData.jsonz"
}
- },
- "type" : "FeatureTrack"
+ }
},
{
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
- "displays" : [
- {
- "displayId" : "prediction:_genemarkhmm-c_elegans_PRJNA13758-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "palevioletred"
- }
- }
- ],
+ "name" : "Prediction: GeneMarkHMM",
+ "trackId" : "c_elegans_PRJNA13758_prediction:_genemarkhmm",
+ "description" : "These are GeneMarkHMM gene predictions provided by Mark Borodovsky.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -10197,17 +9579,26 @@
"Genes",
"Ab-initio predictions"
],
- "trackId" : "c_elegans_PRJNA13758_prediction:_genemarkhmm",
- "description" : "These are GeneMarkHMM gene predictions provided by Mark Borodovsky.",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Prediction: GeneMarkHMM/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Prediction: GeneMarkHMM/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "name" : "Prediction: GeneMarkHMM"
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "prediction:_genemarkhmm-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "palevioletred",
+ "type" : "SvgFeatureRenderer"
+ }
+ }
+ ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ }
},
{
"adapter" : {
@@ -10217,100 +9608,109 @@
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "H_sapiens_proteins-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "renderer" : {
+ "height" : 4,
+ "showLabels" : false,
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
+ },
+ "mouseover" : "jexl:get(feature,'clone')"
+ }
+ ],
+ "trackId" : "c_elegans_PRJNA13758_H_sapiens_proteins",
"name" : "H. sapiens proteins",
"description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ]
+ },
+ {
"category" : [
"Sequence Similarity",
"Proteins"
],
- "trackId" : "c_elegans_PRJNA13758_H_sapiens_proteins",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_elegans_PRJNA13758_C_remanei_proteins",
+ "name" : "C. remanei proteins",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "orange",
- "height" : 4
+ "showLabels" : false,
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
- "displayId" : "H_sapiens_proteins-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "displayId" : "C_remanei_proteins-c_elegans_PRJNA13758-LinearBasicDisplay"
}
- ]
- },
- {
- "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "type" : "FeatureTrack",
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/C. remanei proteins/{refseq}/trackData.jsonz"
}
+ }
+ },
+ {
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/ORFeome PCR Products/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "name" : "C. remanei proteins",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "orange",
- "height" : 4
+ "height" : 6,
+ "color1" : "jexl:get(feature,'amplified')==1?'green':'red'",
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
- "displayId" : "C_remanei_proteins-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "displayId" : "orfeome_pcr_products-c_elegans_PRJNA13758-LinearBasicDisplay"
}
],
+ "trackId" : "c_elegans_PRJNA13758_orfeome_pcr_products",
+ "name" : "ORFeome PCR Products",
+ "description" : "This track contains Orfeome Project primer pairs and RACE tags. These primers were used to amplify C. elegans cDNAs. A positive amplification, shown in green, is evidence that the region between the two primers is transcribed. Failure to amplify, shown in red, suggests either that the gene model is incorrect, or that the gene is expressed at very low levels. Detailed gene models derived from ORFeome sequencing will be added to this display in the future. See Reboul et al. Nat. Genet. 2003 Apr 7 and WORFdb for further information.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "trackId" : "c_elegans_PRJNA13758_C_remanei_proteins"
+ "Genes",
+ "Supporting Evidence"
+ ]
},
{
- "name" : "ORFeome PCR Products",
+ "name" : "Change-of-function alleles",
+ "trackId" : "c_elegans_PRJNA13758_change-of-function_alleles",
+ "description" : "This track shows alleles that generate a putative change-of-function. In this track, the type of mutation is indicated by its glyph: Boxes are deletions or substitutions. Triangles are insertions. Point mutations are diamonds. Color signifies the severity of impact predicted by Ensembl's Variant Effect Predictor. 'HIGH' impacts are red, 'MEDIUM' are yellow, 'LOW' are cyan (light blue), and 'MODIFIER' are purple. This is the same color scheme as is used at the Alliance of Genome Resources.",
"type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/ORFeome PCR Products/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "description" : "This track contains Orfeome Project primer pairs and RACE tags. These primers were used to amplify C. elegans cDNAs. A positive amplification, shown in green, is evidence that the region between the two primers is transcribed. Failure to amplify, shown in red, suggests either that the gene model is incorrect, or that the gene is expressed at very low levels. Detailed gene models derived from ORFeome sequencing will be added to this display in the future. See Reboul et al. Nat. Genet. 2003 Apr 7 and WORFdb for further information.",
- "trackId" : "c_elegans_PRJNA13758_orfeome_pcr_products",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
- "Genes",
- "Supporting Evidence"
- ],
- "displays" : [
- {
- "displayId" : "orfeome_pcr_products-c_elegans_PRJNA13758-LinearBasicDisplay",
- "renderer" : {
- "height" : 6,
- "color1" : "jexl:get(feature,'amplified')==1?'green':'red'",
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay"
- }
+ "Alleles, Variations, RNAi"
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- }
- },
- {
- "name" : "Change-of-function alleles",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -10318,26 +9718,17 @@
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Change-of-function alleles/{refseq}/trackData.jsonz"
}
},
- "type" : "FeatureTrack",
- "description" : "This track shows alleles that generate a putative change-of-function. In this track, the type of mutation is indicated by its glyph: Boxes are deletions or substitutions. Triangles are insertions. Point mutations are diamonds. Color signifies the severity of impact predicted by Ensembl's Variant Effect Predictor. 'HIGH' impacts are red, 'MEDIUM' are yellow, 'LOW' are cyan (light blue), and 'MODIFIER' are purple. This is the same color scheme as is used at the Alliance of Genome Resources.",
- "trackId" : "c_elegans_PRJNA13758_change-of-function_alleles",
- "category" : [
- "Alleles, Variations, RNAi"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
+ "maxHeight" : 5000,
"type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
"showLabels" : false,
- "color1" : "jexl:get(feature,'vep_impact')=='HIGH'?'red':get(feature,'vep_impact')=='MODIFIER'?'purple':get(feature,'vep_impact')=='MODERATE'?'gold':get(feature,'vep_impact')=='LOW'?'cyan':'white'",
- "maxHeight" : 5000,
- "showDescriptions" : false
+ "color1" : "jexl:get(feature,'vep_impact')=='HIGH'?'red':get(feature,'vep_impact')=='MODIFIER'?'purple':get(feature,'vep_impact')=='MODERATE'?'gold':get(feature,'vep_impact')=='LOW'?'cyan':'white'"
},
"mouseover" : "jexl:get(feature,'name')+', '+get(feature,'consequence')",
- "type" : "LinearBasicDisplay",
"displayId" : "change-of-function_alleles-c_elegans_PRJNA13758-LinearBasicDisplay"
}
],
@@ -10346,29 +9737,19 @@
}
},
{
- "trackId" : "c_elegans_PRJNA13758_C_briggsae_proteins",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
"displays" : [
{
"type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "C_briggsae_proteins-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
"height" : 4,
+ "showLabels" : false,
"color1" : "orange",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "C_briggsae_proteins-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')"
}
],
- "name" : "C. briggsae proteins",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -10376,286 +9757,285 @@
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/C. briggsae proteins/{refseq}/trackData.jsonz"
}
},
- "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "C. briggsae proteins",
+ "trackId" : "c_elegans_PRJNA13758_C_briggsae_proteins"
},
{
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz"
+ }
+ },
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "bisque",
+ "showLabels" : false,
"showDescriptions" : false,
"height" : 4
},
"displayId" : "repeat_region_(repeatmasker)-c_elegans_PRJNA13758-LinearBasicDisplay"
}
],
+ "description" : "Repetitive regions identified by RepeatMasker.",
+ "name" : "Repeat Region (RepeatMasker)",
"trackId" : "c_elegans_PRJNA13758_repeat_region_(repeatmasker)",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"Genome Structure",
"Repeats"
],
- "description" : "Repetitive regions identified by RepeatMasker.",
- "name" : "Repeat Region (RepeatMasker)",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack"
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ]
},
{
- "description" : "Transcriptionally Active Regions (TARs) found by the Miller lab from tiling-array projects run as part of the modENCODE project.",
+ "trackId" : "c_elegans_PRJNA13758_transcriptionally_active_region",
"name" : "Transcriptionally Active Region",
+ "description" : "Transcriptionally Active Regions (TARs) found by the Miller lab from tiling-array projects run as part of the modENCODE project.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Genes",
+ "Supporting Evidence"
+ ],
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Transcriptionally Active Region/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Transcriptionally Active Region/{refseq}/trackData.jsonz"
+ }
},
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "transcriptionally_active_region-c_elegans_PRJNA13758-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "green",
- "height" : 5
- }
+ "height" : 5,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "transcriptionally_active_region-c_elegans_PRJNA13758-LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
- "trackId" : "c_elegans_PRJNA13758_transcriptionally_active_region",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "Genes",
- "Supporting Evidence"
- ]
+ }
},
{
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Non-C. elegans Isoseq collection (best)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "green",
"type" : "SvgFeatureRenderer",
+ "color1" : "green",
"height" : 4
},
"displayId" : "non-c._elegans_isoseq_collection_(best)-c_elegans_PRJNA13758-LinearBasicDisplay"
}
],
"trackId" : "non-c._elegans_isoseq_collection_(best)-c_elegans_PRJNA13758",
- "category" : [
- "Sequence Similarity",
- "Nucleotide"
- ],
+ "name" : "Non-C. elegans Isoseq collection (best)",
+ "description" : "IsoSeq from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each IsoSeqsequence.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : "IsoSeq from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each IsoSeqsequence.",
- "name" : "Non-C. elegans Isoseq collection (best)",
+ "type" : "FeatureTrack",
+ "category" : [
+ "Sequence Similarity",
+ "Nucleotide"
+ ]
+ },
+ {
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Non-C. elegans Isoseq collection (best)/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/C. elegans proteins/{refseq}/trackData.jsonz"
}
},
- "type" : "FeatureTrack"
- },
- {
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "C_elegans_proteins-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "orange",
+ "height" : 4,
+ "showLabels" : false
+ },
+ "mouseover" : "jexl:get(feature,'clone')"
+ }
+ ],
+ "trackId" : "c_elegans_PRJNA13758_C_elegans_proteins",
+ "name" : "C. elegans proteins",
+ "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
- ],
- "trackId" : "c_elegans_PRJNA13758_C_elegans_proteins",
+ ]
+ },
+ {
"displays" : [
{
- "mouseover" : "jexl:get(feature,'clone')",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 4,
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "orange"
+ "height" : 7,
+ "color1" : "red"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "C_elegans_proteins-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "displayId" : "mass_spec_peptides-c_elegans_PRJNA13758-LinearBasicDisplay"
}
],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/C. elegans proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Mass spec peptides/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
},
+ "category" : [
+ "Sequence Features",
+ "Translated Features"
+ ],
"type" : "FeatureTrack",
- "name" : "C. elegans proteins",
- "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
- },
- {
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "This track shows peptides identified in mass spec proteomics experiments.",
+ "name" : "Mass spec peptides",
+ "trackId" : "c_elegans_PRJNA13758_mass_spec_peptides"
+ },
+ {
"category" : [
- "Sequence Features",
- "Translated Features"
+ "Sequence Similarity",
+ "Proteins"
],
- "trackId" : "c_elegans_PRJNA13758_mass_spec_peptides",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "C. brenneri proteins",
+ "trackId" : "c_elegans_PRJNA13758_C_brenneri_proteins",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 7,
- "color1" : "red",
+ "showLabels" : false,
+ "height" : 4,
+ "color1" : "orange",
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "mass_spec_peptides-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "C_brenneri_proteins-c_elegans_PRJNA13758-LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Mass spec peptides/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/C. brenneri proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
}
- },
- "name" : "Mass spec peptides",
- "description" : "This track shows peptides identified in mass spec proteomics experiments."
+ }
},
{
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/C. brenneri proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/TEC-RED tags/{refseq}/trackData.jsonz"
}
},
- "name" : "C. brenneri proteins",
- "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "trackId" : "c_elegans_PRJNA13758_C_brenneri_proteins",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
- "color1" : "orange",
- "showLabels" : false,
+ "height" : 5,
+ "color1" : "red",
"type" : "SvgFeatureRenderer"
},
- "displayId" : "C_brenneri_proteins-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "displayId" : "tec-red_tags-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ]
- },
- {
+ ],
+ "description" : "Trans-spliced Exon Coupled RNA End Determination (TEC-RED) tags. TEC-RED uses a method similar to SAGE to identify expressed genes and characterize the 5' end of transcripts.",
+ "name" : "TEC-RED tags",
"trackId" : "c_elegans_PRJNA13758_tec-red_tags",
"category" : [
"Genes",
"Supporting Evidence"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
+ ]
+ },
+ {
"displays" : [
{
+ "displayId" : "sage_tags-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
- "height" : 5,
- "color1" : "red",
- "type" : "SvgFeatureRenderer"
+ "type" : "SvgFeatureRenderer",
+ "height" : 7,
+ "color1" : "lightgray"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "tec-red_tags-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
- "name" : "TEC-RED tags",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/TEC-RED tags/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/SAGE tags/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
"type" : "FeatureTrack",
- "description" : "Trans-spliced Exon Coupled RNA End Determination (TEC-RED) tags. TEC-RED uses a method similar to SAGE to identify expressed genes and characterize the 5' end of transcripts."
- },
- {
- "trackId" : "c_elegans_PRJNA13758_sage_tags",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"Expression"
],
- "displays" : [
- {
- "displayId" : "sage_tags-c_elegans_PRJNA13758-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "lightgray",
- "height" : 7
- }
- }
- ],
"name" : "SAGE tags",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/SAGE tags/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
+ "trackId" : "c_elegans_PRJNA13758_sage_tags",
"description" : "This track indicates the location of Serial Analysis of Gene Expression (SAGE) patterns associated with a tag and its associated genes. Tags shown in grey are either unambiguously mapped to a gene elsewhere or are ambigous due to multiple occurences in genomic or trascript sequences. Colored tags are mapped unambiguously to a single gene or genomic location. Violet and turquoise refer to the plus strand and minus strands, respectively. The number shown above tags is the total number of times this tag was observed in all SAGE experiments."
},
{
- "displays" : [
- {
- "displayId" : "T_muris_proteins-c_elegans_PRJNA13758-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "orange",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 4
- },
- "mouseover" : "jexl:get(feature,'clone')"
- }
- ],
+ "description" : "Matches to WormBase T. muris proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"trackId" : "c_elegans_PRJNA13758_T_muris_proteins",
+ "name" : "T. muris proteins",
"category" : [
"Sequence Similarity",
"Proteins"
@@ -10663,187 +10043,209 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : "Matches to WormBase T. muris proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "T. muris proteins",
+ "type" : "FeatureTrack",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/T. muris proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ }
},
- "type" : "FeatureTrack"
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "height" : 4,
+ "showLabels" : false,
+ "color1" : "orange"
+ },
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "T_muris_proteins-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
- "name" : "Genetic limits",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Genetic limits/{refseq}/trackData.jsonz"
- }
- },
- "type" : "FeatureTrack",
- "description" : "This track shows the maximal extents for genetic loci. Loci that have been interpolated onto the physical map (and whose precise location is unknown) are shown as a thin black span. The physical extent of such loci are determined by interpolating their genetic position onto the physical map using 95% confidence limits. Please note that the actual location of such loci may lay outside of the span depicted. Loci with known sequence connections are shown in turquoise and depicted using the physical span of the gene.",
- "trackId" : "c_elegans_PRJNA13758_genetic_limits",
"category" : [
"Genes",
"Curated Genes"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "displays" : [
- {
- "displayId" : "genetic_limits-c_elegans_PRJNA13758-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
+ "description" : "This track shows the maximal extents for genetic loci. Loci that have been interpolated onto the physical map (and whose precise location is unknown) are shown as a thin black span. The physical extent of such loci are determined by interpolating their genetic position onto the physical map using 95% confidence limits. Please note that the actual location of such loci may lay outside of the span depicted. Loci with known sequence connections are shown in turquoise and depicted using the physical span of the gene.",
+ "name" : "Genetic limits",
+ "trackId" : "c_elegans_PRJNA13758_genetic_limits",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
+ "displays" : [
+ {
+ "displayId" : "genetic_limits-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
+ "height" : 2,
"color1" : "jexl:get(feature,'source')=='interpolated_pmap_position'?'red':'turquoise'",
- "type" : "SvgFeatureRenderer",
- "height" : 2
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Genetic limits/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
}
},
{
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/RNASeq/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
+ "displayId" : "rnaseq-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
+ "displayMode" : "collapse",
"color1" : "black",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
"height" : "jexl:get(feature,'score')>100?50:floor(get(feature,'score')/2)>4?floor(get(feature,'score')/2):4",
- "displayMode" : "collapse",
- "showDescriptions" : false
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
},
"mouseover" : "jexl:'Score: '+get(feature,'score')",
- "type" : "LinearBasicDisplay",
- "displayId" : "rnaseq-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
+ "name" : "RNASeq",
"trackId" : "c_elegans_PRJNA13758_rnaseq",
- "category" : [
- "Expression"
- ],
+ "description" : "These boxes indicate alignments of short read sequences from all available RNASeq projects. The number of reads has been normalised by averaging over the number of libraries. The height of all boxes indicates the relative score of the feature.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : "These boxes indicate alignments of short read sequences from all available RNASeq projects. The number of reads has been normalised by averaging over the number of libraries. The height of all boxes indicates the relative score of the feature.",
- "name" : "RNASeq",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/RNASeq/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack"
+ "category" : [
+ "Expression"
+ ]
},
{
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/PCR Assays/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
+ "category" : [
+ "Reagents"
+ ],
"type" : "FeatureTrack",
- "name" : "PCR Assays",
- "description" : "This track indicates the location of primer pairs that have been created by a number of groups. Click on the element to obtain the left and right oligo sequences, information about the amplification information, and ordering information (if available).",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "category" : [
- "Reagents"
- ],
+ "description" : "This track indicates the location of primer pairs that have been created by a number of groups. Click on the element to obtain the left and right oligo sequences, information about the amplification information, and ordering information (if available).",
+ "name" : "PCR Assays",
"trackId" : "c_elegans_PRJNA13758_pcr_assays",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
"displays" : [
{
"displayId" : "pcr_assays-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
"height" : 4,
- "type" : "SvgFeatureRenderer",
- "color1" : "violet"
+ "color1" : "violet",
+ "type" : "SvgFeatureRenderer"
},
"type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/PCR Assays/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
"trackId" : "c_elegans_PRJNA13758_rnaseq_asymmetries",
- "category" : [
- "Expression"
- ],
+ "name" : "RNASeq Asymmetries",
+ "description" : "Red boxes indicate regions where there are more than 2 times as many forward sense RNASeq reads aligned to the genome as reverse sense reads. This asymmetrical signal has been found empirically to be a sensitive marker for the ends of transcripts. Green boxes indicate regions where there are more than 2 times as many reverse sense RNASeq reads aligned to the genome as forward sense reads. This asymmetrical signal has been found empirically to be sensitive marker for the ends of transcripts. The height of all boxes indicates the relative score of the feature.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Expression"
+ ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/RNASeq Asymmetries/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"mouseover" : "jexl:'Score: '+get(feature,'score')",
"renderer" : {
- "showLabels" : false,
+ "displayMode" : "collapse",
"type" : "SvgFeatureRenderer",
"color1" : "jexl:get(feature,'source')=='RNASeq_R_asymmetry'?'red': get(feature,'source')=='RNASeq_F_asymmetry'?'green':'black'",
- "displayMode" : "collapse",
- "height" : 24
+ "height" : 24,
+ "showLabels" : false
},
- "type" : "LinearBasicDisplay",
"displayId" : "rnaseq_asymmetries-c_elegans_PRJNA13758-LinearBasicDisplay"
}
- ],
- "name" : "RNASeq Asymmetries",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/RNASeq Asymmetries/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "description" : "Red boxes indicate regions where there are more than 2 times as many forward sense RNASeq reads aligned to the genome as reverse sense reads. This asymmetrical signal has been found empirically to be a sensitive marker for the ends of transcripts. Green boxes indicate regions where there are more than 2 times as many reverse sense RNASeq reads aligned to the genome as forward sense reads. This asymmetrical signal has been found empirically to be sensitive marker for the ends of transcripts. The height of all boxes indicates the relative score of the feature."
+ ]
},
{
- "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "D. melanogaster proteins",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
+ }
},
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "D_melanogaster_proteins-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
- "color1" : "orange",
+ "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "height" : 4,
+ "color1" : "orange"
},
- "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "D_melanogaster_proteins-c_elegans_PRJNA13758-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
+ "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"trackId" : "c_elegans_PRJNA13758_D_melanogaster_proteins",
+ "name" : "D. melanogaster proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
+ ],
+ "type" : "FeatureTrack"
},
{
- "name" : "Polysomes",
- "type" : "FeatureTrack",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "polysomes-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "green"
+ }
+ }
+ ],
"adapter" : {
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Polysomes/{refseq}/trackData.jsonz",
@@ -10851,21 +10253,43 @@
},
"type" : "NCListAdapter"
},
- "description" : "This data is from the The Lamm et al. (2011) PMID: 21177965 paper finding regions bound by the polysome fraction of RNAs being actively translated.",
- "trackId" : "c_elegans_PRJNA13758_polysomes",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Expression"
+ ],
+ "trackId" : "c_elegans_PRJNA13758_polysomes",
+ "name" : "Polysomes",
+ "description" : "This data is from the The Lamm et al. (2011) PMID: 21177965 paper finding regions bound by the polysome fraction of RNAs being actively translated."
+ },
+ {
+ "description" : "This track indicates the location of PCR products that have been placed on expression chips produced by the C. elegans Microarray Consortium [ http://cmgm.stanford.edu/~kimlab/wmdirectorybig.html]. The genes corresponding to these products have been clustered by their expression patterns. Click on the profile to get more information about the expression profile of its corresponding gene.",
+ "name" : "Expression chip profiles",
+ "trackId" : "c_elegans_PRJNA13758_expression_chip_profiles",
"category" : [
"Expression"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Expression chip profiles/{refseq}/trackData.jsonz"
+ }
+ },
"displays" : [
{
- "displayId" : "polysomes-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "color1" : "green"
+ "color1" : "orange",
+ "height" : 5
},
+ "displayId" : "expression_chip_profiles-c_elegans_PRJNA13758-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
@@ -10874,41 +10298,20 @@
}
},
{
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
"displays" : [
{
+ "displayId" : "wormbase_nematode_mrnas/ests_(best)-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
- "height" : 5,
- "color1" : "orange",
- "type" : "SvgFeatureRenderer"
+ "type" : "SvgFeatureRenderer",
+ "height" : 4,
+ "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA_BEST'?'lightblue':get(feature,'source')=='BLAT_Caen_EST_BEST'?'green':'black'",
+ "labels" : {
+ "name" : "jexl:get(feature,'species') || get(feature,'id')"
+ }
},
- "type" : "LinearBasicDisplay",
- "displayId" : "expression_chip_profiles-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "Expression"
- ],
- "trackId" : "c_elegans_PRJNA13758_expression_chip_profiles",
- "description" : "This track indicates the location of PCR products that have been placed on expression chips produced by the C. elegans Microarray Consortium [ http://cmgm.stanford.edu/~kimlab/wmdirectorybig.html]. The genes corresponding to these products have been clustered by their expression patterns. Click on the profile to get more information about the expression profile of its corresponding gene.",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Expression chip profiles/{refseq}/trackData.jsonz"
- }
- },
- "type" : "FeatureTrack",
- "name" : "Expression chip profiles"
- },
- {
- "description" : "ESTs and mRNAs from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each cDNA sequence. mRNAs are shown in light blue; ESTs in green.",
- "name" : "WormBase nematode mRNAs/ESTs (best)",
"adapter" : {
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/WormBase nematode mRNAs_ESTs (best)/{refseq}/trackData.jsonz",
@@ -10916,144 +10319,135 @@
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "displays" : [
- {
- "renderer" : {
- "labels" : {
- "name" : "jexl:get(feature,'species') || get(feature,'id')"
- },
- "type" : "SvgFeatureRenderer",
- "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA_BEST'?'lightblue':get(feature,'source')=='BLAT_Caen_EST_BEST'?'green':'black'",
- "height" : 4
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "wormbase_nematode_mrnas/ests_(best)-c_elegans_PRJNA13758-LinearBasicDisplay"
- }
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
- "trackId" : "wormbase_nematode_mrnas/ests_(best)-c_elegans_PRJNA13758",
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Nucleotide"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ]
+ "trackId" : "wormbase_nematode_mrnas/ests_(best)-c_elegans_PRJNA13758",
+ "name" : "WormBase nematode mRNAs/ESTs (best)",
+ "description" : "ESTs and mRNAs from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each cDNA sequence. mRNAs are shown in light blue; ESTs in green."
},
{
- "displays" : [
- {
- "displayId" : "+1_strand-c_elegans_PRJNA13758-LinearWiggleDisplay",
- "maxScore" : 10,
- "type" : "LinearWiggleDisplay",
- "minScore" : -10
- }
- ],
- "category" : [
- "Externally Sourced Resources",
- "Broad Smoothed PhyloCSF"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_+1_strand",
- "description" : "Smoothed PhyloCSF analysis of 26 worm species from their trackhub at https://data.broadinstitute.org/compbio1/PhyloCSFtracks/trackHub/ce11/trackDb.txt. For more information about PhyloCSF, see the documentation at https://github.com/mlin/PhyloCSF/wiki",
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF+1.bw",
"locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ }
},
- "name" : "+1 strand"
- },
- {
"displays" : [
{
- "displayId" : "+2_strand-c_elegans_PRJNA13758-LinearWiggleDisplay",
- "minScore" : -10,
"type" : "LinearWiggleDisplay",
- "maxScore" : 10
+ "maxScore" : 10,
+ "minScore" : -10,
+ "displayId" : "+1_strand-c_elegans_PRJNA13758-LinearWiggleDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_+2_strand",
+ "name" : "+1 strand",
+ "trackId" : "c_elegans_PRJNA13758_+1_strand",
+ "description" : "Smoothed PhyloCSF analysis of 26 worm species from their trackhub at https://data.broadinstitute.org/compbio1/PhyloCSFtracks/trackHub/ce11/trackDb.txt. For more information about PhyloCSF, see the documentation at https://github.com/mlin/PhyloCSF/wiki",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"Externally Sourced Resources",
"Broad Smoothed PhyloCSF"
- ],
+ ]
+ },
+ {
"description" : "Smoothed PhyloCSF analysis of 26 worm species from their trackhub at https://data.broadinstitute.org/compbio1/PhyloCSFtracks/trackHub/ce11/trackDb.txt. For more information about PhyloCSF, see the documentation at https://github.com/mlin/PhyloCSF/wiki",
"name" : "+2 strand",
+ "trackId" : "c_elegans_PRJNA13758_+2_strand",
+ "category" : [
+ "Externally Sourced Resources",
+ "Broad Smoothed PhyloCSF"
+ ],
"type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF+2.bw"
},
"type" : "BigWigAdapter"
- }
+ },
+ "displays" : [
+ {
+ "maxScore" : 10,
+ "displayId" : "+2_strand-c_elegans_PRJNA13758-LinearWiggleDisplay",
+ "minScore" : -10,
+ "type" : "LinearWiggleDisplay"
+ }
+ ]
},
{
"displays" : [
{
- "displayId" : "+3_strand-c_elegans_PRJNA13758-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay",
"maxScore" : 10,
- "minScore" : -10
+ "minScore" : -10,
+ "displayId" : "+3_strand-c_elegans_PRJNA13758-LinearWiggleDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF+3.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"category" : [
"Externally Sourced Resources",
"Broad Smoothed PhyloCSF"
],
- "trackId" : "c_elegans_PRJNA13758_+3_strand",
- "description" : "Smoothed PhyloCSF analysis of 26 worm species from their trackhub at https://data.broadinstitute.org/compbio1/PhyloCSFtracks/trackHub/ce11/trackDb.txt. For more information about PhyloCSF, see the documentation at https://github.com/mlin/PhyloCSF/wiki",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF+3.bw"
- }
- },
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
+ "description" : "Smoothed PhyloCSF analysis of 26 worm species from their trackhub at https://data.broadinstitute.org/compbio1/PhyloCSFtracks/trackHub/ce11/trackDb.txt. For more information about PhyloCSF, see the documentation at https://github.com/mlin/PhyloCSF/wiki",
+ "trackId" : "c_elegans_PRJNA13758_+3_strand",
"name" : "+3 strand"
},
{
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF-1.bw"
+ "uri" : "https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF-1.bw",
+ "locationType" : "UriLocation"
}
},
+ "displays" : [
+ {
+ "maxScore" : 10,
+ "minScore" : -10,
+ "displayId" : "-1_strand-c_elegans_PRJNA13758-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
+ "trackId" : "c_elegans_PRJNA13758_-1_strand",
"name" : "-1 strand",
"description" : "Smoothed PhyloCSF analysis of 26 worm species from their trackhub at https://data.broadinstitute.org/compbio1/PhyloCSFtracks/trackHub/ce11/trackDb.txt. For more information about PhyloCSF, see the documentation at https://github.com/mlin/PhyloCSF/wiki",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"Externally Sourced Resources",
"Broad Smoothed PhyloCSF"
- ],
- "trackId" : "c_elegans_PRJNA13758_-1_strand",
- "displays" : [
- {
- "type" : "LinearWiggleDisplay",
- "maxScore" : 10,
- "minScore" : -10,
- "displayId" : "-1_strand-c_elegans_PRJNA13758-LinearWiggleDisplay"
- }
]
},
{
+ "name" : "-2 strand",
"trackId" : "c_elegans_PRJNA13758_-2_strand",
+ "description" : "Smoothed PhyloCSF analysis of 26 worm species from their trackhub at https://data.broadinstitute.org/compbio1/PhyloCSFtracks/trackHub/ce11/trackDb.txt. For more information about PhyloCSF, see the documentation at https://github.com/mlin/PhyloCSF/wiki",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -11061,56 +10455,69 @@
"Externally Sourced Resources",
"Broad Smoothed PhyloCSF"
],
- "displays" : [
- {
- "displayId" : "-2_strand-c_elegans_PRJNA13758-LinearWiggleDisplay",
- "minScore" : -10,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 10
- }
- ],
- "name" : "-2 strand",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF-2.bw"
- }
+ },
+ "type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "description" : "Smoothed PhyloCSF analysis of 26 worm species from their trackhub at https://data.broadinstitute.org/compbio1/PhyloCSFtracks/trackHub/ce11/trackDb.txt. For more information about PhyloCSF, see the documentation at https://github.com/mlin/PhyloCSF/wiki"
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 10,
+ "displayId" : "-2_strand-c_elegans_PRJNA13758-LinearWiggleDisplay",
+ "minScore" : -10
+ }
+ ]
},
{
+ "category" : [
+ "Externally Sourced Resources",
+ "Broad Smoothed PhyloCSF"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "description" : "Smoothed PhyloCSF analysis of 26 worm species from their trackhub at https://data.broadinstitute.org/compbio1/PhyloCSFtracks/trackHub/ce11/trackDb.txt. For more information about PhyloCSF, see the documentation at https://github.com/mlin/PhyloCSF/wiki",
+ "trackId" : "c_elegans_PRJNA13758_-3_strand",
+ "name" : "-3 strand",
"displays" : [
{
+ "displayId" : "-3_strand-c_elegans_PRJNA13758-LinearWiggleDisplay",
"minScore" : -10,
"maxScore" : 10,
- "type" : "LinearWiggleDisplay",
- "displayId" : "-3_strand-c_elegans_PRJNA13758-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_-3_strand",
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF-3.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ }
+ },
+ {
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "MultiQuantitativeTrack",
"category" : [
"Externally Sourced Resources",
"Broad Smoothed PhyloCSF"
],
+ "trackId" : "multiwiggle_phylo",
+ "name" : "PhyloCSF (Broad)",
"description" : "Smoothed PhyloCSF analysis of 26 worm species from their trackhub at https://data.broadinstitute.org/compbio1/PhyloCSFtracks/trackHub/ce11/trackDb.txt. For more information about PhyloCSF, see the documentation at https://github.com/mlin/PhyloCSF/wiki",
- "name" : "-3 strand",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF-3.bw"
+ "displays" : [
+ {
+ "displayId" : "multiwiggle_phylo-MultiLinearWiggleDisplay",
+ "type" : "MultiLinearWiggleDisplay"
}
- }
- },
- {
+ ],
"adapter" : {
- "type" : "MultiWiggleAdapter",
"bigWigs" : [
"https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF+1.bw",
"https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF+2.bw",
@@ -11118,27 +10525,24 @@
"https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF-1.bw",
"https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF-2.bw",
"https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF-3.bw"
- ]
- },
- "type" : "MultiQuantitativeTrack",
- "name" : "PhyloCSF (Broad)",
- "description" : "Smoothed PhyloCSF analysis of 26 worm species from their trackhub at https://data.broadinstitute.org/compbio1/PhyloCSFtracks/trackHub/ce11/trackDb.txt. For more information about PhyloCSF, see the documentation at https://github.com/mlin/PhyloCSF/wiki",
- "category" : [
- "Externally Sourced Resources",
- "Broad Smoothed PhyloCSF"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "multiwiggle_phylo",
+ ],
+ "type" : "MultiWiggleAdapter"
+ }
+ },
+ {
"displays" : [
{
- "type" : "MultiLinearWiggleDisplay",
- "displayId" : "multiwiggle_phylo-MultiLinearWiggleDisplay"
+ "type" : "LinearVariantDisplay",
+ "displayId" : "cendr_variation-c_elegans_PRJNA13758-LinearVariantDisplay",
+ "renderer" : {
+ "color1" : "jexl:variantColor(feature)",
+ "type" : "SvgFeatureRenderer"
+ }
}
- ]
- },
- {
+ ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"adapter" : {
"index" : {
"location" : {
@@ -11146,278 +10550,260 @@
"locationType" : "UriLocation"
}
},
- "type" : "VcfTabixAdapter",
"vcfGzLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://storage.googleapis.com/elegansvariation.org/releases/current/WI.current.soft-filtered.vcf.gz"
- }
+ "uri" : "https://storage.googleapis.com/elegansvariation.org/releases/current/WI.current.soft-filtered.vcf.gz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "VcfTabixAdapter"
},
- "type" : "VariantTrack",
- "name" : "CeNDR variation",
- "description" : "Strain variant data from https://www.elegansvariation.org/. For more information see Cook DE, Zdraljevic S, Roberts JP, Andersen EC. CeNDR, the Caenorhabditis elegans natural diversity resource. Nucleic Acids Res. 2017 Jan 4;45(D1):D650-D657. doi: 10.1093/nar/gkw893. Epub 2016 Oct 3. PubMed PMID: 27701074; PubMed Central PMCID: PMC5210618. Colors follow the same scheme as ENSEMBL for predicted variants (https://uswest.ensembl.org/info/genome/variation/prediction/predicted_data.html), and variants with no predicted impact are black and variants that don't have recognized predicted consequence are peachpuff (a pale pink-orange). Variants with more than one predicted consequences are colored by the first annotation.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "VariantTrack",
"category" : [
"Externally Sourced Resources",
"Other"
],
"trackId" : "c_elegans_PRJNA13758_cendr_variation",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
- "displays" : [
- {
- "displayId" : "cendr_variation-c_elegans_PRJNA13758-LinearVariantDisplay",
- "type" : "LinearVariantDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "jexl:variantColor(feature)"
- }
- }
- ]
+ "name" : "CeNDR variation",
+ "description" : "Strain variant data from https://www.elegansvariation.org/. For more information see Cook DE, Zdraljevic S, Roberts JP, Andersen EC. CeNDR, the Caenorhabditis elegans natural diversity resource. Nucleic Acids Res. 2017 Jan 4;45(D1):D650-D657. doi: 10.1093/nar/gkw893. Epub 2016 Oct 3. PubMed PMID: 27701074; PubMed Central PMCID: PMC5210618. Colors follow the same scheme as ENSEMBL for predicted variants (https://uswest.ensembl.org/info/genome/variation/prediction/predicted_data.html), and variants with no predicted impact are black and variants that don't have recognized predicted consequence are peachpuff (a pale pink-orange). Variants with more than one predicted consequences are colored by the first annotation."
},
{
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/jbrowse/data/c_elegans/tracks/CRISPR_Cas9 sgRNA predictions/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/jbrowse/data/c_elegans/tracks/CRISPR_Cas9 sgRNA predictions/{refseq}/trackData.jsonz"
}
},
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "crispr_cas9_sgrna_predictions-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "renderer" : {
+ "showDescriptions" : false,
+ "height" : 4,
+ "showLabels" : false,
+ "color1" : "gold",
+ "type" : "SvgFeatureRenderer"
+ }
+ }
+ ],
+ "trackId" : "c_elegans_PRJNA13758-crispr_cas9_sgrna_predictions",
"name" : "CRISPR_Cas9 sgRNA predictions",
"description" : "sgRNA predictions from http://genome.sfu.ca/crispr/. Used by permission.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
+ ]
+ },
+ {
+ "category" : [
+ "Alleles, Variations, RNAi"
],
- "trackId" : "c_elegans_PRJNA13758-crispr_cas9_sgrna_predictions",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "These regions represent concentrated extremely high genetic variation areas that punctuate the autosomes in a non-random distribution. Individual regions correspond to non-overlapping hyper-divergent genomic regions that were identified in at least one isotype when compared to the reference N2 isotype. For more information about this data, see WBPaper00061244.",
+ "name" : "Hyper-divergent regions",
+ "trackId" : "c_elegans_PRJNA13758_hyper-divergent_regions",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"displays" : [
{
- "displayId" : "crispr_cas9_sgrna_predictions-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "gold",
- "showDescriptions" : false,
- "height" : 4
+ "height" : 6,
+ "color1" : "green",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "hyper-divergent_regions-c_elegans_PRJNA13758-LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/jbrowse/data/c_elegans/tracks/Hyper-divergent regions/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
- "description" : "These regions represent concentrated extremely high genetic variation areas that punctuate the autosomes in a non-random distribution. Individual regions correspond to non-overlapping hyper-divergent genomic regions that were identified in at least one isotype when compared to the reference N2 isotype. For more information about this data, see WBPaper00061244.",
- "name" : "Hyper-divergent regions",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/jbrowse/data/c_elegans/tracks/Hyper-divergent regions/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/jbrowse/data/c_elegans/tracks/Hyper-divergent clusters/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "hyper-divergent_clusters-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "green",
- "height" : 6
- },
- "displayId" : "hyper-divergent_regions-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "height" : 6,
+ "color1" : "blue",
+ "type" : "SvgFeatureRenderer"
+ }
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "trackId" : "c_elegans_PRJNA13758_hyper-divergent_regions",
+ "description" : "These represent the smaller regions of clustered genetic variation observed in individual isotypes/strains. WormBase has compressed these clusters to be unique spans shared by multiple isotypes/strains and the individual strains are linked in the feature frame available by clicking on each track feature.",
+ "trackId" : "c_elegans_PRJNA13758_hyper-divergent_clusters",
+ "name" : "Hyper-divergent clusters",
"category" : [
"Alleles, Variations, RNAi"
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
+ ],
+ "type" : "FeatureTrack"
},
{
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/jbrowse/data/c_elegans/tracks/Hyper-divergent clusters/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "name" : "Hyper-divergent clusters",
- "description" : "These represent the smaller regions of clustered genetic variation observed in individual isotypes/strains. WormBase has compressed these clusters to be unique spans shared by multiple isotypes/strains and the individual strains are linked in the feature frame available by clicking on each track feature.",
- "category" : [
- "Alleles, Variations, RNAi"
- ],
+ "name" : "Chromatin fractions extracted with NaCl, 80mM fraction",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Nucleosome Structure_Chromatin fractions extracted with NaCl_ 80mM fraction",
+ "description" : " Adult_Mononucleosomes. Staged C. elegans adults were prepared from a worm strain engineered to express biotin-tagged histone H3.3 (note that the transgene was not induced during this particular experiment). Chromatin isolated from these animals was digested with micrococcal nuclease and extracted with 80 mM NaCl, followed by gel electrophoresis. The gel-purified fraction was used in two-color hybridization experiments with NimbleGen genomic tiling microarrays. The hybridization signal from this fraction was compared to the signal from the input DNA. Scaled log2(ratios) are shown.
For more information, see modENCODE's track detail page",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_hyper-divergent_clusters",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Nucleosome Structure"
+ ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/henikoff/4416_SOH18_80g_WS220.mean.bw",
+ "locationType" : "UriLocation"
+ }
},
"displays" : [
{
- "renderer" : {
- "height" : 6,
- "color1" : "blue",
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "hyper-divergent_clusters-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "displayId" : "Chromatin fractions extracted with NaCl_ 80mM fraction_Chromatin Structure_Nucleosome Structure-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
]
},
{
- "description" : " Adult_Mononucleosomes. Staged C. elegans adults were prepared from a worm strain engineered to express biotin-tagged histone H3.3 (note that the transgene was not induced during this particular experiment). Chromatin isolated from these animals was digested with micrococcal nuclease and extracted with 80 mM NaCl, followed by gel electrophoresis. The gel-purified fraction was used in two-color hybridization experiments with NimbleGen genomic tiling microarrays. The hybridization signal from this fraction was compared to the signal from the input DNA. Scaled log2(ratios) are shown.
For more information, see modENCODE's track detail page",
- "name" : "Chromatin fractions extracted with NaCl, 80mM fraction",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/henikoff/4416_SOH18_80g_WS220.mean.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/henikoff/4417_SOH20_p6_WS220.mean.bw",
"locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ }
},
- "type" : "QuantitativeTrack",
"displays" : [
{
- "displayId" : "Chromatin fractions extracted with NaCl_ 80mM fraction_Chromatin Structure_Nucleosome Structure-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay",
+ "displayId" : "Chromatin fractions extracted with NaCl_ 600mM fraction_Chromatin Structure_Nucleosome Structure-LinearWiggleDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Nucleosome Structure_Chromatin fractions extracted with NaCl_ 80mM fraction",
+ "description" : " Adult_Mononucleosomes. Staged C. elegans adults were prepared from a worm strain engineered to express biotin-tagged histone H3.3 (note that the transgene was not induced during this particular experiment). Chromatin isolated from these animals was digested with micrococcal nuclease and extracted with 80 mM NaCl, followed by gel electrophoresis. The gel-purified fraction was used in two-color hybridization experiments with NimbleGen genomic tiling microarrays. The hybridization signal from this fraction was compared to the signal from the input DNA. Scaled log2(ratios) are shown.
For more information, see modENCODE's track detail page",
+ "name" : "Chromatin fractions extracted with NaCl, 600mM fraction",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Nucleosome Structure_Chromatin fractions extracted with NaCl_ 600mM fraction",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Nucleosome Structure"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
]
},
{
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/henikoff/4418_SOH44_p6p_WS220.mean.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
"type" : "LinearWiggleDisplay",
- "displayId" : "Chromatin fractions extracted with NaCl_ 600mM fraction_Chromatin Structure_Nucleosome Structure-LinearWiggleDisplay"
+ "displayId" : "Chromatin fractions extracted with NaCl_ 600mM Pellet_Chromatin Structure_Nucleosome Structure-LinearWiggleDisplay"
}
],
+ "description" : " Adult_Mononucleosomes. Staged C. elegans adults were prepared from a worm strain engineered to express biotin-tagged histone H3.3 (note that the transgene was not induced during this particular experiment). Chromatin isolated from these animals was digested with micrococcal nuclease and extracted with 80 mM NaCl, followed by gel electrophoresis. The gel-purified fraction was used in two-color hybridization experiments with NimbleGen genomic tiling microarrays. The hybridization signal from this fraction was compared to the signal from the input DNA. Scaled log2(ratios) are shown.
For more information, see modENCODE's track detail page",
+ "name" : "Chromatin fractions extracted with NaCl, 600mM Pellet",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Nucleosome Structure_Chromatin fractions extracted with NaCl_ 600mM Pellet",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Nucleosome Structure"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Nucleosome Structure_Chromatin fractions extracted with NaCl_ 600mM fraction",
- "description" : " Adult_Mononucleosomes. Staged C. elegans adults were prepared from a worm strain engineered to express biotin-tagged histone H3.3 (note that the transgene was not induced during this particular experiment). Chromatin isolated from these animals was digested with micrococcal nuclease and extracted with 80 mM NaCl, followed by gel electrophoresis. The gel-purified fraction was used in two-color hybridization experiments with NimbleGen genomic tiling microarrays. The hybridization signal from this fraction was compared to the signal from the input DNA. Scaled log2(ratios) are shown.
For more information, see modENCODE's track detail page",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/henikoff/4417_SOH20_p6_WS220.mean.bw"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "Chromatin fractions extracted with NaCl, 600mM fraction"
+ ]
},
{
- "name" : "Chromatin fractions extracted with NaCl, 600mM Pellet",
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "displayId" : "Mononucleosomes 80mM NaCl_ Embryo Mononucleosomes_Chromatin Structure_Nucleosome Structure-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/henikoff/4418_SOH44_p6p_WS220.mean.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/henikoff/13401.bw",
"locationType" : "UriLocation"
}
},
- "description" : " Adult_Mononucleosomes. Staged C. elegans adults were prepared from a worm strain engineered to express biotin-tagged histone H3.3 (note that the transgene was not induced during this particular experiment). Chromatin isolated from these animals was digested with micrococcal nuclease and extracted with 80 mM NaCl, followed by gel electrophoresis. The gel-purified fraction was used in two-color hybridization experiments with NimbleGen genomic tiling microarrays. The hybridization signal from this fraction was compared to the signal from the input DNA. Scaled log2(ratios) are shown.
For more information, see modENCODE's track detail page",
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Nucleosome Structure_Chromatin fractions extracted with NaCl_ 600mM Pellet",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Nucleosome Structure"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "displays" : [
- {
- "displayId" : "Chromatin fractions extracted with NaCl_ 600mM Pellet_Chromatin Structure_Nucleosome Structure-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay"
- }
- ]
+ "description" : " Adult_Mononucleosomes. Staged C. elegans adults were prepared from a worm strain engineered to express biotin-tagged histone H3.3 (note that the transgene was not induced during this particular experiment). Chromatin isolated from these animals was digested with micrococcal nuclease and extracted with 80 mM NaCl, followed by gel electrophoresis. The gel-purified fraction was used in two-color hybridization experiments with NimbleGen genomic tiling microarrays. The hybridization signal from this fraction was compared to the signal from the input DNA. Scaled log2(ratios) are shown.
For more information, see modENCODE's track detail page",
+ "name" : "Mononucleosomes 80mM NaCl, Embryo Mononucleosomes",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Nucleosome Structure_Mononucleosomes 80mM NaCl_ Embryo Mononucleosomes"
},
{
"displays" : [
{
"type" : "LinearWiggleDisplay",
- "displayId" : "Mononucleosomes 80mM NaCl_ Embryo Mononucleosomes_Chromatin Structure_Nucleosome Structure-LinearWiggleDisplay"
+ "displayId" : "H3.3 Chromatin fractions extracted with NaCl_ 350mM fraction_Chromatin Structure_Nucleosome Structure-LinearWiggleDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Nucleosome Structure_Mononucleosomes 80mM NaCl_ Embryo Mononucleosomes",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Nucleosome Structure"
- ],
- "description" : " Adult_Mononucleosomes. Staged C. elegans adults were prepared from a worm strain engineered to express biotin-tagged histone H3.3 (note that the transgene was not induced during this particular experiment). Chromatin isolated from these animals was digested with micrococcal nuclease and extracted with 80 mM NaCl, followed by gel electrophoresis. The gel-purified fraction was used in two-color hybridization experiments with NimbleGen genomic tiling microarrays. The hybridization signal from this fraction was compared to the signal from the input DNA. Scaled log2(ratios) are shown.
For more information, see modENCODE's track detail page",
- "name" : "Mononucleosomes 80mM NaCl, Embryo Mononucleosomes",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/henikoff/13401.bw"
- }
- }
- },
- {
- "description" : " Adult_Mononucleosomes. Staged C. elegans adults were prepared from a worm strain engineered to express biotin-tagged histone H3.3 (note that the transgene was not induced during this particular experiment). Chromatin isolated from these animals was digested with micrococcal nuclease and extracted with 80 mM NaCl, followed by gel electrophoresis. The gel-purified fraction was used in two-color hybridization experiments with NimbleGen genomic tiling microarrays. The hybridization signal from this fraction was compared to the signal from the input DNA. Scaled log2(ratios) are shown.
For more information, see modENCODE's track detail page",
- "name" : "H3.3 Chromatin fractions extracted with NaCl, 350mM fraction",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/henikoff/4427_SOH_WS220.mean.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/henikoff/4427_SOH_WS220.mean.bw",
+ "locationType" : "UriLocation"
}
},
"type" : "QuantitativeTrack",
- "displays" : [
- {
- "type" : "LinearWiggleDisplay",
- "displayId" : "H3.3 Chromatin fractions extracted with NaCl_ 350mM fraction_Chromatin Structure_Nucleosome Structure-LinearWiggleDisplay"
- }
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Nucleosome Structure_H3.3 Chromatin fractions extracted with NaCl_ 350mM fraction",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Nucleosome Structure"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ]
+ "name" : "H3.3 Chromatin fractions extracted with NaCl, 350mM fraction",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Nucleosome Structure_H3.3 Chromatin fractions extracted with NaCl_ 350mM fraction",
+ "description" : " Adult_Mononucleosomes. Staged C. elegans adults were prepared from a worm strain engineered to express biotin-tagged histone H3.3 (note that the transgene was not induced during this particular experiment). Chromatin isolated from these animals was digested with micrococcal nuclease and extracted with 80 mM NaCl, followed by gel electrophoresis. The gel-purified fraction was used in two-color hybridization experiments with NimbleGen genomic tiling microarrays. The hybridization signal from this fraction was compared to the signal from the input DNA. Scaled log2(ratios) are shown.
For more information, see modENCODE's track detail page"
},
{
- "displays" : [
- {
- "displayId" : "H3.3 Chromatin fractions extracted with NaCl_ 600mM fraction_Chromatin Structure_Nucleosome Structure-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay"
- }
- ],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -11426,19 +10812,27 @@
"Chromatin Structure",
"Nucleosome Structure"
],
+ "name" : "H3.3 Chromatin fractions extracted with NaCl, 600mM fraction",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Nucleosome Structure_H3.3 Chromatin fractions extracted with NaCl_ 600mM fraction",
"description" : " Adult_Mononucleosomes. Staged C. elegans adults were prepared from a worm strain engineered to express biotin-tagged histone H3.3 (note that the transgene was not induced during this particular experiment). Chromatin isolated from these animals was digested with micrococcal nuclease and extracted with 80 mM NaCl, followed by gel electrophoresis. The gel-purified fraction was used in two-color hybridization experiments with NimbleGen genomic tiling microarrays. The hybridization signal from this fraction was compared to the signal from the input DNA. Scaled log2(ratios) are shown.
For more information, see modENCODE's track detail page",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "displayId" : "H3.3 Chromatin fractions extracted with NaCl_ 600mM fraction_Chromatin Structure_Nucleosome Structure-LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/henikoff/4428_SOH41_p6PD_WS220.mean.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/henikoff/4428_SOH41_p6PD_WS220.mean.bw"
},
"type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "H3.3 Chromatin fractions extracted with NaCl, 600mM fraction"
+ }
},
{
+ "description" : " Adult_Mononucleosomes. Staged C. elegans adults were prepared from a worm strain engineered to express biotin-tagged histone H3.3 (note that the transgene was not induced during this particular experiment). Chromatin isolated from these animals was digested with micrococcal nuclease and extracted with 80 mM NaCl, followed by gel electrophoresis. The gel-purified fraction was used in two-color hybridization experiments with NimbleGen genomic tiling microarrays. The hybridization signal from this fraction was compared to the signal from the input DNA. Scaled log2(ratios) are shown.
For more information, see modENCODE's track detail page",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Nucleosome Structure_H3.3 Chromatin fractions extracted with NaCl_ 80mM fraction",
+ "name" : "H3.3 Chromatin fractions extracted with NaCl, 80mM fraction",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -11447,57 +10841,51 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Nucleosome Structure_H3.3 Chromatin fractions extracted with NaCl_ 80mM fraction",
- "displays" : [
- {
- "type" : "LinearWiggleDisplay",
- "displayId" : "H3.3 Chromatin fractions extracted with NaCl_ 80mM fraction_Chromatin Structure_Nucleosome Structure-LinearWiggleDisplay"
- }
- ],
"type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/henikoff/4422_SOH25_80PD_WS220.mean.bw",
"locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ }
},
- "name" : "H3.3 Chromatin fractions extracted with NaCl, 80mM fraction",
- "description" : " Adult_Mononucleosomes. Staged C. elegans adults were prepared from a worm strain engineered to express biotin-tagged histone H3.3 (note that the transgene was not induced during this particular experiment). Chromatin isolated from these animals was digested with micrococcal nuclease and extracted with 80 mM NaCl, followed by gel electrophoresis. The gel-purified fraction was used in two-color hybridization experiments with NimbleGen genomic tiling microarrays. The hybridization signal from this fraction was compared to the signal from the input DNA. Scaled log2(ratios) are shown.
For more information, see modENCODE's track detail page"
+ "displays" : [
+ {
+ "displayId" : "H3.3 Chromatin fractions extracted with NaCl_ 80mM fraction_Chromatin Structure_Nucleosome Structure-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
+ }
+ ]
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Early Embryo_ AB1791_H3_377098_N2_EEMB",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "description" : "seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Early Embryo_ AB1791_H3_377098_N2_EEMB",
+ "name" : "Transcription Factors ChIP-Seq Early Embryo, AB1791_H3_377098_N2_EEMB",
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq Early Embryo_ AB1791_H3_377098_N2_EEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay",
"minScore" : 121.159116882231,
- "maxScore" : 274.160960249184,
- "type" : "LinearWiggleDisplay"
+ "displayId" : "Transcription Factors ChIP-Seq Early Embryo_ AB1791_H3_377098_N2_EEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 274.160960249184
}
],
- "name" : "Transcription Factors ChIP-Seq Early Embryo, AB1791_H3_377098_N2_EEMB",
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5031.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "description" : "seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5031.bw"
+ }
+ }
},
{
- "description" : "seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Transcription Factors ChIP-Seq Early Embryo, SDQ3927_MRG1_N2_EEMB",
- "type" : "QuantitativeTrack",
"adapter" : {
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6341.bw",
@@ -11508,61 +10896,70 @@
"displays" : [
{
"maxScore" : 126.307407640492,
- "type" : "LinearWiggleDisplay",
"minScore" : 59.2421445213625,
- "displayId" : "Transcription Factors ChIP-Seq Early Embryo_ SDQ3927_MRG1_N2_EEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "displayId" : "Transcription Factors ChIP-Seq Early Embryo_ SDQ3927_MRG1_N2_EEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Early Embryo_ SDQ3927_MRG1_N2_EEMB",
+ "name" : "Transcription Factors ChIP-Seq Early Embryo, SDQ3927_MRG1_N2_EEMB",
+ "description" : "seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
]
},
{
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6329.bw"
- },
- "type" : "BigWigAdapter"
- },
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Early Embryo_ SDQ3838_T26A5.5_N2_EEMB",
"name" : "Transcription Factors ChIP-Seq Early Embryo, SDQ3838_T26A5.5_N2_EEMB",
"description" : "seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Early Embryo_ SDQ3838_T26A5.5_N2_EEMB",
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6329.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "minScore" : 129.808385861092,
- "maxScore" : 310.887835942702,
"type" : "LinearWiggleDisplay",
- "displayId" : "Transcription Factors ChIP-Seq Early Embryo_ SDQ3838_T26A5.5_N2_EEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "minScore" : 129.808385861092,
+ "displayId" : "Transcription Factors ChIP-Seq Early Embryo_ SDQ3838_T26A5.5_N2_EEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 310.887835942702
}
]
},
{
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "maxScore" : 218.456875013217,
+ "displayId" : "Transcription Factors ChIP-Seq Early Embryo_ AB817_8WG16_639746_N2_EEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 88.1372687543616,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6344.bw",
"locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ }
},
- "name" : "Transcription Factors ChIP-Seq Early Embryo, AB817_8WG16_639746_N2_EEMB",
- "description" : "seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -11571,84 +10968,116 @@
"Transcription Factors",
"Transcription and Chromatin"
],
+ "name" : "Transcription Factors ChIP-Seq Early Embryo, AB817_8WG16_639746_N2_EEMB",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Early Embryo_ AB817_8WG16_639746_N2_EEMB",
- "displays" : [
- {
- "maxScore" : 218.456875013217,
- "type" : "LinearWiggleDisplay",
- "minScore" : 88.1372687543616,
- "displayId" : "Transcription Factors ChIP-Seq Early Embryo_ AB817_8WG16_639746_N2_EEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
- }
- ]
+ "description" : "seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
+ "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ3972_COH3_FEM2_AD",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3972_COH3_FEM2_AD",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Transcription and Chromatin"
+ ],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5230.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3972_COH3_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay",
"maxScore" : 128.000849129602,
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3972_COH3_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
"minScore" : 60.8997802127685
}
+ ]
+ },
+ {
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3972_COH3_FEM2_AD",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ5421_CEC7_FEM2_AD",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ5421_CEC7_FEM2_AD",
"description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ3972_COH3_FEM2_AD",
+ "displays" : [
+ {
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ5421_CEC7_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 54.778495079894,
+ "maxScore" : 116.537257817861,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5230.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6375.bw",
+ "locationType" : "UriLocation"
}
- },
- "type" : "QuantitativeTrack"
+ }
},
{
- "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "maxScore" : 214.226116699694,
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ4068_MRG1_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 92.154718510899,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6375.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5233.bw",
"locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ }
},
"type" : "QuantitativeTrack",
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ5421_CEC7_FEM2_AD",
- "displays" : [
- {
- "minScore" : 54.778495079894,
- "maxScore" : 116.537257817861,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ5421_CEC7_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
- }
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ5421_CEC7_FEM2_AD"
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ4068_MRG1_FEM2_AD",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ4068_MRG1_FEM2_AD",
+ "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5227.bw"
+ }
+ },
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ4068_MRG1_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay",
- "maxScore" : 214.226116699694,
- "minScore" : 92.154718510899
+ "maxScore" : 44.6720327364112,
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3965_ZIM1_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 19.2977708030157
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ4068_MRG1_FEM2_AD",
+ "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3965_ZIM1_FEM2_AD",
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ3965_ZIM1_FEM2_AD",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -11657,221 +11086,271 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ4068_MRG1_FEM2_AD",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5233.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
"type" : "QuantitativeTrack"
},
{
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 175.163889686872,
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ0811_RAD51_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 73.0398835966677
+ }
+ ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_3923.bw"
+ }
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3965_ZIM1_FEM2_AD",
+ "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ0811_RAD51_FEM2_AD",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ0811_RAD51_FEM2_AD"
+ },
+ {
"displays" : [
{
- "minScore" : 19.2977708030157,
"type" : "LinearWiggleDisplay",
- "maxScore" : 44.6720327364112,
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3965_ZIM1_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "maxScore" : 55.4163094823452,
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ G0655G0656_HTP3_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 24.3240821291739
}
],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5227.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6272.bw",
+ "locationType" : "UriLocation"
}
},
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Transcription and Chromatin"
+ ],
"type" : "QuantitativeTrack",
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ3965_ZIM1_FEM2_AD",
- "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Transcription Factors ChIP-Seq DH245, G0655G0656_HTP3_FEM2_AD",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ G0655G0656_HTP3_FEM2_AD"
},
{
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_3923.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5224.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ0811_RAD51_FEM2_AD",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3953_REC8_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 10.2005792202037,
+ "maxScore" : 22.5663006672838
+ }
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3953_REC8_FEM2_AD",
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ3953_REC8_FEM2_AD",
"description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ0811_RAD51_FEM2_AD",
- "displays" : [
- {
- "minScore" : 73.0398835966677,
- "maxScore" : 175.163889686872,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ0811_RAD51_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
- }
]
},
{
- "name" : "Transcription Factors ChIP-Seq DH245, G0655G0656_HTP3_FEM2_AD",
+ "displays" : [
+ {
+ "maxScore" : 72.843508647848,
+ "minScore" : 37.5991578537898,
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3989_ASH2_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6272.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5231.bw"
},
"type" : "BigWigAdapter"
},
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
- "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ G0655G0656_HTP3_FEM2_AD",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3989_ASH2_FEM2_AD",
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ3989_ASH2_FEM2_AD",
+ "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ },
+ {
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Transcription and Chromatin"
+ ],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ3949_ZIM3_FEM2_AD",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3949_ZIM3_FEM2_AD",
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq DH245_ G0655G0656_HTP3_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "minScore" : 24.3240821291739,
- "maxScore" : 55.4163094823452,
+ "maxScore" : 22.5063674464426,
+ "minScore" : 9.73860125732607,
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3949_ZIM3_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay"
}
- ]
- },
- {
+ ],
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5224.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5223.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
+ }
+ },
+ {
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5218.bw",
+ "locationType" : "UriLocation"
+ }
},
- "type" : "QuantitativeTrack",
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ3953_REC8_FEM2_AD",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 26.8193651675032,
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3925_ZHP3_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 11.0747905052761
+ }
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3925_ZHP3_FEM2_AD",
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ3925_ZHP3_FEM2_AD",
"description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3953_REC8_FEM2_AD",
+ ]
+ },
+ {
"displays" : [
{
- "minScore" : 10.2005792202037,
- "maxScore" : 22.5663006672838,
"type" : "LinearWiggleDisplay",
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3953_REC8_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "maxScore" : 250.566041226113,
+ "minScore" : 100.006293604617,
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ0835_SCC1_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
}
- ]
- },
- {
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ3989_ASH2_FEM2_AD",
- "type" : "QuantitativeTrack",
+ ],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5231.bw"
- }
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5188.bw"
+ },
+ "type" : "BigWigAdapter"
},
- "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3989_ASH2_FEM2_AD",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "displays" : [
- {
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3989_ASH2_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "maxScore" : 72.843508647848,
- "type" : "LinearWiggleDisplay",
- "minScore" : 37.5991578537898
- }
- ]
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ0835_SCC1_FEM2_AD",
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ0835_SCC1_FEM2_AD",
+ "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "displays" : [
- {
- "minScore" : 9.73860125732607,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 22.5063674464426,
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3949_ZIM3_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
- }
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3949_ZIM3_FEM2_AD",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ3949_ZIM3_FEM2_AD",
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ4501_T09A5.8_FEM2_AD",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ4501_T09A5.8_FEM2_AD",
+ "displays" : [
+ {
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ4501_T09A5.8_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 68.2110500177959,
+ "maxScore" : 171.515000053927,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5223.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_3917.bw"
}
- },
- "type" : "QuantitativeTrack"
+ }
},
{
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6282.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 118.655565071176,
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ0809_COH1_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 52.5764364734881
+ }
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ0809_COH1_FEM2_AD",
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ0809_COH1_FEM2_AD",
+ "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3925_ZHP3_FEM2_AD",
- "displays" : [
- {
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3925_ZHP3_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 26.8193651675032,
- "minScore" : 11.0747905052761
- }
- ],
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5218.bw",
- "locationType" : "UriLocation"
- }
- },
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ3925_ZHP3_FEM2_AD",
- "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ ]
},
{
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -11880,46 +11359,41 @@
"Transcription Factors",
"Transcription and Chromatin"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ0835_SCC1_FEM2_AD",
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ2356_MRE11_FEM2_AD",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ2356_MRE11_FEM2_AD",
+ "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ0835_SCC1_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "maxScore" : 250.566041226113,
"type" : "LinearWiggleDisplay",
- "minScore" : 100.006293604617
+ "maxScore" : 333.130532802508,
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ2356_MRE11_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 164.571575824828
}
],
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5188.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5190.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ0835_SCC1_FEM2_AD",
- "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
},
{
- "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ4501_T09A5.8_FEM2_AD",
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3942_KLE2_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 15.8879865787278,
+ "maxScore" : 39.679050238569
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_3917.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5220.bw"
}
},
- "displays" : [
- {
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ4501_T09A5.8_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "minScore" : 68.2110500177959,
- "maxScore" : 171.515000053927,
- "type" : "LinearWiggleDisplay"
- }
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ4501_T09A5.8_FEM2_AD",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -11927,48 +11401,42 @@
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
+ ],
+ "type" : "QuantitativeTrack",
+ "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3942_KLE2_FEM2_AD",
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ3942_KLE2_FEM2_AD"
},
{
- "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6282.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5209.bw"
}
},
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ0809_COH1_FEM2_AD",
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ0809_COH1_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "minScore" : 52.5764364734881,
- "maxScore" : 118.655565071176,
+ "minScore" : 42.9222345834279,
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3866_MRE11_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 97.4404078285695,
"type" : "LinearWiggleDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ3866_MRE11_FEM2_AD",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3866_MRE11_FEM2_AD",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ0809_COH1_FEM2_AD"
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ]
},
{
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5190.bw",
- "locationType" : "UriLocation"
- }
- },
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ2356_MRE11_FEM2_AD",
- "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -11977,36 +11445,43 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ2356_MRE11_FEM2_AD",
+ "type" : "QuantitativeTrack",
+ "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3853_MSH5_FEM2_AD",
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ3853_MSH5_FEM2_AD",
"displays" : [
{
- "minScore" : 164.571575824828,
- "maxScore" : 333.130532802508,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ2356_MRE11_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "maxScore" : 18.2786614979324,
+ "minScore" : 8.30995829431769,
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3853_MSH5_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
- ]
- },
- {
- "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ3942_KLE2_FEM2_AD",
- "type" : "QuantitativeTrack",
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5220.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5208.bw",
"locationType" : "UriLocation"
}
- },
+ }
+ },
+ {
"displays" : [
{
- "minScore" : 15.8879865787278,
"type" : "LinearWiggleDisplay",
- "maxScore" : 39.679050238569,
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3942_KLE2_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "maxScore" : 173.433245727594,
+ "minScore" : 69.118771090106,
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ4625_T09A5.8_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3942_KLE2_FEM2_AD",
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6007.bw",
+ "locationType" : "UriLocation"
+ }
+ },
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -12014,85 +11489,73 @@
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
- ]
+ ],
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ4625_T09A5.8_FEM2_AD",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ4625_T09A5.8_FEM2_AD",
+ "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ3866_MRE11_FEM2_AD",
+ "displays" : [
+ {
+ "minScore" : 53.0407024895271,
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ5413_CEC7_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 108.124249968264,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5209.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6374.bw",
"locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
"type" : "QuantitativeTrack",
- "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3866_MRE11_FEM2_AD",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ5413_CEC7_FEM2_AD",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ5413_CEC7_FEM2_AD",
+ "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ },
+ {
"displays" : [
{
- "minScore" : 42.9222345834279,
- "maxScore" : 97.4404078285695,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3866_MRE11_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "minScore" : 5.8047973247735,
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ2382_HIM5_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 13.1033252265863,
+ "type" : "LinearWiggleDisplay"
}
- ]
- },
- {
- "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ3853_MSH5_FEM2_AD",
- "type" : "QuantitativeTrack",
+ ],
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5208.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6301.bw"
},
"type" : "BigWigAdapter"
},
- "displays" : [
- {
- "minScore" : 8.30995829431769,
- "maxScore" : 18.2786614979324,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3853_MSH5_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
- }
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3853_MSH5_FEM2_AD",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
- ]
+ ],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ2382_HIM5_FEM2_AD",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ2382_HIM5_FEM2_AD"
},
{
"description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6007.bw"
- }
- },
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ4625_T09A5.8_FEM2_AD",
- "displays" : [
- {
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ4625_T09A5.8_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "minScore" : 69.118771090106,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 173.433245727594
- }
- ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3915_MSH5_FEM2_AD",
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ3915_MSH5_FEM2_AD",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -12101,114 +11564,111 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ4625_T09A5.8_FEM2_AD"
- },
- {
+ "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6374.bw"
- },
- "type" : "BigWigAdapter"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5216.bw",
+ "locationType" : "UriLocation"
+ }
},
- "type" : "QuantitativeTrack",
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ5413_CEC7_FEM2_AD",
- "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Transcription and Chromatin"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ5413_CEC7_FEM2_AD",
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ5413_CEC7_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "minScore" : 53.0407024895271,
- "maxScore" : 108.124249968264,
+ "maxScore" : 20.7170299660231,
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3915_MSH5_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 9.21511988878761,
"type" : "LinearWiggleDisplay"
}
]
},
{
- "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ2382_HIM5_FEM2_AD",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6301.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
"displays" : [
{
- "minScore" : 5.8047973247735,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 13.1033252265863,
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ2382_HIM5_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3907_CHD3_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 83.3495289894759,
+ "maxScore" : 179.138269665078,
+ "type" : "LinearWiggleDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ2382_HIM5_FEM2_AD",
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5214.bw",
+ "locationType" : "UriLocation"
+ }
+ },
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
- ]
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3907_CHD3_FEM2_AD",
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ3907_CHD3_FEM2_AD",
+ "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "displays" : [
- {
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3915_MSH5_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "minScore" : 9.21511988878761,
- "maxScore" : 20.7170299660231,
- "type" : "LinearWiggleDisplay"
- }
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3915_MSH5_FEM2_AD",
"description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ0821_SCC1_FEM2_AD",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ0821_SCC1_FEM2_AD",
+ "displays" : [
+ {
+ "maxScore" : 240.48185739576,
+ "minScore" : 93.9650129406008,
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ0821_SCC1_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5216.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5187.bw"
}
- },
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ3915_MSH5_FEM2_AD"
+ }
},
{
"description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3898_KLE2_FEM2_AD",
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ3898_KLE2_FEM2_AD",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Transcription and Chromatin"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5214.bw"
- }
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6008.bw"
+ },
+ "type" : "BigWigAdapter"
},
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ3907_CHD3_FEM2_AD",
"displays" : [
{
- "type" : "LinearWiggleDisplay",
- "maxScore" : 179.138269665078,
- "minScore" : 83.3495289894759,
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3907_CHD3_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "minScore" : 69.2123270086241,
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3898_KLE2_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 168.27553638977,
+ "type" : "LinearWiggleDisplay"
}
- ],
+ ]
+ },
+ {
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -12217,104 +11677,74 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3907_CHD3_FEM2_AD"
- },
- {
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ0821_SCC1_FEM2_AD",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Transcription and Chromatin"
- ],
+ "type" : "QuantitativeTrack",
+ "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3914_REC8_FEM2_AD",
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ3914_REC8_FEM2_AD",
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ0821_SCC1_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "minScore" : 93.9650129406008,
- "maxScore" : 240.48185739576,
- "type" : "LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 73.755847620207,
+ "minScore" : 35.5150297146683,
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3914_REC8_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
}
],
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ0821_SCC1_FEM2_AD",
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5187.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6278.bw",
"locationType" : "UriLocation"
}
- },
- "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
},
{
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6008.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ3898_KLE2_FEM2_AD",
- "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3898_KLE2_FEM2_AD",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3849_CHD3_FEM2_AD",
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ3849_CHD3_FEM2_AD",
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3898_KLE2_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "maxScore" : 168.27553638977,
- "type" : "LinearWiggleDisplay",
- "minScore" : 69.2123270086241
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3849_CHD3_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 9.57095055183086,
+ "maxScore" : 23.4601531873662,
+ "type" : "LinearWiggleDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5207.bw"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ3914_REC8_FEM2_AD",
"adapter" : {
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6278.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6276.bw"
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3914_REC8_FEM2_AD",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Transcription and Chromatin"
- ],
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3914_REC8_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "maxScore" : 73.755847620207,
"type" : "LinearWiggleDisplay",
- "minScore" : 35.5150297146683
- }
- ]
- },
- {
- "displays" : [
- {
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3849_CHD3_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "minScore" : 9.57095055183086,
- "maxScore" : 23.4601531873662,
- "type" : "LinearWiggleDisplay"
+ "maxScore" : 22.7189663277975,
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ0802_REC8_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 10.1973588881732
}
],
+ "description" : "seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ0802_REC8_FEM2_AD",
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ0802_REC8_FEM2_AD",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -12323,20 +11753,39 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3849_CHD3_FEM2_AD",
- "description" : " seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
+ "type" : "QuantitativeTrack"
+ },
+ {
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5207.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5222.bw"
}
},
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ3849_CHD3_FEM2_AD"
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 20.8746593548769,
+ "minScore" : 9.27383758710939,
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3948_COH3_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ }
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3948_COH3_FEM2_AD",
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ3948_COH3_FEM2_AD",
+ "description" : "seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Transcription and Chromatin"
+ ]
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ0802_REC8_FEM2_AD",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -12345,201 +11794,150 @@
"Transcription Factors",
"Transcription and Chromatin"
],
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ3956_ZHP3_FEM2_AD",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3956_ZHP3_FEM2_AD",
+ "description" : "seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ0802_REC8_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "maxScore" : 22.7189663277975,
- "type" : "LinearWiggleDisplay",
- "minScore" : 10.1973588881732
+ "minScore" : 14.5869962710566,
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3956_ZHP3_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 33.0363523365351,
+ "type" : "LinearWiggleDisplay"
}
],
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ0802_REC8_FEM2_AD",
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6276.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5225.bw",
"locationType" : "UriLocation"
}
- },
- "description" : "seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ0812_COH1_FEM2_AD",
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ0812_COH1_FEM2_AD",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3948_COH3_FEM2_AD",
- "displays" : [
- {
- "minScore" : 9.27383758710939,
- "maxScore" : 20.8746593548769,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3948_COH3_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
- }
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
"type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5222.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5186.bw"
}
},
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ3948_COH3_FEM2_AD",
- "description" : "seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
"displays" : [
{
- "type" : "LinearWiggleDisplay",
- "maxScore" : 33.0363523365351,
- "minScore" : 14.5869962710566,
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ3956_ZHP3_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ0812_COH1_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 43.6527871499016,
+ "maxScore" : 95.1469307572775,
+ "type" : "LinearWiggleDisplay"
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ3956_ZHP3_FEM2_AD",
- "assemblyNames" : [
+ ]
+ },
+ {
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ1665_1666_MRG1_FEM2_AD",
+ "name" : "Transcription Factors ChIP-Seq DH245, SDQ1665_1666_MRG1_FEM2_AD",
+ "description" : "seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "description" : "seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ3956_ZHP3_FEM2_AD",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5225.bw"
- }
- }
- },
- {
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5186.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5189.bw"
}
},
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ0812_COH1_FEM2_AD",
- "description" : "seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Transcription and Chromatin"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ0812_COH1_FEM2_AD",
"displays" : [
{
- "minScore" : 43.6527871499016,
- "maxScore" : 95.1469307572775,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ0812_COH1_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "maxScore" : 152.357139818035,
+ "minScore" : 65.9491561399517,
+ "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ1665_1666_MRG1_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
]
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq DH245_ SDQ1665_1666_MRG1_FEM2_AD",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Transcription and Chromatin"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq DH245_ SDQ1665_1666_MRG1_FEM2_AD_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "maxScore" : 152.357139818035,
"type" : "LinearWiggleDisplay",
- "minScore" : 65.9491561399517
+ "displayId" : "Histone Modifications (H3K79) ChIP-Seq_ AB2621_H3K79me3:361576_N2_L3 _Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 126.614634891918,
+ "maxScore" : 289.474651187631
}
],
- "name" : "Transcription Factors ChIP-Seq DH245, SDQ1665_1666_MRG1_FEM2_AD",
- "type" : "QuantitativeTrack",
"adapter" : {
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5189.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5032.bw",
"locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
- "description" : "seq-SDQ3898_KLE2_FEM2_AD. Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes kle-2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
- "displays" : [
- {
- "minScore" : 126.614634891918,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 289.474651187631,
- "displayId" : "Histone Modifications (H3K79) ChIP-Seq_ AB2621_H3K79me3:361576_N2_L3 _Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
- }
- ],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K79) ChIP-Seq_ AB2621_H3K79me3:361576_N2_L3 ",
- "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5032.bw"
- },
- "type" : "BigWigAdapter"
- },
- "name" : "Histone Modifications (H3K79) ChIP-Seq, AB2621_H3K79me3:361576_N2_L3 "
+ "name" : "Histone Modifications (H3K79) ChIP-Seq, AB2621_H3K79me3:361576_N2_L3 ",
+ "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
"description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K79) ChIP-Seq_ AB3594_H3K79me2:346021_N2_L3",
+ "name" : "Histone Modifications (H3K79) ChIP-Seq, AB3594_H3K79me2:346021_N2_L3",
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5047.bw"
- }
+ },
+ "type" : "BigWigAdapter"
},
- "name" : "Histone Modifications (H3K79) ChIP-Seq, AB3594_H3K79me2:346021_N2_L3",
"displays" : [
{
- "displayId" : "Histone Modifications (H3K79) ChIP-Seq_ AB3594_H3K79me2:346021_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "maxScore" : 406.01816390256,
"type" : "LinearWiggleDisplay",
- "minScore" : 175.974894087845
+ "maxScore" : 406.01816390256,
+ "minScore" : 175.974894087845,
+ "displayId" : "Histone Modifications (H3K79) ChIP-Seq_ AB3594_H3K79me2:346021_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
}
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K79) ChIP-Seq_ AB3594_H3K79me2:346021_N2_L3"
+ ]
},
{
- "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 102.621538851897,
+ "displayId" : "Histone Modifications (H3K23) ChIP-Seq_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 48.0021078211258
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -12547,64 +11945,67 @@
"locationType" : "UriLocation"
}
},
- "type" : "QuantitativeTrack",
- "name" : "Histone Modifications (H3K23) ChIP-Seq",
- "displays" : [
- {
- "displayId" : "Histone Modifications (H3K23) ChIP-Seq_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "minScore" : 48.0021078211258,
- "maxScore" : 102.621538851897,
- "type" : "LinearWiggleDisplay"
- }
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K23) ChIP-Seq"
- },
- {
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications (H3K23) ChIP-Seq",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K23) ChIP-Seq"
+ },
+ {
+ "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-Seq_ UP07449_H3K27me3:24440_N2_L3",
+ "name" : "Histone Modifications (H3K27) ChIP-Seq, UP07449_H3K27me3:24440_N2_L3",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-Seq_ UP07449_H3K27me3:24440_N2_L3",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5045.bw",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "displayId" : "Histone Modifications (H3K27) ChIP-Seq_ UP07449_H3K27me3:24440_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "maxScore" : 270.838586494113,
"type" : "LinearWiggleDisplay",
+ "maxScore" : 270.838586494113,
+ "displayId" : "Histone Modifications (H3K27) ChIP-Seq_ UP07449_H3K27me3:24440_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"minScore" : 107.366233543057
}
- ],
- "type" : "QuantitativeTrack",
+ ]
+ },
+ {
"adapter" : {
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5045.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5044.bw",
"locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
- "name" : "Histone Modifications (H3K27) ChIP-Seq, UP07449_H3K27me3:24440_N2_L3",
- "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
"displays" : [
{
"minScore" : 90.0227892787728,
- "type" : "LinearWiggleDisplay",
+ "displayId" : "Histone Modifications (H3K27) ChIP-Seq_ UP07448_H3K27me1:24439_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"maxScore" : 210.283300844766,
- "displayId" : "Histone Modifications (H3K27) ChIP-Seq_ UP07448_H3K27me1:24439_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
],
+ "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-Seq_ UP07448_H3K27me1:24439_N2_L3",
+ "name" : "Histone Modifications (H3K27) ChIP-Seq, UP07448_H3K27me1:24439_N2_L3",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -12613,27 +12014,41 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-Seq_ UP07448_H3K27me1:24439_N2_L3",
+ "type" : "QuantitativeTrack"
+ },
+ {
+ "name" : "Histone Modifications (H3K27) ChIP-Seq, HK00013_H3K27me3:1E7_N2_L3",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-Seq_ HK00013_H3K27me3:1E7_N2_L3",
"description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
"adapter" : {
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5044.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5051.bw"
},
"type" : "BigWigAdapter"
},
- "name" : "Histone Modifications (H3K27) ChIP-Seq, UP07448_H3K27me1:24439_N2_L3"
- },
- {
"displays" : [
{
- "type" : "LinearWiggleDisplay",
- "maxScore" : 89.8883691423725,
"minScore" : 35.4251618169829,
- "displayId" : "Histone Modifications (H3K27) ChIP-Seq_ HK00013_H3K27me3:1E7_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "displayId" : "Histone Modifications (H3K27) ChIP-Seq_ HK00013_H3K27me3:1E7_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "maxScore" : 89.8883691423725,
+ "type" : "LinearWiggleDisplay"
}
- ],
+ ]
+ },
+ {
+ "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-Seq_ WA30634849_H3K27ac_N2_L3",
+ "name" : "Histone Modifications (H3K27) ChIP-Seq, WA30634849_H3K27ac_N2_L3",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -12642,112 +12057,77 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-Seq_ HK00013_H3K27me3:1E7_N2_L3",
- "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5051.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5054.bw",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "name" : "Histone Modifications (H3K27) ChIP-Seq, HK00013_H3K27me3:1E7_N2_L3"
- },
- {
"displays" : [
{
- "minScore" : 94.2691481046101,
- "type" : "LinearWiggleDisplay",
"maxScore" : 216.593176074576,
- "displayId" : "Histone Modifications (H3K27) ChIP-Seq_ WA30634849_H3K27ac_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "displayId" : "Histone Modifications (H3K27) ChIP-Seq_ WA30634849_H3K27ac_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 94.2691481046101,
+ "type" : "LinearWiggleDisplay"
}
- ],
+ ]
+ },
+ {
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
- "Histone Modifications and Variants"
+ "Chromatin Modifying Enzymes"
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-Seq_ WA30634849_H3K27ac_N2_L3",
- "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5054.bw",
- "locationType" : "UriLocation"
- }
- },
- "name" : "Histone Modifications (H3K27) ChIP-Seq, WA30634849_H3K27ac_N2_L3"
- },
- {
+ "description" : "Chromatin Silencing enzymes. Synchronized C. elegans mixed stage embryos from strain N2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Chromatin Silencing ChIP-chip arrays_ FP00001_HPL2_N2_L3_EGS w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Chromatin Modifying Enzymes"
- ],
+ "name" : "Chromatin Silencing ChIP-chip arrays, FP00001_HPL2_N2_L3_EGS w peaks",
"displays" : [
{
- "displayId" : "Chromatin Silencing ChIP-chip arrays_ FP00001_HPL2_N2_L3_EGS w peaks_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay",
- "maxScore" : 4.287684,
"type" : "LinearWiggleDisplay",
- "minScore" : 0
+ "maxScore" : 4.287684,
+ "minScore" : 0,
+ "displayId" : "Chromatin Silencing ChIP-chip arrays_ FP00001_HPL2_N2_L3_EGS w peaks_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay"
}
],
- "name" : "Chromatin Silencing ChIP-chip arrays, FP00001_HPL2_N2_L3_EGS w peaks",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/FP00001_HPL2_N2_L3_mean.bw"
}
- },
- "type" : "QuantitativeTrack",
- "description" : "Chromatin Silencing enzymes. Synchronized C. elegans mixed stage embryos from strain N2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
},
{
- "name" : "__Chromatin Silencing ChIP-chip arrays, FP00001_HPL2_N2_L3_EGS peaks",
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/11512_details.gff.bb"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/11512_details.gff.bb",
+ "locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
- "description" : "Peak calls for Chromatin Silencing ChIP-chip arrays, FP00001_HPL2_N2_L3_EGS w peaks",
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Chromatin Silencing ChIP-chip arrays_ FP00001_HPL2_N2_L3_EGS w peaks_bigbed_peaks",
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Chromatin Modifying Enzymes"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
+ "displayId" : "Chromatin Silencing ChIP-chip arrays_ FP00001_HPL2_N2_L3_EGS w peaks_Chromatin Structure_Chromatin Modifying Enzymes_bigbed_peaks",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
"type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false
},
- "type" : "LinearBasicDisplay",
- "displayId" : "Chromatin Silencing ChIP-chip arrays_ FP00001_HPL2_N2_L3_EGS w peaks_Chromatin Structure_Chromatin Modifying Enzymes_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
- ]
- },
- {
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Chromatin Silencing ChIP-chip arrays_ SDQ2324_HPL2_N2_LTEMB w peaks",
+ ],
+ "name" : "__Chromatin Silencing ChIP-chip arrays, FP00001_HPL2_N2_L3_EGS peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Chromatin Silencing ChIP-chip arrays_ FP00001_HPL2_N2_L3_EGS w peaks_bigbed_peaks",
+ "description" : "Peak calls for Chromatin Silencing ChIP-chip arrays, FP00001_HPL2_N2_L3_EGS w peaks",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -12755,28 +12135,38 @@
"modENCODE data (2014)",
"Chromatin Structure",
"Chromatin Modifying Enzymes"
- ],
+ ]
+ },
+ {
"displays" : [
{
- "displayId" : "Chromatin Silencing ChIP-chip arrays_ SDQ2324_HPL2_N2_LTEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay",
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 3.87916268875808
+ "displayId" : "Chromatin Silencing ChIP-chip arrays_ SDQ2324_HPL2_N2_LTEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay",
+ "maxScore" : 3.87916268875808,
+ "type" : "LinearWiggleDisplay"
}
],
- "name" : "Chromatin Silencing ChIP-chip arrays, SDQ2324_HPL2_N2_LTEMB w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SDQ2324_HPL2_N2_LTEMB_mean.bw"
- },
- "type" : "BigWigAdapter"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SDQ2324_HPL2_N2_LTEMB_mean.bw",
+ "locationType" : "UriLocation"
+ }
},
- "description" : "Chromatin Silencing enzymes. Synchronized C. elegans mixed stage embryos from strain N2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Chromatin Modifying Enzymes"
+ ],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Chromatin Silencing enzymes. Synchronized C. elegans mixed stage embryos from strain N2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Chromatin Silencing ChIP-chip arrays, SDQ2324_HPL2_N2_LTEMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Chromatin Silencing ChIP-chip arrays_ SDQ2324_HPL2_N2_LTEMB w peaks"
},
{
- "description" : "Peak calls for Chromatin Silencing ChIP-chip arrays, SDQ2324_HPL2_N2_LTEMB w peaks",
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
@@ -12784,21 +12174,23 @@
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "name" : "__Chromatin Silencing ChIP-chip arrays, SDQ2324_HPL2_N2_LTEMB peaks",
"displays" : [
{
- "displayId" : "Chromatin Silencing ChIP-chip arrays_ SDQ2324_HPL2_N2_LTEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes_bigbed_peaks",
"type" : "LinearBasicDisplay",
+ "displayId" : "Chromatin Silencing ChIP-chip arrays_ SDQ2324_HPL2_N2_LTEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes_bigbed_peaks",
"renderer" : {
- "height" : 6,
+ "showLabels" : false,
"showDescriptions" : false,
+ "height" : 6,
"color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "type" : "SvgFeatureRenderer"
}
}
],
+ "name" : "__Chromatin Silencing ChIP-chip arrays, SDQ2324_HPL2_N2_LTEMB peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Chromatin Silencing ChIP-chip arrays_ SDQ2324_HPL2_N2_LTEMB w peaks_bigbed_peaks",
+ "description" : "Peak calls for Chromatin Silencing ChIP-chip arrays, SDQ2324_HPL2_N2_LTEMB w peaks",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -12806,205 +12198,196 @@
"modENCODE data (2014)",
"Chromatin Structure",
"Chromatin Modifying Enzymes"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Chromatin Silencing ChIP-chip arrays_ SDQ2324_HPL2_N2_LTEMB w peaks_bigbed_peaks"
+ ]
},
{
- "description" : "Chromatin Silencing enzymes. Synchronized C. elegans mixed stage embryos from strain N2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Chromatin Silencing ChIP-chip arrays, SDQ4129_Y39G10AR18_N2_MXEMB w peaks",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SDQ4129_Y39G10AR18_N2_MXEMB_mean.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "displays" : [
- {
- "displayId" : "Chromatin Silencing ChIP-chip arrays_ SDQ4129_Y39G10AR18_N2_MXEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay",
- "minScore" : 0,
- "maxScore" : 3.83608591929327,
- "type" : "LinearWiggleDisplay"
- }
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Chromatin Silencing ChIP-chip arrays_ SDQ4129_Y39G10AR18_N2_MXEMB w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Chromatin Modifying Enzymes"
- ]
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Chromatin Silencing ChIP-chip arrays_ SDQ4129_Y39G10AR18_N2_MXEMB w peaks",
+ "name" : "Chromatin Silencing ChIP-chip arrays, SDQ4129_Y39G10AR18_N2_MXEMB w peaks",
+ "description" : "Chromatin Silencing enzymes. Synchronized C. elegans mixed stage embryos from strain N2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "maxScore" : 3.83608591929327,
+ "minScore" : 0,
+ "displayId" : "Chromatin Silencing ChIP-chip arrays_ SDQ4129_Y39G10AR18_N2_MXEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SDQ4129_Y39G10AR18_N2_MXEMB_mean.bw"
+ }
+ }
},
{
"displays" : [
{
- "displayId" : "Chromatin Silencing ChIP-chip arrays_ SDQ4129_Y39G10AR18_N2_MXEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes_bigbed_peaks",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "height" : 6,
+ "showDescriptions" : false
},
+ "displayId" : "Chromatin Silencing ChIP-chip arrays_ SDQ4129_Y39G10AR18_N2_MXEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes_bigbed_peaks",
"type" : "LinearBasicDisplay"
}
],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8515_details.gff.bb"
+ }
+ },
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Chromatin Modifying Enzymes"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Chromatin Silencing ChIP-chip arrays_ SDQ4129_Y39G10AR18_N2_MXEMB w peaks_bigbed_peaks",
"description" : "Peak calls for Chromatin Silencing ChIP-chip arrays, SDQ4129_Y39G10AR18_N2_MXEMB w peaks",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8515_details.gff.bb",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "__Chromatin Silencing ChIP-chip arrays, SDQ4129_Y39G10AR18_N2_MXEMB peaks"
+ "name" : "__Chromatin Silencing ChIP-chip arrays, SDQ4129_Y39G10AR18_N2_MXEMB peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Chromatin Silencing ChIP-chip arrays_ SDQ4129_Y39G10AR18_N2_MXEMB w peaks_bigbed_peaks"
},
{
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SDQ35mean.wig_mean_WS220.bw"
- },
- "type" : "BigWigAdapter"
- },
- "name" : "CBP-1 ChIP-chip arrays",
- "description" : "Transcription and Chromatin. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the chromodomain-containing protein MRG-1. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Transcription and Chromatin. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the chromodomain-containing protein MRG-1. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "CBP-1 ChIP-chip arrays",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_CBP-1 ChIP-chip arrays",
"displays" : [
{
"type" : "LinearWiggleDisplay",
- "maxScore" : 2.66140334353535,
"minScore" : 0.911763103366667,
- "displayId" : "CBP-1 ChIP-chip arrays_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "displayId" : "CBP-1 ChIP-chip arrays_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 2.66140334353535
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SDQ35mean.wig_mean_WS220.bw",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_No Antibody (IGG) ChIP-chip arrays_ NIGG_N2_MXEMB w peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Transcription and Chromatin"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
"displayId" : "No Antibody (IGG) ChIP-chip arrays_ NIGG_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
+ "minScore" : 0,
"maxScore" : 2.46037172856149,
- "minScore" : 0
+ "type" : "LinearWiggleDisplay"
}
],
- "name" : "No Antibody (IGG) ChIP-chip arrays, NIGG_N2_MXEMB w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB46540_NIGG_N2_MXEMB_mean.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB46540_NIGG_N2_MXEMB_mean.bw",
+ "locationType" : "UriLocation"
}
},
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Transcription and Chromatin"
+ ],
+ "name" : "No Antibody (IGG) ChIP-chip arrays, NIGG_N2_MXEMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_No Antibody (IGG) ChIP-chip arrays_ NIGG_N2_MXEMB w peaks",
"description" : "Transcription and Chromatin. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the chromodomain-containing protein MRG-1. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "description" : "Peak calls for No Antibody (IGG) ChIP-chip arrays, NIGG_N2_MXEMB w peaks",
"type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7847_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Transcription and Chromatin"
+ ],
"name" : "__No Antibody (IGG) ChIP-chip arrays, NIGG_N2_MXEMB peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_No Antibody (IGG) ChIP-chip arrays_ NIGG_N2_MXEMB w peaks_bigbed_peaks",
+ "description" : "Peak calls for No Antibody (IGG) ChIP-chip arrays, NIGG_N2_MXEMB w peaks",
"displays" : [
{
+ "displayId" : "No Antibody (IGG) ChIP-chip arrays_ NIGG_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
"renderer" : {
"type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "deeppink",
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
+ "color1" : "deeppink"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "No Antibody (IGG) ChIP-chip arrays_ NIGG_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Transcription and Chromatin"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_No Antibody (IGG) ChIP-chip arrays_ NIGG_N2_MXEMB w peaks_bigbed_peaks"
- },
- {
- "name" : "No Antibody (IGG) ChIP-chip arrays, IGG_N2_L3",
"adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JA00002_IGG_N2_L3_mean_WS220.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7847_details.gff.bb"
}
- },
+ }
+ },
+ {
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
- "description" : "Transcription and Chromatin. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the chromodomain-containing protein MRG-1. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_No Antibody (IGG) ChIP-chip arrays_ IGG_N2_L3",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_No Antibody (IGG) ChIP-chip arrays_ IGG_N2_L3",
+ "name" : "No Antibody (IGG) ChIP-chip arrays, IGG_N2_L3",
+ "description" : "Transcription and Chromatin. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the chromodomain-containing protein MRG-1. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "displayId" : "No Antibody (IGG) ChIP-chip arrays_ IGG_N2_L3_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
"maxScore" : 2.14935274798244,
- "minScore" : 0.575286406834205
+ "minScore" : 0.575286406834205,
+ "displayId" : "No Antibody (IGG) ChIP-chip arrays_ IGG_N2_L3_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
- ]
- },
- {
- "name" : "MES-4 ChIP-chip arrays, SGF3165_FLAG_MES4FLAG_EEMB",
- "type" : "QuantitativeTrack",
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SGF3165_FLAG_MES4FLAG_EEMB_mean_WS220.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JA00002_IGG_N2_L3_mean_WS220.bw"
}
- },
+ }
+ },
+ {
"description" : "Transcription and Chromatin. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the chromodomain-containing protein MRG-1. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_MES-4 ChIP-chip arrays_ SGF3165_FLAG_MES4FLAG_EEMB",
+ "name" : "MES-4 ChIP-chip arrays, SGF3165_FLAG_MES4FLAG_EEMB",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -13013,64 +12396,64 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SGF3165_FLAG_MES4FLAG_EEMB_mean_WS220.bw"
+ }
+ },
"displays" : [
{
- "displayId" : "MES-4 ChIP-chip arrays_ SGF3165_FLAG_MES4FLAG_EEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "maxScore" : 2.26427490708411,
"type" : "LinearWiggleDisplay",
- "minScore" : 0.827610719337758
+ "maxScore" : 2.26427490708411,
+ "minScore" : 0.827610719337758,
+ "displayId" : "MES-4 ChIP-chip arrays_ SGF3165_FLAG_MES4FLAG_EEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
}
]
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_MES-4 ChIP-chip arrays_ SDQ0791_MES4_N2_EEMB",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "Transcription and Chromatin. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the chromodomain-containing protein MRG-1. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "MES-4 ChIP-chip arrays, SDQ0791_MES4_N2_EEMB",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_MES-4 ChIP-chip arrays_ SDQ0791_MES4_N2_EEMB",
"displays" : [
{
"displayId" : "MES-4 ChIP-chip arrays_ SDQ0791_MES4_N2_EEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
"minScore" : 0.99161427506215,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 2.8221644698853
+ "maxScore" : 2.8221644698853,
+ "type" : "LinearWiggleDisplay"
}
],
- "name" : "MES-4 ChIP-chip arrays, SDQ0791_MES4_N2_EEMB",
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SDQ0791_MES4_N2_EEMB_mean_WS220.bw"
- },
- "type" : "BigWigAdapter"
- },
- "description" : "Transcription and Chromatin. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the chromodomain-containing protein MRG-1. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
+ }
},
{
- "displays" : [
- {
- "displayId" : "MES-4 ChIP-chip arrays_ MES4FLAG_N2_EEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "minScore" : 0.379671666837783,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 1.15052020253873
- }
- ],
+ "description" : "Transcription and Chromatin. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the chromodomain-containing protein MRG-1. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_MES-4 ChIP-chip arrays_ MES4FLAG_N2_EEMB",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "MES-4 ChIP-chip arrays, MES4FLAG_N2_EEMB",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "description" : "Transcription and Chromatin. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the chromodomain-containing protein MRG-1. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "MES-4 ChIP-chip arrays, MES4FLAG_N2_EEMB",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
@@ -13078,17 +12461,21 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/NA_MES4FLAG_EEMB_mean_WS220.bw",
"locationType" : "UriLocation"
}
- }
- },
- {
+ },
"displays" : [
{
- "minScore" : 0.901446226431906,
"type" : "LinearWiggleDisplay",
- "maxScore" : 2.67074614070274,
- "displayId" : "MRG-1 ChIP-chip arrays_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "maxScore" : 1.15052020253873,
+ "displayId" : "MES-4 ChIP-chip arrays_ MES4FLAG_N2_EEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 0.379671666837783
}
- ],
+ ]
+ },
+ {
+ "name" : "MRG-1 ChIP-chip arrays",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_MRG-1 ChIP-chip arrays",
+ "description" : "Transcription and Chromatin. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the chromodomain-containing protein MRG-1. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -13097,29 +12484,24 @@
"Transcription Factors",
"Transcription and Chromatin"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_MRG-1 ChIP-chip arrays",
- "description" : "Transcription and Chromatin. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the chromodomain-containing protein MRG-1. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SDQ0790_MRG1_N2_EEMB_mean.wig_mean_WS220.bw",
"locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ }
},
- "type" : "QuantitativeTrack",
- "name" : "MRG-1 ChIP-chip arrays"
+ "displays" : [
+ {
+ "displayId" : "MRG-1 ChIP-chip arrays_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 0.901446226431906,
+ "maxScore" : 2.67074614070274,
+ "type" : "LinearWiggleDisplay"
+ }
+ ]
},
{
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00006_ZFP1_N2_MXEMB_mean.wig_mean.bw",
- "locationType" : "UriLocation"
- }
- },
"type" : "QuantitativeTrack",
- "name" : "ZFP-1 ChIP-chip arrays, JL00006_ZFP1_N2_MXEMB",
- "description" : "Transcription and Chromatin. Synchronized C. elegans mixed embryos from strains RB774 (which contains a zfp-1 knockout allele) and N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes chromatin-associated protein ZFP-1. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -13128,128 +12510,126 @@
"Transcription Factors",
"Transcription and Chromatin"
],
+ "name" : "ZFP-1 ChIP-chip arrays, JL00006_ZFP1_N2_MXEMB",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_ZFP-1 ChIP-chip arrays_ JL00006_ZFP1_N2_MXEMB",
+ "description" : "Transcription and Chromatin. Synchronized C. elegans mixed embryos from strains RB774 (which contains a zfp-1 knockout allele) and N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes chromatin-associated protein ZFP-1. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "maxScore" : 3.27687725717023,
"type" : "LinearWiggleDisplay",
"minScore" : 1.16846949486618,
- "displayId" : "ZFP-1 ChIP-chip arrays_ JL00006_ZFP1_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "displayId" : "ZFP-1 ChIP-chip arrays_ JL00006_ZFP1_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 3.27687725717023
}
- ]
- },
- {
- "description" : "Transcription and Chromatin. Synchronized C. elegans mixed embryos from strains RB774 (which contains a zfp-1 knockout allele) and N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes chromatin-associated protein ZFP-1. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
+ ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SDQ3517_ZFP1_N2_MXEMB_mean.bw"
- },
- "type" : "BigWigAdapter"
- },
- "name" : "ZFP-1 ChIP-chip arrays, SDQ3517_ZFP1_N2_MXEMB",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00006_ZFP1_N2_MXEMB_mean.wig_mean.bw",
+ "locationType" : "UriLocation"
+ }
+ }
+ },
+ {
"displays" : [
{
+ "displayId" : "ZFP-1 ChIP-chip arrays_ SDQ3517_ZFP1_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
"minScore" : 0.836520986113303,
"maxScore" : 2.55521510943425,
- "type" : "LinearWiggleDisplay",
- "displayId" : "ZFP-1 ChIP-chip arrays_ SDQ3517_ZFP1_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
],
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SDQ3517_ZFP1_N2_MXEMB_mean.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_ZFP-1 ChIP-chip arrays_ SDQ3517_ZFP1_N2_MXEMB"
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_ZFP-1 ChIP-chip arrays_ SDQ3517_ZFP1_N2_MXEMB",
+ "name" : "ZFP-1 ChIP-chip arrays, SDQ3517_ZFP1_N2_MXEMB",
+ "description" : "Transcription and Chromatin. Synchronized C. elegans mixed embryos from strains RB774 (which contains a zfp-1 knockout allele) and N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes chromatin-associated protein ZFP-1. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "displays" : [
- {
- "displayId" : "ZFP-1 ChIP-chip arrays_ ZFP1_RB774_MXEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 3.05632088097994,
- "minScore" : 0
- }
- ],
+ "name" : "ZFP-1 ChIP-chip arrays, ZFP1_RB774_MXEMB w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_ZFP-1 ChIP-chip arrays_ ZFP1_RB774_MXEMB w peaks",
+ "description" : "Transcription and Chromatin. Synchronized C. elegans mixed embryos from strains RB774 (which contains a zfp-1 knockout allele) and N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes chromatin-associated protein ZFP-1. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : "Transcription and Chromatin. Synchronized C. elegans mixed embryos from strains RB774 (which contains a zfp-1 knockout allele) and N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes chromatin-associated protein ZFP-1. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "ZFP-1 ChIP-chip arrays, ZFP1_RB774_MXEMB w peaks",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00006_ZFP1_RB774_MXEMB_1_A_13805901_MA2Cscore.bw"
- },
- "type" : "BigWigAdapter"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00006_ZFP1_RB774_MXEMB_1_A_13805901_MA2Cscore.bw",
+ "locationType" : "UriLocation"
+ }
},
- "type" : "QuantitativeTrack"
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "displayId" : "ZFP-1 ChIP-chip arrays_ ZFP1_RB774_MXEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 3.05632088097994
+ }
+ ]
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_ZFP-1 ChIP-chip arrays_ ZFP1_RB774_MXEMB w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "Peak calls for ZFP-1 ChIP-chip arrays, ZFP1_RB774_MXEMB w peaks",
+ "name" : "__ZFP-1 ChIP-chip arrays, ZFP1_RB774_MXEMB peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_ZFP-1 ChIP-chip arrays_ ZFP1_RB774_MXEMB w peaks_bigbed_peaks",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "ZFP-1 ChIP-chip arrays_ ZFP1_RB774_MXEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
"showLabels" : false,
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay"
+ "height" : 6,
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "name" : "__ZFP-1 ChIP-chip arrays, ZFP1_RB774_MXEMB peaks",
"adapter" : {
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7817_details.gff.bb"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7817_details.gff.bb",
+ "locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Peak calls for ZFP-1 ChIP-chip arrays, ZFP1_RB774_MXEMB w peaks"
+ }
},
{
"displays" : [
{
- "type" : "LinearWiggleDisplay",
- "maxScore" : 2.09993207874373,
+ "displayId" : "Core Histones ChIP-chip arrays_ H3_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"minScore" : 0.713077585985433,
- "displayId" : "Core Histones ChIP-chip arrays_ H3_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "maxScore" : 2.09993207874373,
+ "type" : "LinearWiggleDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Core Histones ChIP-chip arrays_ H3_N2_L3",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
- "description" : "Core Histones. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes core histone H3. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Core Histones ChIP-chip arrays, H3_N2_L3",
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
@@ -13257,19 +12637,6 @@
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack"
- },
- {
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB1791_H3_N2_L3_mean.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "Core Histones ChIP-chip arrays, AB1791_H3_N2_L3 w peaks",
- "description" : "Core Histones. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes core histone H3. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -13278,17 +12645,45 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Core Histones ChIP-chip arrays_ AB1791_H3_N2_L3 w peaks",
+ "type" : "QuantitativeTrack",
+ "description" : "Core Histones. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes core histone H3. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Core Histones ChIP-chip arrays_ H3_N2_L3",
+ "name" : "Core Histones ChIP-chip arrays, H3_N2_L3"
+ },
+ {
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB1791_H3_N2_L3_mean.bw"
+ }
+ },
"displays" : [
{
"maxScore" : 2.95322111523054,
- "type" : "LinearWiggleDisplay",
+ "displayId" : "Core Histones ChIP-chip arrays_ AB1791_H3_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"minScore" : 0,
- "displayId" : "Core Histones ChIP-chip arrays_ AB1791_H3_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
+ ],
+ "description" : "Core Histones. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes core histone H3. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Core Histones ChIP-chip arrays, AB1791_H3_N2_L3 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Core Histones ChIP-chip arrays_ AB1791_H3_N2_L3 w peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
]
},
{
+ "name" : "__Core Histones ChIP-chip arrays, AB1791_H3_N2_L3 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Core Histones ChIP-chip arrays_ AB1791_H3_N2_L3 w peaks_bigbed_peaks",
+ "description" : "Peak calls for Core Histones ChIP-chip arrays, AB1791_H3_N2_L3 w peaks",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -13297,61 +12692,73 @@
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Core Histones ChIP-chip arrays_ AB1791_H3_N2_L3 w peaks_bigbed_peaks",
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9450_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
- "displayId" : "Core Histones ChIP-chip arrays_ AB1791_H3_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"type" : "LinearBasicDisplay",
+ "displayId" : "Core Histones ChIP-chip arrays_ AB1791_H3_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
"type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "showDescriptions" : false,
+ "height" : 6,
+ "showLabels" : false,
+ "color1" : "deeppink"
}
}
- ],
+ ]
+ },
+ {
"adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9450_details.gff.bb"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/MP05858_H4DAM1636076_N2_L3_mean_WS220.bw"
}
},
- "type" : "FeatureTrack",
- "name" : "__Core Histones ChIP-chip arrays, AB1791_H3_N2_L3 peaks",
- "description" : "Peak calls for Core Histones ChIP-chip arrays, AB1791_H3_N2_L3 w peaks"
- },
- {
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
+ "displays" : [
+ {
+ "displayId" : "Core Histones ChIP-chip arrays_ MP05858_H4DAM1636076_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 0.76445880658195,
+ "maxScore" : 2.235329716915,
+ "type" : "LinearWiggleDisplay"
+ }
],
+ "description" : "Core Histones. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes core histone H3. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Core Histones ChIP-chip arrays_ MP05858_H4DAM1636076_N2_L3",
+ "name" : "Core Histones ChIP-chip arrays, MP05858_H4DAM1636076_N2_L3",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Core Histones ChIP-chip arrays_ MP05858_H4DAM1636076_N2_L3",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack"
+ },
+ {
"displays" : [
{
"type" : "LinearWiggleDisplay",
- "maxScore" : 2.235329716915,
- "minScore" : 0.76445880658195,
- "displayId" : "Core Histones ChIP-chip arrays_ MP05858_H4DAM1636076_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "displayId" : "Core Histones ChIP-chip arrays_ H3609253_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 0.686520266046716,
+ "maxScore" : 2.26309171529308
}
],
- "type" : "QuantitativeTrack",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/MP05858_H4DAM1636076_N2_L3_mean_WS220.bw"
- }
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB1791_H3609253_N2_EEMB_mean_WS220.bw"
+ },
+ "type" : "BigWigAdapter"
},
- "name" : "Core Histones ChIP-chip arrays, MP05858_H4DAM1636076_N2_L3",
- "description" : "Core Histones. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes core histone H3. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -13360,27 +12767,19 @@
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "name" : "Core Histones ChIP-chip arrays, H3609253_N2_EEMB",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Core Histones ChIP-chip arrays_ H3609253_N2_EEMB",
+ "description" : "Core Histones. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes core histone H3. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ },
+ {
"displays" : [
{
- "type" : "LinearWiggleDisplay",
- "maxScore" : 2.26309171529308,
- "minScore" : 0.686520266046716,
- "displayId" : "Core Histones ChIP-chip arrays_ H3609253_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "minScore" : 0.727478920309329,
+ "displayId" : "Core Histones ChIP-chip arrays_ H3144_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "maxScore" : 2.16387551608888,
+ "type" : "LinearWiggleDisplay"
}
],
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB1791_H3609253_N2_EEMB_mean_WS220.bw",
- "locationType" : "UriLocation"
- }
- },
- "type" : "QuantitativeTrack",
- "name" : "Core Histones ChIP-chip arrays, H3609253_N2_EEMB",
- "description" : "Core Histones. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes core histone H3. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -13388,47 +12787,36 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AR0144_H3144_N2_L3_mean_WS220.bw"
}
},
- "type" : "QuantitativeTrack",
- "name" : "Core Histones ChIP-chip arrays, H3144_N2_L3",
- "description" : "Core Histones. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes core histone H3. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Core Histones ChIP-chip arrays_ H3144_N2_L3",
+ "description" : "Core Histones. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes core histone H3. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Core Histones ChIP-chip arrays, H3144_N2_L3",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Core Histones ChIP-chip arrays_ H3144_N2_L3"
+ },
+ {
"displays" : [
{
- "displayId" : "Core Histones ChIP-chip arrays_ H3144_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay",
- "maxScore" : 2.16387551608888,
- "minScore" : 0.727478920309329
+ "maxScore" : 1.80304457496358,
+ "displayId" : "Core Histones ChIP-chip arrays_ H3144_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 0.574904709737981
}
- ]
- },
- {
- "description" : "Core Histones. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes core histone H3. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Core Histones ChIP-chip arrays, H3144_N2_EEMB",
- "type" : "QuantitativeTrack",
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AR0144_H3144_N2_EEMB_mean_WS220.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AR0144_H3144_N2_EEMB_mean_WS220.bw"
}
},
- "displays" : [
- {
- "displayId" : "Core Histones ChIP-chip arrays_ H3144_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "minScore" : 0.574904709737981,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 1.80304457496358
- }
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Core Histones ChIP-chip arrays_ H3144_N2_EEMB",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -13436,39 +12824,59 @@
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
- ]
+ ],
+ "name" : "Core Histones ChIP-chip arrays, H3144_N2_EEMB",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Core Histones ChIP-chip arrays_ H3144_N2_EEMB",
+ "description" : "Core Histones. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes core histone H3. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
"displays" : [
{
- "minScore" : 0.71591400430528,
- "maxScore" : 2.06792122516751,
"type" : "LinearWiggleDisplay",
- "displayId" : "Core Histones ChIP-chip arrays_ H3144_N2_L3_LM_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "displayId" : "Core Histones ChIP-chip arrays_ H3144_N2_L3_LM_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 0.71591400430528,
+ "maxScore" : 2.06792122516751
}
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Core Histones ChIP-chip arrays_ H3144_N2_L3_LM",
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AR0144_H3144_N2_L3_LM_mean_WS220.bw"
+ }
+ },
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "description" : "Core Histones. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes core histone H3. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Core Histones ChIP-chip arrays_ H3144_N2_L3_LM",
"name" : "Core Histones ChIP-chip arrays, H3144_N2_L3_LM",
+ "description" : "Core Histones. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes core histone H3. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ },
+ {
"adapter" : {
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AR0144_H3144_N2_L3_LM_mean_WS220.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/15018.bw",
"locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack"
- },
- {
+ "displays" : [
+ {
+ "maxScore" : 2.994566,
+ "displayId" : "Centromere Specificaton ChIP-chip arrays_ SDQ0804_HCP3_N2_LTEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
+ "description" : "Cenromere Specificaton and Kinetochore Function. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the centromere-binding protein HCP-3 (CENP-A). After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Centromere Specificaton ChIP-chip arrays_ SDQ0804_HCP3_N2_LTEMB w peaks",
+ "name" : "Centromere Specificaton ChIP-chip arrays, SDQ0804_HCP3_N2_LTEMB w peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -13477,132 +12885,109 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "displays" : [
- {
- "displayId" : "Centromere Specificaton ChIP-chip arrays_ SDQ0804_HCP3_N2_LTEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay",
- "minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 2.994566
- }
- ],
- "name" : "Centromere Specificaton ChIP-chip arrays, SDQ0804_HCP3_N2_LTEMB w peaks",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/15018.bw",
- "locationType" : "UriLocation"
- }
- },
- "type" : "QuantitativeTrack",
- "description" : "Cenromere Specificaton and Kinetochore Function. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the centromere-binding protein HCP-3 (CENP-A). After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "type" : "QuantitativeTrack"
},
{
- "description" : "Peak calls for Centromere Specificaton ChIP-chip arrays, SDQ0804_HCP3_N2_LTEMB w peaks",
"name" : "__Centromere Specificaton ChIP-chip arrays, SDQ0804_HCP3_N2_LTEMB peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Centromere Specificaton ChIP-chip arrays_ SDQ0804_HCP3_N2_LTEMB w peaks_bigbed_peaks",
+ "description" : "Peak calls for Centromere Specificaton ChIP-chip arrays, SDQ0804_HCP3_N2_LTEMB w peaks",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Chromatin Modifying Enzymes"
+ ],
"adapter" : {
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/15021_details.gff.bb"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/15021_details.gff.bb",
+ "locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "Centromere Specificaton ChIP-chip arrays_ SDQ0804_HCP3_N2_LTEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes_bigbed_peaks",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay"
+ "showDescriptions" : false,
+ "height" : 6
+ }
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Centromere Specificaton ChIP-chip arrays_ SDQ0804_HCP3_N2_LTEMB w peaks_bigbed_peaks",
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Chromatin Modifying Enzymes"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
]
},
{
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Centromere Specificaton ChIP-chip arrays_ OD00079_HCP3_N2_EEMB w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Chromatin Modifying Enzymes"
],
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Centromere Specificaton ChIP-chip arrays_ OD00079_HCP3_N2_EEMB w peaks",
+ "name" : "Centromere Specificaton ChIP-chip arrays, OD00079_HCP3_N2_EEMB w peaks",
+ "description" : "Cenromere Specificaton and Kinetochore Function. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the centromere-binding protein HCP-3 (CENP-A). After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
+ "maxScore" : 2.362567,
"displayId" : "Centromere Specificaton ChIP-chip arrays_ OD00079_HCP3_N2_EEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay",
"minScore" : 0,
- "maxScore" : 2.362567,
"type" : "LinearWiggleDisplay"
}
],
- "name" : "Centromere Specificaton ChIP-chip arrays, OD00079_HCP3_N2_EEMB w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/OD00079_HCP3_N2_EEMB_WS220.bw",
- "locationType" : "UriLocation"
- }
- },
- "description" : "Cenromere Specificaton and Kinetochore Function. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the centromere-binding protein HCP-3 (CENP-A). After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/OD00079_HCP3_N2_EEMB_WS220.bw"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
"displays" : [
{
- "displayId" : "Centromere Specificaton ChIP-chip arrays_ OD00079_HCP3_N2_EEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
+ "showDescriptions" : false,
"height" : 6,
- "showDescriptions" : false
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "Centromere Specificaton ChIP-chip arrays_ OD00079_HCP3_N2_EEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/15016_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Chromatin Modifying Enzymes"
],
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Centromere Specificaton ChIP-chip arrays_ OD00079_HCP3_N2_EEMB w peaks_bigbed_peaks",
- "description" : "Peak calls for Centromere Specificaton ChIP-chip arrays, OD00079_HCP3_N2_EEMB w peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/15016_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "__Centromere Specificaton ChIP-chip arrays, OD00079_HCP3_N2_EEMB peaks"
+ "name" : "__Centromere Specificaton ChIP-chip arrays, OD00079_HCP3_N2_EEMB peaks",
+ "description" : "Peak calls for Centromere Specificaton ChIP-chip arrays, OD00079_HCP3_N2_EEMB w peaks"
},
{
- "displays" : [
- {
- "displayId" : "Centromere Specificaton ChIP-chip arrays_ OD00079_HCP3_N2_MXEMB_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 2.92,
- "minScore" : 1.15407755731613
- }
- ],
+ "description" : "Cenromere Specificaton and Kinetochore Function. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the centromere-binding protein HCP-3 (CENP-A). After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Centromere Specificaton ChIP-chip arrays_ OD00079_HCP3_N2_MXEMB",
+ "name" : "Centromere Specificaton ChIP-chip arrays, OD00079_HCP3_N2_MXEMB",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -13611,58 +12996,53 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : "Cenromere Specificaton and Kinetochore Function. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the centromere-binding protein HCP-3 (CENP-A). After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Centromere Specificaton ChIP-chip arrays, OD00079_HCP3_N2_MXEMB",
"type" : "QuantitativeTrack",
"adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/OD00079_HCP3_N2_MXEMB_mean_WS220.bw",
- "locationType" : "UriLocation"
- }
- }
- },
- {
- "name" : "Centromere Specificaton ChIP-chip arrays, OD00001_HCP3_N2_MXEMB",
- "adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/OD00001_HCP3_N2_MXEMB_mean.wig_mean_WS220.bw"
- }
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/OD00079_HCP3_N2_MXEMB_mean_WS220.bw"
+ },
+ "type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "description" : "Cenromere Specificaton and Kinetochore Function. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the centromere-binding protein HCP-3 (CENP-A). After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Centromere Specificaton ChIP-chip arrays_ OD00001_HCP3_N2_MXEMB",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Chromatin Modifying Enzymes"
- ],
"displays" : [
{
- "displayId" : "Centromere Specificaton ChIP-chip arrays_ OD00001_HCP3_N2_MXEMB_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay",
"maxScore" : 2.92,
- "minScore" : 1.1540798442179
+ "displayId" : "Centromere Specificaton ChIP-chip arrays_ OD00079_HCP3_N2_MXEMB_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay",
+ "minScore" : 1.15407755731613
}
]
},
{
- "name" : "Centromere Specificaton ChIP-chip arrays, SDQ0803_KNL2_N2_LTemb",
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "displayId" : "Centromere Specificaton ChIP-chip arrays_ OD00001_HCP3_N2_MXEMB_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay",
+ "minScore" : 1.1540798442179,
+ "maxScore" : 2.92,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/15158.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/OD00001_HCP3_N2_MXEMB_mean.wig_mean_WS220.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Chromatin Modifying Enzymes"
+ ],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"description" : "Cenromere Specificaton and Kinetochore Function. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the centromere-binding protein HCP-3 (CENP-A). After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Centromere Specificaton ChIP-chip arrays_ SDQ0803_KNL2_N2_LTemb",
+ "name" : "Centromere Specificaton ChIP-chip arrays, OD00001_HCP3_N2_MXEMB",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Centromere Specificaton ChIP-chip arrays_ OD00001_HCP3_N2_MXEMB"
+ },
+ {
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -13671,64 +13051,88 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
+ "description" : "Cenromere Specificaton and Kinetochore Function. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the centromere-binding protein HCP-3 (CENP-A). After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Centromere Specificaton ChIP-chip arrays_ SDQ0803_KNL2_N2_LTemb",
+ "name" : "Centromere Specificaton ChIP-chip arrays, SDQ0803_KNL2_N2_LTemb",
"displays" : [
{
- "minScore" : 1.65864498045814,
"type" : "LinearWiggleDisplay",
"maxScore" : 5.00589388017619,
+ "minScore" : 1.65864498045814,
"displayId" : "Centromere Specificaton ChIP-chip arrays_ SDQ0803_KNL2_N2_LTemb_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay"
}
- ]
- },
- {
- "description" : "Cenromere Specificaton and Kinetochore Function. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the centromere-binding protein HCP-3 (CENP-A). After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Centromere Specificaton ChIP-chip arrays, OD00079_HCP3_N2_EEMB (15012)",
+ ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/15012.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/15158.bw"
+ }
+ }
+ },
+ {
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/15012.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
"displays" : [
{
- "displayId" : "Centromere Specificaton ChIP-chip arrays_ OD00079_HCP3_N2_EEMB (15012)_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay",
"minScore" : 1.21921491615181,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 3.165395
+ "displayId" : "Centromere Specificaton ChIP-chip arrays_ OD00079_HCP3_N2_EEMB (15012)_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay",
+ "maxScore" : 3.165395,
+ "type" : "LinearWiggleDisplay"
}
],
+ "description" : "Cenromere Specificaton and Kinetochore Function. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the centromere-binding protein HCP-3 (CENP-A). After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Centromere Specificaton ChIP-chip arrays, OD00079_HCP3_N2_EEMB (15012)",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Centromere Specificaton ChIP-chip arrays_ OD00079_HCP3_N2_EEMB (15012)",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Chromatin Modifying Enzymes"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
]
},
{
"description" : "Cenromere Specificaton and Kinetochore Function. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the centromere-binding protein HCP-3 (CENP-A). After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Centromere Specificaton ChIP-chip arrays_ OD00079_HCP3_N2_LTEMB w peaks",
"name" : "Centromere Specificaton ChIP-chip arrays, OD00079_HCP3_N2_LTEMB w peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Chromatin Modifying Enzymes"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/15006.bw"
- }
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/15006.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
"displays" : [
{
- "displayId" : "Centromere Specificaton ChIP-chip arrays_ OD00079_HCP3_N2_LTEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay",
"maxScore" : 2.91275,
- "minScore" : 0
+ "minScore" : 0,
+ "displayId" : "Centromere Specificaton ChIP-chip arrays_ OD00079_HCP3_N2_LTEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay"
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Centromere Specificaton ChIP-chip arrays_ OD00079_HCP3_N2_LTEMB w peaks",
+ ]
+ },
+ {
+ "description" : "Peak calls for Centromere Specificaton ChIP-chip arrays, OD00079_HCP3_N2_LTEMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Centromere Specificaton ChIP-chip arrays_ OD00079_HCP3_N2_LTEMB w peaks_bigbed_peaks",
+ "name" : "__Centromere Specificaton ChIP-chip arrays, OD00079_HCP3_N2_LTEMB peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -13736,89 +13140,59 @@
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
- },
- {
- "description" : "Peak calls for Centromere Specificaton ChIP-chip arrays, OD00079_HCP3_N2_LTEMB w peaks",
+ ],
+ "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/15010_details.gff.bb"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/15010_details.gff.bb",
+ "locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "name" : "__Centromere Specificaton ChIP-chip arrays, OD00079_HCP3_N2_LTEMB peaks",
"displays" : [
{
- "displayId" : "Centromere Specificaton ChIP-chip arrays_ OD00079_HCP3_N2_LTEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes_bigbed_peaks",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
"color1" : "deeppink",
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
+ "showLabels" : false
},
+ "displayId" : "Centromere Specificaton ChIP-chip arrays_ OD00079_HCP3_N2_LTEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes_bigbed_peaks",
"type" : "LinearBasicDisplay"
}
- ],
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Chromatin Modifying Enzymes"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Centromere Specificaton ChIP-chip arrays_ OD00079_HCP3_N2_LTEMB w peaks_bigbed_peaks"
+ ]
},
{
- "displays" : [
- {
- "minScore" : 1.65652172185312,
- "maxScore" : 4.99945976319126,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Centromere Specificaton ChIP-chip arrays_ SDQ0810_KNL2_N2_LTemb_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay"
- }
- ],
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Centromere Specificaton ChIP-chip arrays_ SDQ0810_KNL2_N2_LTemb",
+ "name" : "Centromere Specificaton ChIP-chip arrays, SDQ0810_KNL2_N2_LTemb",
+ "description" : "Cenromere Specificaton and Kinetochore Function. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the centromere-binding protein HCP-3 (CENP-A). After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Chromatin Modifying Enzymes"
],
- "description" : "Cenromere Specificaton and Kinetochore Function. Synchronized C. elegans early embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes the centromere-binding protein HCP-3 (CENP-A). After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Centromere Specificaton ChIP-chip arrays, SDQ0810_KNL2_N2_LTemb",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/15159.bw"
- }
+ },
+ "type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack"
- },
- {
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Transcription and Chromatin"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ DPY27_YPT47_MXEMB",
"displays" : [
{
"type" : "LinearWiggleDisplay",
- "maxScore" : 4.4558921896778,
- "minScore" : 1.47044442259367,
- "displayId" : "Dosage Compensation ChIP-chip arrays_ DPY27_YPT47_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "maxScore" : 4.99945976319126,
+ "displayId" : "Centromere Specificaton ChIP-chip arrays_ SDQ0810_KNL2_N2_LTemb_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay",
+ "minScore" : 1.65652172185312
}
- ],
+ ]
+ },
+ {
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -13826,19 +13200,29 @@
"locationType" : "UriLocation"
}
},
- "type" : "QuantitativeTrack",
- "name" : "Dosage Compensation ChIP-chip arrays, DPY27_YPT47_MXEMB",
- "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
"displays" : [
{
- "displayId" : "Dosage Compensation ChIP-chip arrays_ SDC3_YPT47_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "maxScore" : 4.2371049121796,
- "type" : "LinearWiggleDisplay",
- "minScore" : 1.39824462101927
+ "maxScore" : 4.4558921896778,
+ "displayId" : "Dosage Compensation ChIP-chip arrays_ DPY27_YPT47_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 1.47044442259367,
+ "type" : "LinearWiggleDisplay"
}
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ DPY27_YPT47_MXEMB",
+ "name" : "Dosage Compensation ChIP-chip arrays, DPY27_YPT47_MXEMB",
+ "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Transcription and Chromatin"
+ ]
+ },
+ {
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -13847,44 +13231,85 @@
"Transcription Factors",
"Transcription and Chromatin"
],
+ "name" : "Dosage Compensation ChIP-chip arrays, SDC3_YPT47_MXEMB",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ SDC3_YPT47_MXEMB",
"description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "displayId" : "Dosage Compensation ChIP-chip arrays_ SDC3_YPT47_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 1.39824462101927,
+ "maxScore" : 4.2371049121796,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00002_SDC3_YPT47_MXemb_mean.wig_mean_WS220.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00002_SDC3_YPT47_MXemb_mean.wig_mean_WS220.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "Dosage Compensation ChIP-chip arrays, SDC3_YPT47_MXEMB"
+ }
},
{
- "name" : "Dosage Compensation ChIP-chip arrays, DPY27_N2_MXEMB w peaks",
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "minScore" : 0,
+ "displayId" : "Dosage Compensation ChIP-chip arrays_ DPY27_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 2.40766669744746,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00001_DPY27_N2_MXemb_mean_WS220.bw"
- },
- "type" : "BigWigAdapter"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00001_DPY27_N2_MXemb_mean_WS220.bw",
+ "locationType" : "UriLocation"
+ }
},
- "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ DPY27_N2_MXEMB w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ DPY27_N2_MXEMB w peaks",
+ "name" : "Dosage Compensation ChIP-chip arrays, DPY27_N2_MXEMB w peaks",
+ "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ },
+ {
+ "name" : "__Dosage Compensation ChIP-chip arrays, DPY27_N2_MXEMB peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ DPY27_N2_MXEMB w peaks_bigbed_peaks",
+ "description" : "Peak calls for Dosage Compensation ChIP-chip arrays, DPY27_N2_MXEMB w peaks",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Transcription and Chromatin"
+ ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4500_details.gff.bb"
+ }
+ },
"displays" : [
{
- "displayId" : "Dosage Compensation ChIP-chip arrays_ DPY27_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 2.40766669744746,
- "minScore" : 0
+ "type" : "LinearBasicDisplay",
+ "displayId" : "Dosage Compensation ChIP-chip arrays_ DPY27_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
+ "height" : 6,
+ "showDescriptions" : false,
+ "showLabels" : false
+ }
}
]
},
@@ -13894,83 +13319,45 @@
"Transcription Factors",
"Transcription and Chromatin"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ DPY27_N2_MXEMB w peaks_bigbed_peaks",
+ "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Dosage Compensation ChIP-chip arrays, DPY28_N2_MXEMB",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ DPY28_N2_MXEMB",
"displays" : [
{
- "renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "Dosage Compensation ChIP-chip arrays_ DPY27_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks"
+ "type" : "LinearWiggleDisplay",
+ "minScore" : 1.22266339680173,
+ "displayId" : "Dosage Compensation ChIP-chip arrays_ DPY28_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 3.80655574788404
}
],
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4500_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "__Dosage Compensation ChIP-chip arrays, DPY27_N2_MXEMB peaks",
- "description" : "Peak calls for Dosage Compensation ChIP-chip arrays, DPY27_N2_MXEMB w peaks"
- },
- {
- "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Dosage Compensation ChIP-chip arrays, DPY28_N2_MXEMB",
- "type" : "QuantitativeTrack",
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00012_DPY28_N2_MXemb_mean_WS220.bw"
},
"type" : "BigWigAdapter"
- },
+ }
+ },
+ {
"displays" : [
{
"type" : "LinearWiggleDisplay",
- "maxScore" : 3.80655574788404,
- "minScore" : 1.22266339680173,
- "displayId" : "Dosage Compensation ChIP-chip arrays_ DPY28_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "maxScore" : 4.16803452497911,
+ "minScore" : 1.37545139324311,
+ "displayId" : "Dosage Compensation ChIP-chip arrays_ DPY27_N2_L4_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ DPY28_N2_MXEMB",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Transcription and Chromatin"
- ]
- },
- {
- "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Dosage Compensation ChIP-chip arrays, DPY27_N2_L4",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00001_DPY27_N2_L4_mean_WS220.bw",
- "locationType" : "UriLocation"
- }
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00001_DPY27_N2_L4_mean_WS220.bw"
+ },
+ "type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "displays" : [
- {
- "displayId" : "Dosage Compensation ChIP-chip arrays_ DPY27_N2_L4_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "maxScore" : 4.16803452497911,
- "type" : "LinearWiggleDisplay",
- "minScore" : 1.37545139324311
- }
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ DPY27_N2_L4",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -13978,18 +13365,28 @@
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
+ ],
+ "type" : "QuantitativeTrack",
+ "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ DPY27_N2_L4",
+ "name" : "Dosage Compensation ChIP-chip arrays, DPY27_N2_L4"
},
{
"displays" : [
{
- "minScore" : 1.41396970644281,
"type" : "LinearWiggleDisplay",
"maxScore" : 4.28475668619034,
- "displayId" : "Dosage Compensation ChIP-chip arrays_ DPY27_YPT41_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "displayId" : "Dosage Compensation ChIP-chip arrays_ DPY27_YPT41_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 1.41396970644281
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ DPY27_YPT41_MXEMB",
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00001_DPY27_YPT41_MXemb_mean_WS220.bw",
+ "locationType" : "UriLocation"
+ }
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -13998,112 +13395,104 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Dosage Compensation ChIP-chip arrays, DPY27_YPT41_MXEMB",
"type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00001_DPY27_YPT41_MXemb_mean_WS220.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- }
+ "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ DPY27_YPT41_MXEMB",
+ "name" : "Dosage Compensation ChIP-chip arrays, DPY27_YPT41_MXEMB"
},
{
- "name" : "Dosage Compensation ChIP-chip arrays, SDC3_N2_MXEMB w peaks",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00002_SDC3_N2_MXemb_mean.wig_mean_WS220.bw"
- },
- "type" : "BigWigAdapter"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00002_SDC3_N2_MXemb_mean.wig_mean_WS220.bw",
+ "locationType" : "UriLocation"
+ }
},
- "type" : "QuantitativeTrack",
- "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ SDC3_N2_MXEMB w peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Transcription and Chromatin"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
+ "displayId" : "Dosage Compensation ChIP-chip arrays_ SDC3_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
"maxScore" : 1.60896239264551,
- "displayId" : "Dosage Compensation ChIP-chip arrays_ SDC3_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
+ ],
+ "name" : "Dosage Compensation ChIP-chip arrays, SDC3_N2_MXEMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ SDC3_N2_MXEMB w peaks",
+ "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Transcription and Chromatin"
]
},
{
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "Dosage Compensation ChIP-chip arrays_ SDC3_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
+ "renderer" : {
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ }
+ }
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4496_details.gff.bb"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4496_details.gff.bb",
+ "locationType" : "UriLocation"
}
},
- "name" : "__Dosage Compensation ChIP-chip arrays, SDC3_N2_MXEMB peaks",
- "description" : "Peak calls for Dosage Compensation ChIP-chip arrays, SDC3_N2_MXEMB w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ SDC3_N2_MXEMB w peaks_bigbed_peaks",
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "displayId" : "Dosage Compensation ChIP-chip arrays_ SDC3_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks"
- }
- ]
+ "name" : "__Dosage Compensation ChIP-chip arrays, SDC3_N2_MXEMB peaks",
+ "description" : "Peak calls for Dosage Compensation ChIP-chip arrays, SDC3_N2_MXEMB w peaks"
},
{
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00004_MIX1_N2_MXemb_mean_WS220.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "minScore" : 0,
- "maxScore" : 3.58503263665519,
"type" : "LinearWiggleDisplay",
- "displayId" : "Dosage Compensation ChIP-chip arrays_ MIX1_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "minScore" : 0,
+ "displayId" : "Dosage Compensation ChIP-chip arrays_ MIX1_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 3.58503263665519
}
],
+ "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Dosage Compensation ChIP-chip arrays, MIX1_N2_MXEMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ MIX1_N2_MXEMB w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ MIX1_N2_MXEMB w peaks",
- "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00004_MIX1_N2_MXemb_mean_WS220.bw"
- },
- "type" : "BigWigAdapter"
- },
- "name" : "Dosage Compensation ChIP-chip arrays, MIX1_N2_MXEMB w peaks"
+ ]
},
{
- "description" : "Peak calls for Dosage Compensation ChIP-chip arrays, MIX1_N2_MXEMB w peaks",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
@@ -14111,90 +13500,91 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/1363_details.gff.bb"
}
},
- "name" : "__Dosage Compensation ChIP-chip arrays, MIX1_N2_MXEMB peaks",
"displays" : [
{
- "displayId" : "Dosage Compensation ChIP-chip arrays_ MIX1_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
"type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
- }
+ "showDescriptions" : false,
+ "height" : 6,
+ "color1" : "deeppink"
+ },
+ "displayId" : "Dosage Compensation ChIP-chip arrays_ MIX1_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks"
}
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ MIX1_N2_MXEMB w peaks_bigbed_peaks",
+ "name" : "__Dosage Compensation ChIP-chip arrays, MIX1_N2_MXEMB peaks",
+ "description" : "Peak calls for Dosage Compensation ChIP-chip arrays, MIX1_N2_MXEMB w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ MIX1_N2_MXEMB w peaks_bigbed_peaks"
+ ]
},
{
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00002_SDC3_N2_MXEMB_1_A_WS220.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
"name" : "Dosage Compensation ChIP-chip arrays, SDC3_N2_MXEMB_1_A",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ SDC3_N2_MXEMB_1_A",
"description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ SDC3_N2_MXEMB_1_A",
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00002_SDC3_N2_MXEMB_1_A_WS220.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "displayId" : "Dosage Compensation ChIP-chip arrays_ SDC3_N2_MXEMB_1_A_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "minScore" : 1.41907426523731,
+ "type" : "LinearWiggleDisplay",
"maxScore" : 4.30022504617366,
- "type" : "LinearWiggleDisplay"
+ "displayId" : "Dosage Compensation ChIP-chip arrays_ SDC3_N2_MXEMB_1_A_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 1.41907426523731
}
]
},
{
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "maxScore" : 4.92,
+ "displayId" : "Dosage Compensation ChIP-chip arrays_ DPY27_N2_MXEMB_1_A_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 1.65001628098527,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00001_DPY27_N2_MXEMB_1_A_WS220.bw"
- },
- "type" : "BigWigAdapter"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00001_DPY27_N2_MXEMB_1_A_WS220.bw",
+ "locationType" : "UriLocation"
+ }
},
- "name" : "Dosage Compensation ChIP-chip arrays, DPY27_N2_MXEMB_1_A",
- "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ DPY27_N2_MXEMB_1_A",
- "displays" : [
- {
- "displayId" : "Dosage Compensation ChIP-chip arrays_ DPY27_N2_MXEMB_1_A_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "minScore" : 1.65001628098527,
- "maxScore" : 4.92,
- "type" : "LinearWiggleDisplay"
- }
- ]
+ "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Dosage Compensation ChIP-chip arrays, DPY27_N2_MXEMB_1_A",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ DPY27_N2_MXEMB_1_A"
},
{
- "name" : "Dosage Compensation ChIP-chip arrays w peaks",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -14202,30 +13592,40 @@
"locationType" : "UriLocation"
}
},
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "minScore" : 0,
+ "displayId" : "Dosage Compensation ChIP-chip arrays w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 4.2800903446134,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "Dosage Compensation ChIP-chip arrays w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "displays" : [
- {
- "minScore" : 0,
- "maxScore" : 4.2800903446134,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Dosage Compensation ChIP-chip arrays w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
- }
- ]
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack"
},
{
"description" : "Peak calls for Dosage Compensation ChIP-chip arrays w peaks",
"name" : "__Dosage Compensation ChIP-chip arrays peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays w peaks_bigbed_peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Transcription and Chromatin"
+ ],
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
@@ -14235,37 +13635,35 @@
},
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "Dosage Compensation ChIP-chip arrays w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
"color1" : "deeppink",
"showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false,
"type" : "SvgFeatureRenderer"
},
- "displayId" : "Dosage Compensation ChIP-chip arrays w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays w peaks_bigbed_peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Transcription and Chromatin"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
]
},
{
"displays" : [
{
- "minScore" : 0.885668532256687,
- "maxScore" : 2.68384403714148,
"type" : "LinearWiggleDisplay",
- "displayId" : "Dosage Compensation ChIP-chip arrays_ SDQ314_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "minScore" : 0.885668532256687,
+ "displayId" : "Dosage Compensation ChIP-chip arrays_ SDQ314_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 2.68384403714148
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ SDQ314",
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SDQ314mean_WS220.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -14274,66 +13672,52 @@
"Transcription Factors",
"Transcription and Chromatin"
],
- "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"name" : "Dosage Compensation ChIP-chip arrays, SDQ314",
- "type" : "QuantitativeTrack",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ SDQ314",
+ "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ },
+ {
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SDQ314mean_WS220.bw"
- }
- }
- },
- {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00005_SDC2_N2_MXemb_mean_WS220.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "minScore" : 0.988611769595302,
"type" : "LinearWiggleDisplay",
"maxScore" : 2.99579324119788,
- "displayId" : "Dosage Compensation ChIP-chip arrays_ JL00005_SDC2_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "displayId" : "Dosage Compensation ChIP-chip arrays_ JL00005_SDC2_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 0.988611769595302
}
],
+ "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Dosage Compensation ChIP-chip arrays, JL00005_SDC2_N2_MXEMB",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ JL00005_SDC2_N2_MXEMB",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ JL00005_SDC2_N2_MXEMB",
- "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00005_SDC2_N2_MXemb_mean_WS220.bw"
- },
- "type" : "BigWigAdapter"
- },
- "name" : "Dosage Compensation ChIP-chip arrays, JL00005_SDC2_N2_MXEMB"
+ ]
},
{
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ SDQ3146_SDC2_N2_MXEMB",
+ "name" : "Dosage Compensation ChIP-chip arrays, SDQ3146_SDC2_N2_MXEMB",
+ "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "displays" : [
- {
- "displayId" : "Dosage Compensation ChIP-chip arrays_ SDQ3146_SDC2_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 2.68384403714148,
- "minScore" : 0.885668532256687
- }
- ],
- "name" : "Dosage Compensation ChIP-chip arrays, SDQ3146_SDC2_N2_MXEMB",
- "type" : "QuantitativeTrack",
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
@@ -14341,18 +13725,32 @@
},
"type" : "BigWigAdapter"
},
- "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "minScore" : 0.885668532256687,
+ "displayId" : "Dosage Compensation ChIP-chip arrays_ SDQ3146_SDC2_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 2.68384403714148
+ }
+ ]
},
{
"displays" : [
{
- "displayId" : "Dosage Compensation ChIP-chip arrays_ SDC3_N2_MXEMB_1_B_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay",
- "maxScore" : 3.79329182479829,
- "minScore" : 1.25178630218344
+ "displayId" : "Dosage Compensation ChIP-chip arrays_ SDC3_N2_MXEMB_1_B_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 1.25178630218344,
+ "maxScore" : 3.79329182479829
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ SDC3_N2_MXEMB_1_B",
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00002_SDC3_N2_MXEMB_1_B_WS220.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -14361,35 +13759,11 @@
"Transcription Factors",
"Transcription and Chromatin"
],
- "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"name" : "Dosage Compensation ChIP-chip arrays, SDC3_N2_MXEMB_1_B",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00002_SDC3_N2_MXEMB_1_B_WS220.bw"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack"
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ SDC3_N2_MXEMB_1_B",
+ "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Transcription and Chromatin"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ DPY27_11dh_MXEMB",
- "displays" : [
- {
- "displayId" : "Dosage Compensation ChIP-chip arrays_ DPY27_11dh_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "minScore" : 1.43411596826223,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 4.34580596443101
- }
- ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -14397,19 +13771,18 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00001_DPY27_11dh_MXemb_mean_WS220.bw"
}
},
- "type" : "QuantitativeTrack",
- "name" : "Dosage Compensation ChIP-chip arrays, DPY27_11dh_MXEMB",
- "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
"displays" : [
{
- "minScore" : 1.63536977973214,
- "maxScore" : 4.15,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Dosage Compensation ChIP-chip arrays_ IGG_N2_EEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "maxScore" : 4.34580596443101,
+ "minScore" : 1.43411596826223,
+ "displayId" : "Dosage Compensation ChIP-chip arrays_ DPY27_11dh_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
],
+ "name" : "Dosage Compensation ChIP-chip arrays, DPY27_11dh_MXEMB",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ DPY27_11dh_MXEMB",
+ "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -14417,21 +13790,13 @@
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
- ],
+ ]
+ },
+ {
+ "name" : "Dosage Compensation ChIP-chip arrays, IGG_N2_EEMB",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ IGG_N2_EEMB",
"description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SS00050_IGG_N2_EEMB_mean_WS220.bw"
- }
- },
- "name" : "Dosage Compensation ChIP-chip arrays, IGG_N2_EEMB"
- },
- {
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ DPY26_N2_MXEMB w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -14440,28 +13805,64 @@
"Transcription Factors",
"Transcription and Chromatin"
],
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SS00050_IGG_N2_EEMB_mean_WS220.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "maxScore" : 3.93950007467915,
"type" : "LinearWiggleDisplay",
- "minScore" : 0,
- "displayId" : "Dosage Compensation ChIP-chip arrays_ DPY26_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "maxScore" : 4.15,
+ "displayId" : "Dosage Compensation ChIP-chip arrays_ IGG_N2_EEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 1.63536977973214
}
- ],
+ ]
+ },
+ {
+ "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"name" : "Dosage Compensation ChIP-chip arrays, DPY26_N2_MXEMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ DPY26_N2_MXEMB w peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Transcription and Chromatin"
+ ],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/JL00003_DPY26_N2_MXemb_mean_WS220.bw"
- },
- "type" : "BigWigAdapter"
+ }
},
- "type" : "QuantitativeTrack",
- "description" : "Dosage Compensation and Chromosome Organization. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with antibodies that recognize the dosage compensation and condensin proteins. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "displays" : [
+ {
+ "displayId" : "Dosage Compensation ChIP-chip arrays_ DPY26_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 3.93950007467915,
+ "type" : "LinearWiggleDisplay"
+ }
+ ]
},
{
"description" : "Peak calls for Dosage Compensation ChIP-chip arrays, DPY26_N2_MXEMB w peaks",
+ "name" : "__Dosage Compensation ChIP-chip arrays, DPY26_N2_MXEMB peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ DPY26_N2_MXEMB w peaks_bigbed_peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Transcription and Chromatin"
+ ],
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
@@ -14469,83 +13870,63 @@
"locationType" : "UriLocation"
}
},
- "name" : "__Dosage Compensation ChIP-chip arrays, DPY26_N2_MXEMB peaks",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
"color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false
},
- "type" : "LinearBasicDisplay",
"displayId" : "Dosage Compensation ChIP-chip arrays_ DPY26_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks"
}
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Transcription and Chromatin"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-chip arrays_ DPY26_N2_MXEMB w peaks_bigbed_peaks"
+ ]
},
{
"displays" : [
{
- "minScore" : 0,
"type" : "LinearWiggleDisplay",
"maxScore" : 3.74,
- "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ UP07448_H3K27ME124439_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ UP07448_H3K27ME124439_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 0
}
],
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/UP07448_H3K27ME124439_N2_L3_mean.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "Histone Modifications (H3K27) ChIP-chip arrays, UP07448_H3K27ME124439_N2_L3 w peaks",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-chip arrays_ UP07448_H3K27ME124439_N2_L3 w peaks",
- "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/UP07448_H3K27ME124439_N2_L3_mean.bw"
- },
- "type" : "BigWigAdapter"
- },
- "name" : "Histone Modifications (H3K27) ChIP-chip arrays, UP07448_H3K27ME124439_N2_L3 w peaks"
+ "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "color1" : "deeppink",
"height" : 6,
"showDescriptions" : false,
- "color1" : "deeppink",
"showLabels" : false,
"type" : "SvgFeatureRenderer"
},
- "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ UP07448_H3K27ME124439_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
+ "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ UP07448_H3K27ME124439_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-chip arrays_ UP07448_H3K27ME124439_N2_L3 w peaks_bigbed_peaks",
- "description" : "Peak calls for Histone Modifications (H3K27) ChIP-chip arrays, UP07448_H3K27ME124439_N2_L3 w peaks",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
@@ -14553,12 +13934,20 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7932_details.gff.bb"
}
},
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
"type" : "FeatureTrack",
- "name" : "__Histone Modifications (H3K27) ChIP-chip arrays, UP07448_H3K27ME124439_N2_L3 peaks"
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Peak calls for Histone Modifications (H3K27) ChIP-chip arrays, UP07448_H3K27ME124439_N2_L3 w peaks",
+ "name" : "__Histone Modifications (H3K27) ChIP-chip arrays, UP07448_H3K27ME124439_N2_L3 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-chip arrays_ UP07448_H3K27ME124439_N2_L3 w peaks_bigbed_peaks"
},
{
- "name" : "Histone Modifications (H3K27) ChIP-chip arrays, TJ00001_H3K27ME18835_N2_EEMB w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -14566,8 +13955,17 @@
"locationType" : "UriLocation"
}
},
+ "displays" : [
+ {
+ "maxScore" : 4.037691,
+ "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ TJ00001_H3K27ME18835_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-chip arrays_ TJ00001_H3K27ME18835_N2_EEMB w peaks",
+ "name" : "Histone Modifications (H3K27) ChIP-chip arrays, TJ00001_H3K27ME18835_N2_EEMB w peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -14576,61 +13974,59 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack"
+ },
+ {
"displays" : [
{
- "minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 4.037691,
- "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ TJ00001_H3K27ME18835_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "type" : "LinearBasicDisplay",
+ "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ TJ00001_H3K27ME18835_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
+ "renderer" : {
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ }
}
- ]
- },
- {
- "name" : "__Histone Modifications (H3K27) ChIP-chip arrays, TJ00001_H3K27ME18835_N2_EEMB peaks",
+ ],
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9349_details.gff.bb"
- }
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9349_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "description" : "Peak calls for Histone Modifications (H3K27) ChIP-chip arrays, TJ00001_H3K27ME18835_N2_EEMB w peaks",
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-chip arrays_ TJ00001_H3K27ME18835_N2_EEMB w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Peak calls for Histone Modifications (H3K27) ChIP-chip arrays, TJ00001_H3K27ME18835_N2_EEMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-chip arrays_ TJ00001_H3K27ME18835_N2_EEMB w peaks_bigbed_peaks",
+ "name" : "__Histone Modifications (H3K27) ChIP-chip arrays, TJ00001_H3K27ME18835_N2_EEMB peaks"
+ },
+ {
"displays" : [
{
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
- },
- "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ TJ00001_H3K27ME18835_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
+ "maxScore" : 5.09574210136197,
+ "minScore" : 1.75529489344945,
+ "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ AB4729_H3K27AC361571_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
- ]
- },
- {
- "name" : "Histone Modifications (H3K27) ChIP-chip arrays, AB4729_H3K27AC361571_N2_L3",
+ ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB4729_H3K27AC361571_N2_L3_mean_WS220.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB4729_H3K27AC361571_N2_L3_mean_WS220.bw"
+ }
},
"type" : "QuantitativeTrack",
- "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-chip arrays_ AB4729_H3K27AC361571_N2_L3",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -14639,189 +14035,177 @@
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "displays" : [
- {
- "type" : "LinearWiggleDisplay",
- "maxScore" : 5.09574210136197,
- "minScore" : 1.75529489344945,
- "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ AB4729_H3K27AC361571_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
- }
- ]
+ "name" : "Histone Modifications (H3K27) ChIP-chip arrays, AB4729_H3K27AC361571_N2_L3",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-chip arrays_ AB4729_H3K27AC361571_N2_L3",
+ "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "Histone Modifications (H3K27) ChIP-chip arrays, HK00013_H3K27ME31E7_N2_EEMB w peaks",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-chip arrays_ HK00013_H3K27ME31E7_N2_EEMB w peaks",
+ "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ HK00013_H3K27ME31E7_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "minScore" : 0,
"type" : "LinearWiggleDisplay",
+ "minScore" : 0,
+ "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ HK00013_H3K27ME31E7_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"maxScore" : 2.45
}
],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00013_H3K27ME31E7_N2_EEMB_mean.bw"
- }
- },
- "type" : "QuantitativeTrack",
- "name" : "Histone Modifications (H3K27) ChIP-chip arrays, HK00013_H3K27ME31E7_N2_EEMB w peaks",
- "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
- "description" : "Peak calls for Histone Modifications (H3K27) ChIP-chip arrays, HK00013_H3K27ME31E7_N2_EEMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-chip arrays_ HK00013_H3K27ME31E7_N2_EEMB w peaks_bigbed_peaks",
"name" : "__Histone Modifications (H3K27) ChIP-chip arrays, HK00013_H3K27ME31E7_N2_EEMB peaks",
+ "description" : "Peak calls for Histone Modifications (H3K27) ChIP-chip arrays, HK00013_H3K27ME31E7_N2_EEMB w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7828_details.gff.bb"
- }
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
+ "color1" : "deeppink",
"height" : 6,
- "type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
"showLabels" : false,
- "color1" : "deeppink"
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ HK00013_H3K27ME31E7_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-chip arrays_ HK00013_H3K27ME31E7_N2_EEMB w peaks_bigbed_peaks",
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
]
},
{
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/WA30634849_H3K27AC_N2_EEMB_mean.bw",
+ "locationType" : "UriLocation"
+ }
+ },
+ "displays" : [
+ {
+ "maxScore" : 4.33,
+ "minScore" : 0,
+ "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ WA30634849_H3K27AC_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-chip arrays_ WA30634849_H3K27AC_N2_EEMB w peaks",
+ "name" : "Histone Modifications (H3K27) ChIP-chip arrays, WA30634849_H3K27AC_N2_EEMB w peaks",
+ "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-chip arrays_ WA30634849_H3K27AC_N2_EEMB w peaks",
- "displays" : [
- {
- "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ WA30634849_H3K27AC_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 4.33
- }
- ],
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/WA30634849_H3K27AC_N2_EEMB_mean.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "name" : "Histone Modifications (H3K27) ChIP-chip arrays, WA30634849_H3K27AC_N2_EEMB w peaks",
- "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ ]
},
{
- "name" : "__Histone Modifications (H3K27) ChIP-chip arrays, WA30634849_H3K27AC_N2_EEMB peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8677_details.gff.bb"
- }
- },
"description" : "Peak calls for Histone Modifications (H3K27) ChIP-chip arrays, WA30634849_H3K27AC_N2_EEMB w peaks",
+ "name" : "__Histone Modifications (H3K27) ChIP-chip arrays, WA30634849_H3K27AC_N2_EEMB peaks",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-chip arrays_ WA30634849_H3K27AC_N2_EEMB w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8677_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
- "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ WA30634849_H3K27AC_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
+ "type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
"height" : 6,
- "showDescriptions" : false
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ WA30634849_H3K27AC_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
}
]
},
{
- "name" : "Histone Modifications (H3K27) ChIP-chip arrays, AB4729_H3K27AC361571_N2_EEMB",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB4729_H3K27AC361571_N2_EEMB_WS220.bw",
- "locationType" : "UriLocation"
- }
- },
"description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications (H3K27) ChIP-chip arrays, AB4729_H3K27AC361571_N2_EEMB",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-chip arrays_ AB4729_H3K27AC361571_N2_EEMB",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB4729_H3K27AC361571_N2_EEMB_WS220.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ AB4729_H3K27AC361571_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay",
"maxScore" : 4.69172796844374,
- "minScore" : 1.68897022958643
+ "minScore" : 1.68897022958643,
+ "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ AB4729_H3K27AC361571_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
}
]
},
{
- "displays" : [
- {
- "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ UP07448_H3K27ME124439_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "maxScore" : 4.31,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
- }
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-chip arrays_ UP07448_H3K27ME124439_N2_EEMB w peaks",
+ "name" : "Histone Modifications (H3K27) ChIP-chip arrays, UP07448_H3K27ME124439_N2_EEMB w peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-chip arrays_ UP07448_H3K27ME124439_N2_EEMB w peaks",
- "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
"adapter" : {
"bigWigLocation" : {
@@ -14830,119 +14214,137 @@
},
"type" : "BigWigAdapter"
},
- "name" : "Histone Modifications (H3K27) ChIP-chip arrays, UP07448_H3K27ME124439_N2_EEMB w peaks"
- },
- {
"displays" : [
{
- "renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ UP07448_H3K27ME124439_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
+ "maxScore" : 4.31,
+ "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ UP07448_H3K27ME124439_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
}
- ],
+ ]
+ },
+ {
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-chip arrays_ UP07448_H3K27ME124439_N2_EEMB w peaks_bigbed_peaks",
+ "name" : "__Histone Modifications (H3K27) ChIP-chip arrays, UP07448_H3K27ME124439_N2_EEMB peaks",
+ "description" : "Peak calls for Histone Modifications (H3K27) ChIP-chip arrays, UP07448_H3K27ME124439_N2_EEMB w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "description" : "Peak calls for Histone Modifications (H3K27) ChIP-chip arrays, UP07448_H3K27ME124439_N2_EEMB w peaks",
- "name" : "__Histone Modifications (H3K27) ChIP-chip arrays, UP07448_H3K27ME124439_N2_EEMB peaks",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7934_details.gff.bb",
"locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- }
+ }
+ },
+ "displays" : [
+ {
+ "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ UP07448_H3K27ME124439_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
+ "renderer" : {
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00013_H3K27ME31E7_N2_L3_mean_WS220.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00013_H3K27ME31E7_N2_L3_mean_WS220.bw"
}
},
- "name" : "Histone Modifications (H3K27) ChIP-chip arrays, H3K27ME31E7_N2_L3",
- "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-chip arrays_ H3K27ME31E7_N2_L3",
"displays" : [
{
- "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ H3K27ME31E7_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
"maxScore" : 4.07737736138774,
- "minScore" : 1.29193452925795
+ "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ H3K27ME31E7_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 1.29193452925795,
+ "type" : "LinearWiggleDisplay"
}
- ]
- },
- {
+ ],
+ "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-chip arrays_ H3K27ME31E7_N2_L3",
+ "name" : "Histone Modifications (H3K27) ChIP-chip arrays, H3K27ME31E7_N2_L3",
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack"
+ },
+ {
+ "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-chip arrays_ WA30634849_H3K27AC_N2_L3",
+ "name" : "Histone Modifications (H3K27) ChIP-chip arrays, WA30634849_H3K27AC_N2_L3",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K27) ChIP-chip arrays_ WA30634849_H3K27AC_N2_L3",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/WA30634849_H3K27AC_N2_L3_mean_WS220.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "minScore" : 1.41889911573776,
"type" : "LinearWiggleDisplay",
"maxScore" : 4.11696701738715,
- "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ WA30634849_H3K27AC_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "displayId" : "Histone Modifications (H3K27) ChIP-chip arrays_ WA30634849_H3K27AC_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 1.41889911573776
+ }
+ ]
+ },
+ {
+ "displays" : [
+ {
+ "maxScore" : 4.14,
+ "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ H3K36ME22C3_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 2.06981113558344,
+ "type" : "LinearWiggleDisplay"
}
],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/WA30634849_H3K27AC_N2_L3_mean_WS220.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00012_H3K36ME22C3_N2_EEMB_mean_WS220.bw",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigWigAdapter"
},
"type" : "QuantitativeTrack",
- "name" : "Histone Modifications (H3K27) ChIP-chip arrays, WA30634849_H3K27AC_N2_L3",
- "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
+ "name" : "Histone Modifications (H3K36) ChIP-chip arrays, H3K36ME22C3_N2_EEMB",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ H3K36ME22C3_N2_EEMB",
+ "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00012_H3K36ME22C3_N2_EEMB_mean_WS220.bw"
- }
- },
- "name" : "Histone Modifications (H3K36) ChIP-chip arrays, H3K36ME22C3_N2_EEMB",
- "displays" : [
- {
- "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ H3K36ME22C3_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "maxScore" : 4.14,
- "type" : "LinearWiggleDisplay",
- "minScore" : 2.06981113558344
- }
- ],
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -14951,48 +14353,31 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ H3K36ME22C3_N2_EEMB"
- },
- {
+ "type" : "QuantitativeTrack",
"description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ AB9048_H3K36ME1206009_N2_EEMB",
"name" : "Histone Modifications (H3K36) ChIP-chip arrays, AB9048_H3K36ME1206009_N2_EEMB",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB9048_H3K36ME1206009_N2_EEMB_mean_WS220.bw"
- }
- },
"displays" : [
{
- "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ AB9048_H3K36ME1206009_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "minScore" : 1.12362532972286,
"maxScore" : 3.30341009006927,
+ "minScore" : 1.12362532972286,
+ "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ AB9048_H3K36ME1206009_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ AB9048_H3K36ME1206009_N2_EEMB",
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ]
- },
- {
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00001_H3K36ME3_13C9_N2_YA_1_OID30311_MA2Cscore.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB9048_H3K36ME1206009_N2_EEMB_mean_WS220.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
+ }
+ },
+ {
"name" : "Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_YA_s7 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_YA_s7 w peaks",
"description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -15001,125 +14386,138 @@
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_YA_s7 w peaks",
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00001_H3K36ME3_13C9_N2_YA_1_OID30311_MA2Cscore.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
+ "maxScore" : 3.527688,
"displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_YA_s7 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"minScore" : 0,
- "maxScore" : 3.527688,
"type" : "LinearWiggleDisplay"
}
]
},
{
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_YA_s7 w peaks_bigbed_peaks",
+ "name" : "__Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_YA_s7 peaks",
+ "description" : "Peak calls for Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_YA_s7 w peaks",
"displays" : [
{
- "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_YA_s7 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
+ "showLabels" : false,
"showDescriptions" : false,
- "height" : 6
- }
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_YA_s7 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8659_details.gff.bb",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8659_details.gff.bb"
}
- },
- "name" : "__Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_YA_s7 peaks",
- "description" : "Peak calls for Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_YA_s7 w peaks"
+ }
},
{
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_LTEMB w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00001_H3K36ME3_13C9_N2_LTEMB_1_OID30311_MA2Cscore.bw",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "minScore" : 0,
"maxScore" : 3.815772,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_LTEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_LTEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
}
],
"name" : "Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_LTEMB w peaks",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00001_H3K36ME3_13C9_N2_LTEMB_1_OID30311_MA2Cscore.bw"
- }
- },
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_LTEMB w peaks",
+ "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"type" : "QuantitativeTrack",
- "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_LTEMB w peaks_bigbed_peaks",
+ ]
+ },
+ {
"displays" : [
{
- "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_LTEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"type" : "LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
+ "showLabels" : false,
"showDescriptions" : false,
- "height" : 6
- }
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_LTEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
}
],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8629_details.gff.bb",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8629_details.gff.bb"
}
},
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
"name" : "__Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_LTEMB peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_LTEMB w peaks_bigbed_peaks",
"description" : "Peak calls for Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_LTEMB w peaks"
},
{
- "name" : "Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_L4 w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00001_H3K36ME3_13C9_N2_L4_1_OID30311_MA2Cscore.bw"
- }
+ },
+ "type" : "BigWigAdapter"
},
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "minScore" : 0,
+ "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L4 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "maxScore" : 3.468124
+ }
+ ],
"description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L4 w peaks",
+ "name" : "Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_L4 w peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -15128,39 +14526,30 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "displays" : [
- {
- "type" : "LinearWiggleDisplay",
- "maxScore" : 3.468124,
- "minScore" : 0,
- "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L4 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
- }
- ]
+ "type" : "QuantitativeTrack"
},
{
- "description" : "Peak calls for Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_L4 w peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8658_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "__Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_L4 peaks",
"displays" : [
{
- "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L4 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink",
"showDescriptions" : false,
- "height" : 6
+ "height" : 6,
+ "showLabels" : false,
+ "color1" : "deeppink"
},
+ "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L4 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"type" : "LinearBasicDisplay"
}
],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8658_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -15169,20 +14558,26 @@
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L4 w peaks_bigbed_peaks"
+ "name" : "__Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_L4 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L4 w peaks_bigbed_peaks",
+ "description" : "Peak calls for Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_L4 w peaks"
},
{
- "name" : "Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_L1 w peaks",
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "minScore" : 0,
+ "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L1 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "maxScore" : 3.399566,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00001_H3K36ME3_13C9_N2_L1_1_OID30311_MA2Cscore.bw"
- },
- "type" : "BigWigAdapter"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00001_H3K36ME3_13C9_N2_L1_1_OID30311_MA2Cscore.bw",
+ "locationType" : "UriLocation"
+ }
},
- "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L1 w peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -15191,60 +14586,36 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "displays" : [
- {
- "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L1 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "maxScore" : 3.399566,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
- }
- ]
+ "type" : "QuantitativeTrack",
+ "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L1 w peaks",
+ "name" : "Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_L1 w peaks"
},
{
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8652_details.gff.bb"
+ }
+ },
"displays" : [
{
- "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L1 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
+ "showLabels" : false,
"showDescriptions" : false,
+ "height" : 6,
"color1" : "deeppink",
- "showLabels" : false,
"type" : "SvgFeatureRenderer"
- }
+ },
+ "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L1 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
}
],
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "__Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_L1 peaks",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L1 w peaks_bigbed_peaks",
"description" : "Peak calls for Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_L1 w peaks",
"type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8652_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "__Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_L1 peaks"
- },
- {
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00012_H3K36ME22C3_N2_L3_mean_WS220.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "Histone Modifications (H3K36) ChIP-chip arrays, H3K36ME22C3_N2_L3",
- "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -15252,78 +14623,109 @@
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
+ ]
+ },
+ {
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
+ "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications (H3K36) ChIP-chip arrays, H3K36ME22C3_N2_L3",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ H3K36ME22C3_N2_L3",
"displays" : [
{
- "maxScore" : 3.98,
- "type" : "LinearWiggleDisplay",
"minScore" : 1.40536410531076,
- "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ H3K36ME22C3_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ H3K36ME22C3_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "maxScore" : 3.98,
+ "type" : "LinearWiggleDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00012_H3K36ME22C3_N2_L3_mean_WS220.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ AB9050_H3K36ME3_N2_L3",
+ "name" : "Histone Modifications (H3K36) ChIP-chip arrays, AB9050_H3K36ME3_N2_L3",
+ "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ AB9050_H3K36ME3_N2_L3",
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB9050_H3K36ME3_N2_L3_mean_WS220.bw"
+ }
+ },
"displays" : [
{
- "minScore" : 1.92049187356116,
"type" : "LinearWiggleDisplay",
"maxScore" : 3.73,
+ "minScore" : 1.92049187356116,
"displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ AB9050_H3K36ME3_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
}
- ],
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB9050_H3K36ME3_N2_L3_mean_WS220.bw",
- "locationType" : "UriLocation"
- }
- },
- "name" : "Histone Modifications (H3K36) ChIP-chip arrays, AB9050_H3K36ME3_N2_L3",
- "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ ]
},
{
- "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Histone Modifications (H3K36) ChIP-chip arrays, AM39379_H3K36AC29108001_N2_EEMB w peaks",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/15033.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
"displays" : [
{
- "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ AM39379_H3K36AC29108001_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "maxScore" : 4.323493,
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 4.323493
+ "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ AM39379_H3K36AC29108001_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ AM39379_H3K36AC29108001_N2_EEMB w peaks",
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/15033.bw"
+ }
+ },
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
+ ],
+ "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications (H3K36) ChIP-chip arrays, AM39379_H3K36AC29108001_N2_EEMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ AM39379_H3K36AC29108001_N2_EEMB w peaks"
},
{
- "description" : "Peak calls for Histone Modifications (H3K36) ChIP-chip arrays, AM39379_H3K36AC29108001_N2_EEMB w peaks",
- "name" : "__Histone Modifications (H3K36) ChIP-chip arrays, AM39379_H3K36AC29108001_N2_EEMB peaks",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ AM39379_H3K36AC29108001_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
+ "renderer" : {
+ "showDescriptions" : false,
+ "height" : 6,
+ "showLabels" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ }
+ }
+ ],
"adapter" : {
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/15036_details.gff.bb",
@@ -15331,32 +14733,20 @@
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "displays" : [
- {
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ AM39379_H3K36AC29108001_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
- }
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ AM39379_H3K36AC29108001_N2_EEMB w peaks_bigbed_peaks",
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ]
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ AM39379_H3K36AC29108001_N2_EEMB w peaks_bigbed_peaks",
+ "name" : "__Histone Modifications (H3K36) ChIP-chip arrays, AM39379_H3K36AC29108001_N2_EEMB peaks",
+ "description" : "Peak calls for Histone Modifications (H3K36) ChIP-chip arrays, AM39379_H3K36AC29108001_N2_EEMB w peaks"
},
{
- "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"adapter" : {
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00001_H3K36ME313C9_N2_EEMB_mean_WS220.bw",
@@ -15364,57 +14754,65 @@
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "name" : "Histone Modifications (H3K36) ChIP-chip arrays, H3K36ME313C9_N2_EEMB",
"displays" : [
{
- "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ H3K36ME313C9_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "maxScore" : 4.03,
"type" : "LinearWiggleDisplay",
- "minScore" : 2.0557441218973
+ "minScore" : 2.0557441218973,
+ "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ H3K36ME313C9_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "maxScore" : 4.03
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications (H3K36) ChIP-chip arrays, H3K36ME313C9_N2_EEMB",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ H3K36ME313C9_N2_EEMB",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ H3K36ME313C9_N2_EEMB"
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ]
},
{
- "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00001_H3K36ME313C9_N2_L3_mean_WS220.bw",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "name" : "Histone Modifications (H3K36) ChIP-chip arrays, H3K36ME313C9_N2_L3",
"displays" : [
{
+ "minScore" : 1.5229639264305,
"displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ H3K36ME313C9_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
"maxScore" : 4.06686038312273,
- "minScore" : 1.5229639264305
+ "type" : "LinearWiggleDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications (H3K36) ChIP-chip arrays, H3K36ME313C9_N2_L3",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ H3K36ME313C9_N2_L3",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ H3K36ME313C9_N2_L3"
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ]
},
{
- "name" : "Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_L2 w peaks",
+ "displays" : [
+ {
+ "maxScore" : 3.488541,
+ "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L2 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00001_H3K36ME3_13C9_N2_L2_1_OID30311_MA2Cscore.bw",
@@ -15422,247 +14820,238 @@
},
"type" : "BigWigAdapter"
},
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
"description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L2 w peaks",
+ "name" : "Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_L2 w peaks"
+ },
+ {
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L2 w peaks_bigbed_peaks",
+ "name" : "__Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_L2 peaks",
+ "description" : "Peak calls for Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_L2 w peaks",
"displays" : [
{
- "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L2 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "minScore" : 0,
- "maxScore" : 3.488541,
- "type" : "LinearWiggleDisplay"
- }
- ]
- },
- {
- "displays" : [
- {
+ "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L2 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
+ "color1" : "deeppink",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
+ "height" : 6,
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L2 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L2 w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
- "description" : "Peak calls for Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_L2 w peaks",
- "name" : "__Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_L2 peaks",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8630_details.gff.bb"
- },
- "type" : "BigBedAdapter"
+ }
}
},
{
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L3 w peaks",
"displays" : [
{
- "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay",
"maxScore" : 3.538532,
- "minScore" : 0
+ "minScore" : 0,
+ "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
}
],
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00001_H3K36ME3_13C9_N2_L3_1_OID30311_MA2Cscore.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00001_H3K36ME3_13C9_N2_L3_1_OID30311_MA2Cscore.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
- "name" : "Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_L3 w peaks",
- "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L3 w peaks",
+ "name" : "Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_L3 w peaks"
},
{
"displays" : [
{
- "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
"height" : 6,
- "showDescriptions" : false
- }
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8651_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L3 w peaks_bigbed_peaks",
- "description" : "Peak calls for Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_L3 w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8651_details.gff.bb",
- "locationType" : "UriLocation"
- }
- },
+ "description" : "Peak calls for Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_L3 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_L3 w peaks_bigbed_peaks",
"name" : "__Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_L3 peaks"
},
{
- "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB9049_H3K36ME2608457_N2_EEMB_WS220.bw"
- },
- "type" : "BigWigAdapter"
- },
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
+ "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ H3K36ME2608457_N2_EEMB",
"name" : "Histone Modifications (H3K36) ChIP-chip arrays, H3K36ME2608457_N2_EEMB",
"displays" : [
{
- "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ H3K36ME2608457_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "minScore" : 2.72308286320489,
"maxScore" : 5.18,
+ "minScore" : 2.72308286320489,
+ "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ H3K36ME2608457_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ H3K36ME2608457_N2_EEMB"
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB9049_H3K36ME2608457_N2_EEMB_WS220.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
"displays" : [
{
- "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ AB9048_H3K36ME1206009_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay",
- "maxScore" : 4.37326288267427,
- "minScore" : 0
+ "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ AB9048_H3K36ME1206009_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 4.37326288267427
}
],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB9048_H3K36ME1206009_N2_L3_mean.bw"
+ }
+ },
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ AB9048_H3K36ME1206009_N2_L3 w peaks",
"description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB9048_H3K36ME1206009_N2_L3_mean.bw"
- },
- "type" : "BigWigAdapter"
- },
- "name" : "Histone Modifications (H3K36) ChIP-chip arrays, AB9048_H3K36ME1206009_N2_L3 w peaks"
+ "name" : "Histone Modifications (H3K36) ChIP-chip arrays, AB9048_H3K36ME1206009_N2_L3 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ AB9048_H3K36ME1206009_N2_L3 w peaks"
},
{
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ AB9048_H3K36ME1206009_N2_L3 w peaks_bigbed_peaks",
+ "name" : "__Histone Modifications (H3K36) ChIP-chip arrays, AB9048_H3K36ME1206009_N2_L3 peaks",
+ "description" : "Peak calls for Histone Modifications (H3K36) ChIP-chip arrays, AB9048_H3K36ME1206009_N2_L3 w peaks",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ AB9048_H3K36ME1206009_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
"color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ AB9048_H3K36ME1206009_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
],
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7766_details.gff.bb",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "__Histone Modifications (H3K36) ChIP-chip arrays, AB9048_H3K36ME1206009_N2_L3 peaks",
- "description" : "Peak calls for Histone Modifications (H3K36) ChIP-chip arrays, AB9048_H3K36ME1206009_N2_L3 w peaks"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7766_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ }
},
{
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/NA_N2_EEMB_mean.wig_mean_WS220.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ NA_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
"maxScore" : 3.97427419798789,
- "minScore" : 1.251210485336
+ "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ NA_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 1.251210485336,
+ "type" : "LinearWiggleDisplay"
}
],
+ "name" : "Histone Modifications (H3K36) ChIP-chip arrays, NA_N2_EEMB",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ NA_N2_EEMB",
+ "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Histone Modifications (H3K36) ChIP-chip arrays, NA_N2_EEMB",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/NA_N2_EEMB_mean.wig_mean_WS220.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack"
+ ]
},
{
- "name" : "Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_EEMB w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -15670,61 +15059,51 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00001_H3K36ME3_13C9_N2_EEMB_1_OID30311_MA2Cscore.bw"
}
},
- "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_EEMB w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
"displays" : [
{
+ "type" : "LinearWiggleDisplay",
"displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"minScore" : 0,
- "maxScore" : 3.83226,
- "type" : "LinearWiggleDisplay"
+ "maxScore" : 3.83226
}
- ]
- },
- {
+ ],
+ "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_EEMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_EEMB w peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_EEMB w peaks_bigbed_peaks",
+ ]
+ },
+ {
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8611_details.gff.bb"
+ }
+ },
"displays" : [
{
- "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"type" : "LinearBasicDisplay",
+ "displayId" : "Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
}
}
],
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8611_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
+ "description" : "Peak calls for Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_EEMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-chip arrays_ HK00001_H3K36ME3_13C9_N2_EEMB w peaks_bigbed_peaks",
"name" : "__Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_EEMB peaks",
- "description" : "Peak calls for Histone Modifications (H3K36) ChIP-chip arrays, HK00001_H3K36ME3_13C9_N2_EEMB w peaks"
- },
- {
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L3 w peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -15733,69 +15112,72 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack"
+ },
+ {
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
+ "name" : "Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_L3 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L3 w peaks",
+ "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
"maxScore" : 4.91734895056465,
- "type" : "LinearWiggleDisplay",
"minScore" : 0,
- "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
],
- "name" : "Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_L3 w peaks",
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/WA30534819_H3K4ME3_N2_L3_1_OID28399_MA2Cscore.bw"
},
"type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
},
{
- "description" : "Peak calls for Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_L3 w peaks",
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8474_details.gff.bb",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8474_details.gff.bb"
},
"type" : "BigBedAdapter"
},
- "name" : "__Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_L3 peaks",
"displays" : [
{
- "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"type" : "LinearBasicDisplay",
+ "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
"type" : "SvgFeatureRenderer",
+ "height" : 6,
+ "showDescriptions" : false,
"showLabels" : false,
"color1" : "deeppink"
}
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "Peak calls for Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_L3 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L3 w peaks_bigbed_peaks",
+ "name" : "__Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_L3 peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L3 w peaks_bigbed_peaks"
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack"
},
{
- "displays" : [
- {
- "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L2 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "minScore" : 0,
- "maxScore" : 5.15096374549998,
- "type" : "LinearWiggleDisplay"
- }
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L2 w peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -15804,70 +15186,77 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L2 w peaks",
"name" : "Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_L2 w peaks",
+ "displays" : [
+ {
+ "maxScore" : 5.15096374549998,
+ "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L2 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/WA30534819_H3K4ME3_N2_L2_1_OID28399_MA2Cscore.bw"
},
"type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack"
+ }
},
{
+ "name" : "__Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_L2 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L2 w peaks_bigbed_peaks",
+ "description" : "Peak calls for Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_L2 w peaks",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L2 w peaks_bigbed_peaks",
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8471_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
+ "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L2 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "deeppink",
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L2 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
- }
- ],
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8471_details.gff.bb",
- "locationType" : "UriLocation"
+ "type" : "LinearBasicDisplay"
}
- },
- "name" : "__Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_L2 peaks",
- "description" : "Peak calls for Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_L2 w peaks"
+ ]
},
{
- "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/WA30534819_H3K4ME3_N2_L1_1_OID28399_MA2Cscore.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_L1 w peaks",
"displays" : [
{
"displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L1 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 0,
"maxScore" : 5.02558483580298,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
+ "type" : "LinearWiggleDisplay"
}
],
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/WA30534819_H3K4ME3_N2_L1_1_OID28399_MA2Cscore.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -15876,10 +15265,11 @@
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L1 w peaks"
+ "name" : "Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_L1 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L1 w peaks",
+ "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L1 w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -15888,33 +15278,44 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "description" : "Peak calls for Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_L1 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L1 w peaks_bigbed_peaks",
+ "name" : "__Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_L1 peaks",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6
},
- "type" : "LinearBasicDisplay",
"displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L1 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
}
],
- "name" : "__Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_L1 peaks",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9056_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Peak calls for Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_L1 w peaks"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9056_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
- "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ AB8895_H3K4ME1733246_N2_EEMB",
"name" : "Histone Modifications (H3K4) ChIP-chip arrays, AB8895_H3K4ME1733246_N2_EEMB",
+ "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -15922,98 +15323,98 @@
"locationType" : "UriLocation"
}
},
- "type" : "QuantitativeTrack",
"displays" : [
{
- "minScore" : 0.850927495993089,
- "maxScore" : 2.49735604846391,
"type" : "LinearWiggleDisplay",
- "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ AB8895_H3K4ME1733246_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ AB8895_H3K4ME1733246_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 0.850927495993089,
+ "maxScore" : 2.49735604846391
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ AB8895_H3K4ME1733246_N2_EEMB",
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
]
},
{
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/WA30834809_H3K4ME2_N2_EEMB_mean_WS220.bw"
+ }
+ },
"displays" : [
{
- "minScore" : 0,
"maxScore" : 4.03,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ H3K4ME2_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ H3K4ME2_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
}
],
+ "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications (H3K4) ChIP-chip arrays, H3K4ME2_N2_EEMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ H3K4ME2_N2_EEMB w peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ H3K4ME2_N2_EEMB w peaks",
- "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/WA30834809_H3K4ME2_N2_EEMB_mean_WS220.bw"
- }
- },
- "name" : "Histone Modifications (H3K4) ChIP-chip arrays, H3K4ME2_N2_EEMB w peaks"
+ ]
},
{
- "description" : "Peak calls for Histone Modifications (H3K4) ChIP-chip arrays, H3K4ME2_N2_EEMB w peaks",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8679_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8679_details.gff.bb"
+ }
},
- "type" : "FeatureTrack",
- "name" : "__Histone Modifications (H3K4) ChIP-chip arrays, H3K4ME2_N2_EEMB peaks",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ H3K4ME2_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"renderer" : {
- "color1" : "deeppink",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
"height" : 6,
- "showDescriptions" : false
- },
- "type" : "LinearBasicDisplay"
+ "showDescriptions" : false,
+ "showLabels" : false
+ }
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "Peak calls for Histone Modifications (H3K4) ChIP-chip arrays, H3K4ME2_N2_EEMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ H3K4ME2_N2_EEMB w peaks_bigbed_peaks",
+ "name" : "__Histone Modifications (H3K4) ChIP-chip arrays, H3K4ME2_N2_EEMB peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ H3K4ME2_N2_EEMB w peaks_bigbed_peaks"
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack"
},
{
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/MP07030_H3K4ME2_DAM1570816_N2_EEMB_mean_WS220.bw",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "minScore" : 1.53854445012769,
"type" : "LinearWiggleDisplay",
- "maxScore" : 3.17,
- "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ MP07030_H3K4ME2_DAM1570816_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ MP07030_H3K4ME2_DAM1570816_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 1.53854445012769,
+ "maxScore" : 3.17
}
],
+ "name" : "Histone Modifications (H3K4) ChIP-chip arrays, MP07030_H3K4ME2_DAM1570816_N2_EEMB",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ MP07030_H3K4ME2_DAM1570816_N2_EEMB",
+ "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -16021,58 +15422,38 @@
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
- ],
- "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Histone Modifications (H3K4) ChIP-chip arrays, MP07030_H3K4ME2_DAM1570816_N2_EEMB",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/MP07030_H3K4ME2_DAM1570816_N2_EEMB_mean_WS220.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- }
+ ]
},
{
- "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_LTEMB w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/WA30534819_H3K4ME3_N2_LTEMB_1_OID28399_MA2Cscore.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/WA30534819_H3K4ME3_N2_LTEMB_1_OID28399_MA2Cscore.bw"
+ }
},
"displays" : [
{
"maxScore" : 5.16834486700607,
- "type" : "LinearWiggleDisplay",
+ "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_LTEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"minScore" : 0,
- "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_LTEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
],
+ "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_LTEMB w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_LTEMB w peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
- ]
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack"
},
{
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8462_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "__Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_LTEMB peaks",
- "description" : "Peak calls for Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_LTEMB w peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -16081,145 +15462,153 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "description" : "Peak calls for Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_LTEMB w peaks",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_LTEMB w peaks_bigbed_peaks",
+ "name" : "__Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_LTEMB peaks",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_LTEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
"showDescriptions" : false,
"height" : 6,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay"
- }
- ]
+ "showLabels" : false
+ }
+ }
+ ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8462_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ }
},
{
"displays" : [
{
- "maxScore" : 3.18295750520151,
"type" : "LinearWiggleDisplay",
"minScore" : 1.0570759767165,
- "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ AB8895_H3K4ME1733246_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ AB8895_H3K4ME1733246_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "maxScore" : 3.18295750520151
}
],
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB8895_H3K4ME1733246_N2_L3_mean_WS220.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ AB8895_H3K4ME1733246_N2_L3",
- "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB8895_H3K4ME1733246_N2_L3_mean_WS220.bw"
- }
- },
- "type" : "QuantitativeTrack",
- "name" : "Histone Modifications (H3K4) ChIP-chip arrays, AB8895_H3K4ME1733246_N2_L3"
+ "name" : "Histone Modifications (H3K4) ChIP-chip arrays, AB8895_H3K4ME1733246_N2_L3",
+ "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
+ "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications (H3K4) ChIP-chip arrays, H3K4ME3_N2_L3",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ H3K4ME3_N2_L3",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "displays" : [
- {
- "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ H3K4ME3_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 4.32160363220401,
- "minScore" : 1.55342919862732
- }
- ],
- "name" : "Histone Modifications (H3K4) ChIP-chip arrays, H3K4ME3_N2_L3",
"type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AR0169_H3K4me3_N2_L3_mean_WS220.bw"
- }
+ },
+ "type" : "BigWigAdapter"
},
- "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "displays" : [
+ {
+ "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ H3K4ME3_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 1.55342919862732,
+ "maxScore" : 4.32160363220401,
+ "type" : "LinearWiggleDisplay"
+ }
+ ]
},
{
"description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_L4 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L4 w peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
"type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/WA30534819_H3K4ME3_N2_L4_1_OID28399_MA2Cscore.bw",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigWigAdapter"
},
- "name" : "Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_L4 w peaks",
"displays" : [
{
- "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L4 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
"maxScore" : 4.675462,
- "minScore" : 0
+ "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L4 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
}
+ ]
+ },
+ {
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L4 w peaks_bigbed_peaks",
+ "name" : "__Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_L4 peaks",
+ "description" : "Peak calls for Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_L4 w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L4 w peaks"
- },
- {
- "description" : "Peak calls for Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_L4 w peaks",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8477_details.gff.bb"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8477_details.gff.bb",
+ "locationType" : "UriLocation"
}
},
- "name" : "__Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_L4 peaks",
"displays" : [
{
+ "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L4 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showLabels" : false,
"showDescriptions" : false,
"height" : 6,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "deeppink"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L4 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
- ],
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_L4 w peaks_bigbed_peaks"
+ ]
},
{
- "name" : "Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_EEMB w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/WA30534819_H3K4ME3_N2_EEMB_1_OID28399_MA2Cscore.bw",
@@ -16227,50 +15616,41 @@
},
"type" : "BigWigAdapter"
},
- "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_EEMB w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
"displays" : [
{
- "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "maxScore" : 4.335177,
"type" : "LinearWiggleDisplay",
- "minScore" : 0
+ "minScore" : 0,
+ "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "maxScore" : 4.335177
}
- ]
- },
- {
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_EEMB w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
],
+ "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_EEMB w peaks",
+ "name" : "Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_EEMB w peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack"
+ },
+ {
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
+ "showLabels" : false,
"showDescriptions" : false,
"height" : 6
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
+ }
}
],
- "name" : "__Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_EEMB peaks",
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
@@ -16278,10 +15658,7 @@
},
"type" : "BigBedAdapter"
},
- "description" : "Peak calls for Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_EEMB w peaks"
- },
- {
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ H3K4ME2_N2_L3",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -16290,215 +15667,230 @@
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "name" : "__Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_EEMB peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_EEMB w peaks_bigbed_peaks",
+ "description" : "Peak calls for Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_EEMB w peaks"
+ },
+ {
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/WA30834809_H3K4ME2_N2_L3_mean_WS220.bw",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ H3K4ME2_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "minScore" : 1.62582299864596,
+ "type" : "LinearWiggleDisplay",
"maxScore" : 4.64249393529078,
- "type" : "LinearWiggleDisplay"
+ "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ H3K4ME2_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 1.62582299864596
}
],
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ H3K4ME2_N2_L3",
"name" : "Histone Modifications (H3K4) ChIP-chip arrays, H3K4ME2_N2_L3",
+ "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ]
+ },
+ {
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/WA30834809_H3K4ME2_N2_L3_mean_WS220.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/WA30534819_H3K4ME3_N2_YA_1_OID28399_MA2Cscore.bw",
"locationType" : "UriLocation"
}
},
- "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
"displays" : [
{
- "type" : "LinearWiggleDisplay",
"maxScore" : 4.631936,
"minScore" : 0,
- "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_YA w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_YA w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
],
+ "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_YA w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_YA w peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_YA w peaks",
- "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/WA30534819_H3K4ME3_N2_YA_1_OID28399_MA2Cscore.bw",
- "locationType" : "UriLocation"
- }
- },
- "name" : "Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_YA w peaks"
+ ]
},
{
"description" : "Peak calls for Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_YA w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_YA w peaks_bigbed_peaks",
"name" : "__Histone Modifications (H3K4) ChIP-chip arrays, WA30534819_H3K4ME3_N2_YA peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8468_details.gff.bb"
- }
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8468_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
"height" : 6,
- "showDescriptions" : false
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_YA w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ WA30534819_H3K4ME3_N2_YA w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
]
},
{
- "name" : "Histone Modifications (H3K4) ChIP-chip arrays, H3K4ME3_N2_EEMB w peaks",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 4.21,
+ "minScore" : 0,
+ "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ H3K4ME3_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/WA30534819_H3K4ME3_N2_EEMB_mean_WS220.bw",
"locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ }
},
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
"description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ H3K4ME3_N2_EEMB w peaks",
+ "name" : "Histone Modifications (H3K4) ChIP-chip arrays, H3K4ME3_N2_EEMB w peaks"
+ },
+ {
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ H3K4ME3_N2_EEMB w peaks_bigbed_peaks",
+ "name" : "__Histone Modifications (H3K4) ChIP-chip arrays, H3K4ME3_N2_EEMB peaks",
+ "description" : "Peak calls for Histone Modifications (H3K4) ChIP-chip arrays, H3K4ME3_N2_EEMB w peaks",
"displays" : [
{
- "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ H3K4ME3_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 4.21,
- "minScore" : 0
- }
- ]
- },
- {
- "displays" : [
- {
- "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ H3K4ME3_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"type" : "LinearBasicDisplay",
+ "displayId" : "Histone Modifications (H3K4) ChIP-chip arrays_ H3K4ME3_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"renderer" : {
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
+ "showDescriptions" : false,
"height" : 6,
- "showDescriptions" : false
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
}
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-chip arrays_ H3K4ME3_N2_EEMB w peaks_bigbed_peaks",
- "description" : "Peak calls for Histone Modifications (H3K4) ChIP-chip arrays, H3K4ME3_N2_EEMB w peaks",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8505_details.gff.bb",
"locationType" : "UriLocation"
}
- },
- "type" : "FeatureTrack",
- "name" : "__Histone Modifications (H3K4) ChIP-chip arrays, H3K4ME3_N2_EEMB peaks"
+ }
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K79) ChIP-chip arrays_ AB2886_H3K79ME1361912_N2_MXEMB w peaks",
"displays" : [
{
+ "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ AB2886_H3K79ME1361912_N2_MXEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
"maxScore" : 3.47,
- "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ AB2886_H3K79ME1361912_N2_MXEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
],
- "type" : "QuantitativeTrack",
"adapter" : {
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB2886_H3K79ME1361912_N2_MXEMB_mean.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB2886_H3K79ME1361912_N2_MXEMB_mean.bw"
},
"type" : "BigWigAdapter"
},
- "name" : "Histone Modifications (H3K79) ChIP-chip arrays, AB2886_H3K79ME1361912_N2_MXEMB w peaks",
- "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K79) ChIP-chip arrays_ AB2886_H3K79ME1361912_N2_MXEMB w peaks",
+ "name" : "Histone Modifications (H3K79) ChIP-chip arrays, AB2886_H3K79ME1361912_N2_MXEMB w peaks"
},
{
- "description" : "Peak calls for Histone Modifications (H3K79) ChIP-chip arrays, AB2886_H3K79ME1361912_N2_MXEMB w peaks",
- "name" : "__Histone Modifications (H3K79) ChIP-chip arrays, AB2886_H3K79ME1361912_N2_MXEMB peaks",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7873_details.gff.bb",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ AB2886_H3K79ME1361912_N2_MXEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"renderer" : {
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
+ "showDescriptions" : false,
"height" : 6,
- "showDescriptions" : false
- },
- "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ AB2886_H3K79ME1361912_N2_MXEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ }
}
],
+ "description" : "Peak calls for Histone Modifications (H3K79) ChIP-chip arrays, AB2886_H3K79ME1361912_N2_MXEMB w peaks",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K79) ChIP-chip arrays_ AB2886_H3K79ME1361912_N2_MXEMB w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "__Histone Modifications (H3K79) ChIP-chip arrays, AB2886_H3K79ME1361912_N2_MXEMB peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
- ]
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack"
},
{
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -16507,38 +15899,46 @@
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "name" : "Histone Modifications (H3K79) ChIP-chip arrays, AB2621_H3K79ME3361576_N2_MXEMB w peaks",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K79) ChIP-chip arrays_ AB2621_H3K79ME3361576_N2_MXEMB w peaks",
+ "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "maxScore" : 3.72757210565808,
"type" : "LinearWiggleDisplay",
- "minScore" : 0,
- "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ AB2621_H3K79ME3361576_N2_MXEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "maxScore" : 3.72757210565808,
+ "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ AB2621_H3K79ME3361576_N2_MXEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 0
}
],
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB2621_H3K79ME3361576_N2_MXEMB_mean.bw"
}
- },
- "name" : "Histone Modifications (H3K79) ChIP-chip arrays, AB2621_H3K79ME3361576_N2_MXEMB w peaks",
- "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
},
{
- "name" : "__Histone Modifications (H3K79) ChIP-chip arrays, AB2621_H3K79ME3361576_N2_MXEMB peaks",
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ AB2621_H3K79ME3361576_N2_MXEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
+ "renderer" : {
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7859_details.gff.bb",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigBedAdapter"
},
- "description" : "Peak calls for Histone Modifications (H3K79) ChIP-chip arrays, AB2621_H3K79ME3361576_N2_MXEMB w peaks",
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K79) ChIP-chip arrays_ AB2621_H3K79ME3361576_N2_MXEMB w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -16547,31 +15947,28 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "description" : "Peak calls for Histone Modifications (H3K79) ChIP-chip arrays, AB2621_H3K79ME3361576_N2_MXEMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K79) ChIP-chip arrays_ AB2621_H3K79ME3361576_N2_MXEMB w peaks_bigbed_peaks",
+ "name" : "__Histone Modifications (H3K79) ChIP-chip arrays, AB2621_H3K79ME3361576_N2_MXEMB peaks"
+ },
+ {
"displays" : [
{
- "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ AB2621_H3K79ME3361576_N2_MXEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
- "renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "type" : "LinearBasicDisplay"
+ "maxScore" : 3.21,
+ "minScore" : 0,
+ "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ AB3594_H3K79ME2346021_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
- ]
- },
- {
+ ],
"adapter" : {
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB3594_H3K79ME2_346021_N2_L3_mean.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB3594_H3K79ME2_346021_N2_L3_mean.bw"
},
"type" : "BigWigAdapter"
},
"type" : "QuantitativeTrack",
- "name" : "Histone Modifications (H3K79) ChIP-chip arrays, AB3594_H3K79ME2346021_N2_L3 w peaks",
- "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -16580,89 +15977,77 @@
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "name" : "Histone Modifications (H3K79) ChIP-chip arrays, AB3594_H3K79ME2346021_N2_L3 w peaks",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K79) ChIP-chip arrays_ AB3594_H3K79ME2346021_N2_L3 w peaks",
- "displays" : [
- {
- "maxScore" : 3.21,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0,
- "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ AB3594_H3K79ME2346021_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
- }
- ]
+ "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 6,
- "showDescriptions" : false
- },
- "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ AB3594_H3K79ME2346021_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
- }
- ],
+ "description" : "Peak calls for Histone Modifications (H3K79) ChIP-chip arrays, AB3594_H3K79ME2346021_N2_L3 w peaks",
+ "name" : "__Histone Modifications (H3K79) ChIP-chip arrays, AB3594_H3K79ME2346021_N2_L3 peaks",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K79) ChIP-chip arrays_ AB3594_H3K79ME2346021_N2_L3 w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "description" : "Peak calls for Histone Modifications (H3K79) ChIP-chip arrays, AB3594_H3K79ME2346021_N2_L3 w peaks",
- "name" : "__Histone Modifications (H3K79) ChIP-chip arrays, AB3594_H3K79ME2346021_N2_L3 peaks",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7856_details.gff.bb"
- },
- "type" : "BigBedAdapter"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7856_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
},
- "type" : "FeatureTrack"
- },
- {
"displays" : [
{
- "minScore" : 1.61338293863936,
- "maxScore" : 4.5,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ H3K79ME3361576_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
+ "height" : 6,
+ "showLabels" : false,
+ "color1" : "deeppink"
+ },
+ "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ AB3594_H3K79ME2346021_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
- ],
+ ]
+ },
+ {
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K79) ChIP-chip arrays_ H3K79ME3361576_N2_EEMB",
+ "name" : "Histone Modifications (H3K79) ChIP-chip arrays, H3K79ME3361576_N2_EEMB",
+ "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K79) ChIP-chip arrays_ H3K79ME3361576_N2_EEMB",
- "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB2621_H3K79ME3361576_N2_EEMB_mean_WS220.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB2621_H3K79ME3361576_N2_EEMB_mean_WS220.bw",
+ "locationType" : "UriLocation"
}
},
- "name" : "Histone Modifications (H3K79) ChIP-chip arrays, H3K79ME3361576_N2_EEMB"
- },
- {
"displays" : [
{
- "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ H3K79ME2346021_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "maxScore" : 4.29,
"type" : "LinearWiggleDisplay",
- "minScore" : 1.57113450349554
+ "maxScore" : 4.5,
+ "minScore" : 1.61338293863936,
+ "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ H3K79ME3361576_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
}
- ],
+ ]
+ },
+ {
+ "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K79) ChIP-chip arrays_ H3K79ME2346021_N2_EEMB",
+ "name" : "Histone Modifications (H3K79) ChIP-chip arrays, H3K79ME2346021_N2_EEMB",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -16671,18 +16056,32 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Histone Modifications (H3K79) ChIP-chip arrays, H3K79ME2346021_N2_EEMB",
+ "type" : "QuantitativeTrack",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB3594_H3K79ME2346021_N2_EEMB_mean_WS220.bw",
- "locationType" : "UriLocation"
- }
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB3594_H3K79ME2346021_N2_EEMB_mean_WS220.bw"
+ },
+ "type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack"
+ "displays" : [
+ {
+ "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ H3K79ME2346021_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 1.57113450349554,
+ "maxScore" : 4.29,
+ "type" : "LinearWiggleDisplay"
+ }
+ ]
},
{
+ "displays" : [
+ {
+ "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ AB2621_H3K79ME3_361576_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 3.27,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -16690,62 +16089,55 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB2621_H3K79ME3_361576_N2_L3_mean.bw"
}
},
- "type" : "QuantitativeTrack",
- "name" : "Histone Modifications (H3K79) ChIP-chip arrays, AB2621_H3K79ME3_361576_N2_L3 w peaks",
- "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K79) ChIP-chip arrays_ AB2621_H3K79ME3_361576_N2_L3 w peaks",
- "displays" : [
- {
- "minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 3.27,
- "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ AB2621_H3K79ME3_361576_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
- }
- ]
+ "name" : "Histone Modifications (H3K79) ChIP-chip arrays, AB2621_H3K79ME3_361576_N2_L3 w peaks",
+ "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "description" : "Peak calls for Histone Modifications (H3K79) ChIP-chip arrays, AB2621_H3K79ME3_361576_N2_L3 w peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9091_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "__Histone Modifications (H3K79) ChIP-chip arrays, AB2621_H3K79ME3_361576_N2_L3 peaks",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
"height" : 6,
"showDescriptions" : false,
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
"showLabels" : false
},
"displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ AB2621_H3K79ME3_361576_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
}
],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9091_details.gff.bb"
+ }
+ },
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K79) ChIP-chip arrays_ AB2621_H3K79ME3_361576_N2_L3 w peaks_bigbed_peaks"
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K79) ChIP-chip arrays_ AB2621_H3K79ME3_361576_N2_L3 w peaks_bigbed_peaks",
+ "name" : "__Histone Modifications (H3K79) ChIP-chip arrays, AB2621_H3K79ME3_361576_N2_L3 peaks",
+ "description" : "Peak calls for Histone Modifications (H3K79) ChIP-chip arrays, AB2621_H3K79ME3_361576_N2_L3 w peaks"
},
{
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -16754,50 +16146,49 @@
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "name" : "Histone Modifications (H3K79) ChIP-chip arrays, AB3594_H3K79ME2346021_N2_MXEMB w peaks",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K79) ChIP-chip arrays_ AB3594_H3K79ME2346021_N2_MXEMB w peaks",
+ "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ AB3594_H3K79ME2346021_N2_MXEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "minScore" : 0,
"type" : "LinearWiggleDisplay",
- "maxScore" : 4.21
+ "maxScore" : 4.21,
+ "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ AB3594_H3K79ME2346021_N2_MXEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 0
}
],
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB3594_H3K79ME2346021_N2_MXEMB_mean.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB3594_H3K79ME2346021_N2_MXEMB_mean.bw"
}
- },
- "name" : "Histone Modifications (H3K79) ChIP-chip arrays, AB3594_H3K79ME2346021_N2_MXEMB w peaks",
- "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
},
{
- "description" : "Peak calls for Histone Modifications (H3K79) ChIP-chip arrays, AB3594_H3K79ME2346021_N2_MXEMB w peaks",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7867_details.gff.bb",
"locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ }
},
- "name" : "__Histone Modifications (H3K79) ChIP-chip arrays, AB3594_H3K79ME2346021_N2_MXEMB peaks",
"displays" : [
{
- "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ AB3594_H3K79ME2346021_N2_MXEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"type" : "LinearBasicDisplay",
"renderer" : {
+ "color1" : "deeppink",
"showDescriptions" : false,
"height" : 6,
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "deeppink"
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ AB3594_H3K79ME2346021_N2_MXEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
}
],
+ "description" : "Peak calls for Histone Modifications (H3K79) ChIP-chip arrays, AB3594_H3K79ME2346021_N2_MXEMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K79) ChIP-chip arrays_ AB3594_H3K79ME2346021_N2_MXEMB w peaks_bigbed_peaks",
+ "name" : "__Histone Modifications (H3K79) ChIP-chip arrays, AB3594_H3K79ME2346021_N2_MXEMB peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -16806,46 +16197,27 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K79) ChIP-chip arrays_ AB3594_H3K79ME2346021_N2_MXEMB w peaks_bigbed_peaks"
+ "type" : "FeatureTrack"
},
{
- "type" : "QuantitativeTrack",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB2886_H3K79ME1361912_N2_EEMB_mean_WS220.bw"
- }
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB2886_H3K79ME1361912_N2_EEMB_mean_WS220.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
},
- "name" : "Histone Modifications (H3K79) ChIP-chip arrays, H3K79ME1361912_N2_EEMB",
- "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K79) ChIP-chip arrays_ H3K79ME1361912_N2_EEMB",
"displays" : [
{
- "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ H3K79ME1361912_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay",
"maxScore" : 4.66328894994542,
+ "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ H3K79ME1361912_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"minScore" : 1.53888535348199
}
- ]
- },
- {
- "displays" : [
- {
- "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ AB2886_H3K79ME1_361912_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "maxScore" : 3.39,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
- }
],
+ "description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K79) ChIP-chip arrays_ H3K79ME1361912_N2_EEMB",
+ "name" : "Histone Modifications (H3K79) ChIP-chip arrays, H3K79ME1361912_N2_EEMB",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -16854,150 +16226,174 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack"
+ },
+ {
+ "name" : "Histone Modifications (H3K79) ChIP-chip arrays, AB2886_H3K79ME1_361912_N2_L3 w peaks",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K79) ChIP-chip arrays_ AB2886_H3K79ME1_361912_N2_L3 w peaks",
"description" : "H3K4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB2886_H3K79ME1_361912_N2_L3_mean.bw"
- }
+ },
+ "type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "name" : "Histone Modifications (H3K79) ChIP-chip arrays, AB2886_H3K79ME1_361912_N2_L3 w peaks"
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 3.39,
+ "minScore" : 0,
+ "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ AB2886_H3K79ME1_361912_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ }
+ ]
},
{
- "name" : "__Histone Modifications (H3K79) ChIP-chip arrays, AB2886_H3K79ME1_361912_N2_L3 peaks",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7815_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
"description" : "Peak calls for Histone Modifications (H3K79) ChIP-chip arrays, AB2886_H3K79ME1_361912_N2_L3 w peaks",
+ "name" : "__Histone Modifications (H3K79) ChIP-chip arrays, AB2886_H3K79ME1_361912_N2_L3 peaks",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K79) ChIP-chip arrays_ AB2886_H3K79ME1_361912_N2_L3 w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7815_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink",
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ AB2886_H3K79ME1_361912_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
+ "displayId" : "Histone Modifications (H3K79) ChIP-chip arrays_ AB2886_H3K79ME1_361912_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
]
},
{
"displays" : [
{
- "type" : "LinearWiggleDisplay",
- "maxScore" : 4.08761322717135,
+ "displayId" : "Histone Modifications (H3K9) ChIP-chip arrays_ H3K9ME3_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"minScore" : 1.50301236496655,
- "displayId" : "Histone Modifications (H3K9) ChIP-chip arrays_ H3K9ME3_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "maxScore" : 4.08761322717135,
+ "type" : "LinearWiggleDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K9) ChIP-chip arrays_ H3K9ME3_N2_L3",
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/H3K9me3_mean_WS220.bw"
+ }
+ },
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "description" : "H3K9 modifications. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K9) ChIP-chip arrays_ H3K9ME3_N2_L3",
"name" : "Histone Modifications (H3K9) ChIP-chip arrays, H3K9ME3_N2_L3",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/H3K9me3_mean_WS220.bw"
- }
- }
+ "description" : "H3K9 modifications. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00009_H3K9ME32F3_N2_L3_mean_WS220.bw",
- "locationType" : "UriLocation"
- }
- },
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
- "name" : "Histone Modifications (H3K9) ChIP-chip arrays, H3K9ME32F3_N2_L3",
- "description" : "H3K9 modifications. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K9) ChIP-chip arrays_ H3K9ME32F3_N2_L3",
+ "name" : "Histone Modifications (H3K9) ChIP-chip arrays, H3K9ME32F3_N2_L3",
+ "description" : "H3K9 modifications. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
"displayId" : "Histone Modifications (H3K9) ChIP-chip arrays_ H3K9ME32F3_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"minScore" : 1.71119524470694,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 4.77937952941497
+ "maxScore" : 4.77937952941497,
+ "type" : "LinearWiggleDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00009_H3K9ME32F3_N2_L3_mean_WS220.bw",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
- "description" : "H3K9 modifications. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K9) ChIP-chip arrays_ AB8896_H3K9ME1104560_N2_EEMB",
"name" : "Histone Modifications (H3K9) ChIP-chip arrays, AB8896_H3K9ME1104560_N2_EEMB",
+ "description" : "H3K9 modifications. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB8896_H3K9ME1104560_N2_EEMB_WS220.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB8896_H3K9ME1104560_N2_EEMB_WS220.bw",
+ "locationType" : "UriLocation"
}
},
"displays" : [
{
- "maxScore" : 2.8352858925573,
"type" : "LinearWiggleDisplay",
+ "displayId" : "Histone Modifications (H3K9) ChIP-chip arrays_ AB8896_H3K9ME1104560_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"minScore" : 0.962444344543907,
- "displayId" : "Histone Modifications (H3K9) ChIP-chip arrays_ AB8896_H3K9ME1104560_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "maxScore" : 2.8352858925573
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K9) ChIP-chip arrays_ AB8896_H3K9ME1104560_N2_EEMB",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
]
},
{
+ "displays" : [
+ {
+ "maxScore" : 5.25497163813994,
+ "displayId" : "Histone Modifications (H3K9) ChIP-chip arrays_ H3K9ME3_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 1.90834064058618,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/UP07442_H3K9ME3_N2_EEMB_mean_WS220.bw"
- }
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/UP07442_H3K9ME3_N2_EEMB_mean_WS220.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "name" : "Histone Modifications (H3K9) ChIP-chip arrays, H3K9ME3_N2_EEMB",
- "description" : "H3K9 modifications. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -17006,75 +16402,77 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
+ "description" : "H3K9 modifications. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K9) ChIP-chip arrays_ H3K9ME3_N2_EEMB",
+ "name" : "Histone Modifications (H3K9) ChIP-chip arrays, H3K9ME3_N2_EEMB"
+ },
+ {
"displays" : [
{
- "displayId" : "Histone Modifications (H3K9) ChIP-chip arrays_ H3K9ME3_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "minScore" : 1.90834064058618,
"type" : "LinearWiggleDisplay",
- "maxScore" : 5.25497163813994
+ "maxScore" : 7.14,
+ "minScore" : 2.74346926164881,
+ "displayId" : "Histone Modifications (H3K9) ChIP-chip arrays_ H3K9ME32F3_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
}
- ]
- },
- {
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00009_H3K9ME32F3_N2_EEMB_mean_WS220.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00009_H3K9ME32F3_N2_EEMB_mean_WS220.bw",
+ "locationType" : "UriLocation"
}
},
- "type" : "QuantitativeTrack",
- "name" : "Histone Modifications (H3K9) ChIP-chip arrays, H3K9ME32F3_N2_EEMB",
- "description" : "H3K9 modifications. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K9) ChIP-chip arrays_ H3K9ME32F3_N2_EEMB",
- "displays" : [
- {
- "minScore" : 2.74346926164881,
- "maxScore" : 7.14,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Histone Modifications (H3K9) ChIP-chip arrays_ H3K9ME32F3_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
- }
- ]
+ "name" : "Histone Modifications (H3K9) ChIP-chip arrays, H3K9ME32F3_N2_EEMB",
+ "description" : "H3K9 modifications. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "description" : "H3K9 modifications. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Histone Modifications (H3K9) ChIP-chip arrays, H3K9ME26D11_N2_L3",
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00008_H3K9ME26D11_N2_L3_mean_WS220.bw"
- },
- "type" : "BigWigAdapter"
+ }
},
"displays" : [
{
- "displayId" : "Histone Modifications (H3K9) ChIP-chip arrays_ H3K9ME26D11_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay",
"maxScore" : 4.32026972001594,
+ "displayId" : "Histone Modifications (H3K9) ChIP-chip arrays_ H3K9ME26D11_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"minScore" : 1.53288900760526
}
],
+ "description" : "H3K9 modifications. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications (H3K9) ChIP-chip arrays, H3K9ME26D11_N2_L3",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K9) ChIP-chip arrays_ H3K9ME26D11_N2_L3",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
]
},
{
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB8898_H3K9ME3339901_N2_EEMB_WS220.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
"displayId" : "Histone Modifications (H3K9) ChIP-chip arrays_ H3K9ME3339901_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
@@ -17083,7 +16481,10 @@
"type" : "LinearWiggleDisplay"
}
],
+ "name" : "Histone Modifications (H3K9) ChIP-chip arrays, H3K9ME3339901_N2_EEMB",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K9) ChIP-chip arrays_ H3K9ME3339901_N2_EEMB",
+ "description" : "H3K9 modifications. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -17091,207 +16492,189 @@
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
- ],
- "description" : "H3K9 modifications. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Histone Modifications (H3K9) ChIP-chip arrays, H3K9ME3339901_N2_EEMB",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB8898_H3K9ME3339901_N2_EEMB_WS220.bw"
- }
- }
+ ]
},
{
"description" : "H3K9 modifications. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K9) ChIP-chip arrays_ AB9045_H3K9ME1291918_N2_EEMB",
"name" : "Histone Modifications (H3K9) ChIP-chip arrays, AB9045_H3K9ME1291918_N2_EEMB",
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB9045_H3K9ME1291918_N2_EEMB_mean_WS220.bw",
"locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ }
},
- "type" : "QuantitativeTrack",
"displays" : [
{
"type" : "LinearWiggleDisplay",
- "maxScore" : 4.64,
+ "displayId" : "Histone Modifications (H3K9) ChIP-chip arrays_ AB9045_H3K9ME1291918_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"minScore" : 1.67880340297999,
- "displayId" : "Histone Modifications (H3K9) ChIP-chip arrays_ AB9045_H3K9ME1291918_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "maxScore" : 4.64
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K9) ChIP-chip arrays_ AB9045_H3K9ME1291918_N2_EEMB",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
]
},
{
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K9) ChIP-chip arrays_ H3K9ME26D11_N2_EEMB",
+ "name" : "Histone Modifications (H3K9) ChIP-chip arrays, H3K9ME26D11_N2_EEMB",
+ "description" : "H3K9 modifications. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K9) ChIP-chip arrays_ H3K9ME26D11_N2_EEMB",
- "displays" : [
- {
- "maxScore" : 4.61668279547888,
- "type" : "LinearWiggleDisplay",
- "minScore" : 1.57040532250803,
- "displayId" : "Histone Modifications (H3K9) ChIP-chip arrays_ H3K9ME26D11_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
- }
- ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HK00008_H3K9ME26D11_N2_EEMB_mean_WS220.bw"
- },
- "type" : "BigWigAdapter"
+ }
},
- "type" : "QuantitativeTrack",
- "name" : "Histone Modifications (H3K9) ChIP-chip arrays, H3K9ME26D11_N2_EEMB",
- "description" : "H3K9 modifications. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "minScore" : 1.57040532250803,
+ "displayId" : "Histone Modifications (H3K9) ChIP-chip arrays_ H3K9ME26D11_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "maxScore" : 4.61668279547888
+ }
+ ]
},
{
+ "description" : "H3K9 modifications. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications (H3K9) ChIP-chip arrays, NA_N2_EEMB",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K9) ChIP-chip arrays_ NA_N2_EEMB",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "displays" : [
- {
- "displayId" : "Histone Modifications (H3K9) ChIP-chip arrays_ NA_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "maxScore" : 3.97427419798789,
- "type" : "LinearWiggleDisplay",
- "minScore" : 1.251210485336
- }
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
- "name" : "Histone Modifications (H3K9) ChIP-chip arrays, NA_N2_EEMB",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/NA_N2_EEMB_mean.wig_mean_WS220.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/NA_N2_EEMB_mean.wig_mean_WS220.bw"
}
},
- "type" : "QuantitativeTrack",
- "description" : "H3K9 modifications. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "displays" : [
+ {
+ "maxScore" : 3.97427419798789,
+ "displayId" : "Histone Modifications (H3K9) ChIP-chip arrays_ NA_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 1.251210485336,
+ "type" : "LinearWiggleDisplay"
+ }
+ ]
},
{
"displays" : [
{
- "displayId" : "Histone Modifications (H3K9) ChIP-chip arrays_ AB9045_H3K9ME1291918_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "minScore" : 1.36270986044627,
+ "type" : "LinearWiggleDisplay",
"maxScore" : 3.92639351650383,
- "type" : "LinearWiggleDisplay"
+ "displayId" : "Histone Modifications (H3K9) ChIP-chip arrays_ AB9045_H3K9ME1291918_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 1.36270986044627
}
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K9) ChIP-chip arrays_ AB9045_H3K9ME1291918_N2_L3",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB9045_H3K9ME1291918_N2_L3_mean_WS220.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "description" : "H3K9 modifications. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Histone Modifications (H3K9) ChIP-chip arrays, AB9045_H3K9ME1291918_N2_L3",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB9045_H3K9ME1291918_N2_L3_mean_WS220.bw",
- "locationType" : "UriLocation"
- }
- }
+ "description" : "H3K9 modifications. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K9) ChIP-chip arrays_ AB9045_H3K9ME1291918_N2_L3",
+ "name" : "Histone Modifications (H3K9) ChIP-chip arrays, AB9045_H3K9ME1291918_N2_L3"
},
{
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/MP07329_H4K16ACDAM1612187_N2_EEMB_mean.bw"
- }
- },
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-chip arrays_ MP07329_H4K16ACDAM1612187_N2_EEMB w peaks",
"name" : "Histone Modifications (H4) ChIP-chip arrays, MP07329_H4K16ACDAM1612187_N2_EEMB w peaks",
"description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-chip arrays_ MP07329_H4K16ACDAM1612187_N2_EEMB w peaks",
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/MP07329_H4K16ACDAM1612187_N2_EEMB_mean.bw"
+ }
+ },
"displays" : [
{
- "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ MP07329_H4K16ACDAM1612187_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 4.22
+ "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ MP07329_H4K16ACDAM1612187_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "maxScore" : 4.22,
+ "type" : "LinearWiggleDisplay"
}
]
},
{
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-chip arrays_ MP07329_H4K16ACDAM1612187_N2_EEMB w peaks_bigbed_peaks",
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9337_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
- "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ MP07329_H4K16ACDAM1612187_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
"type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
+ "showDescriptions" : false,
+ "height" : 6,
"showLabels" : false
- }
+ },
+ "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ MP07329_H4K16ACDAM1612187_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
}
],
+ "description" : "Peak calls for Histone Modifications (H4) ChIP-chip arrays, MP07329_H4K16ACDAM1612187_N2_EEMB w peaks",
"name" : "__Histone Modifications (H4) ChIP-chip arrays, MP07329_H4K16ACDAM1612187_N2_EEMB peaks",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9337_details.gff.bb"
- }
- },
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-chip arrays_ MP07329_H4K16ACDAM1612187_N2_EEMB w peaks_bigbed_peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
"type" : "FeatureTrack",
- "description" : "Peak calls for Histone Modifications (H4) ChIP-chip arrays, MP07329_H4K16ACDAM1612187_N2_EEMB w peaks"
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ]
},
{
- "displays" : [
- {
- "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ AB15823_H4K8AC487128_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "minScore" : 0.689024179121877,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 2.00673993673296
- }
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-chip arrays_ AB15823_H4K8AC487128_N2_L3",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -17300,166 +16683,203 @@
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"name" : "Histone Modifications (H4) ChIP-chip arrays, AB15823_H4K8AC487128_N2_L3",
- "type" : "QuantitativeTrack",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-chip arrays_ AB15823_H4K8AC487128_N2_L3",
+ "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ AB15823_H4K8AC487128_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 0.689024179121877,
+ "maxScore" : 2.00673993673296,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB15823_H4K8AC487128_N2_L3_mean_WS220.bw"
- }
+ },
+ "type" : "BigWigAdapter"
}
},
{
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/DISN147_H4K20ME1_001_N2_L3_mean.bw"
+ }
+ },
"displays" : [
{
- "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ DISN147_H4K20ME1_001_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "minScore" : 0,
+ "type" : "LinearWiggleDisplay",
"maxScore" : 4.69943008199871,
- "type" : "LinearWiggleDisplay"
+ "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ DISN147_H4K20ME1_001_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 0
}
],
+ "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications (H4) ChIP-chip arrays, DISN147_H4K20ME1_001_N2_L3 w peaks",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-chip arrays_ DISN147_H4K20ME1_001_N2_L3 w peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
+ ]
+ },
+ {
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
],
- "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Histone Modifications (H4) ChIP-chip arrays, DISN147_H4K20ME1_001_N2_L3 w peaks",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/DISN147_H4K20ME1_001_N2_L3_mean.bw",
- "locationType" : "UriLocation"
- }
- },
- "type" : "QuantitativeTrack"
- },
- {
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Peak calls for Histone Modifications (H4) ChIP-chip arrays, DISN147_H4K20ME1_001_N2_L3 w peaks",
+ "name" : "__Histone Modifications (H4) ChIP-chip arrays, DISN147_H4K20ME1_001_N2_L3 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-chip arrays_ DISN147_H4K20ME1_001_N2_L3 w peaks_bigbed_peaks",
"displays" : [
{
- "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ DISN147_H4K20ME1_001_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
+ "color1" : "deeppink",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
- }
+ "height" : 6,
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ DISN147_H4K20ME1_001_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
}
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-chip arrays_ DISN147_H4K20ME1_001_N2_L3 w peaks_bigbed_peaks",
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : "Peak calls for Histone Modifications (H4) ChIP-chip arrays, DISN147_H4K20ME1_001_N2_L3 w peaks",
- "name" : "__Histone Modifications (H4) ChIP-chip arrays, DISN147_H4K20ME1_001_N2_L3 peaks",
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8606_details.gff.bb",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8606_details.gff.bb"
},
"type" : "BigBedAdapter"
}
},
{
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/DISN147_H4K20ME1001_N2_LTEMB_mean.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "Histone Modifications (H4) ChIP-chip arrays, DISN147_H4K20ME1001_N2_LTEMB w peaks",
- "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications (H4) ChIP-chip arrays, DISN147_H4K20ME1001_N2_LTEMB w peaks",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-chip arrays_ DISN147_H4K20ME1001_N2_LTEMB w peaks",
"displays" : [
{
- "maxScore" : 5.128101,
"type" : "LinearWiggleDisplay",
+ "maxScore" : 5.128101,
"minScore" : 0,
"displayId" : "Histone Modifications (H4) ChIP-chip arrays_ DISN147_H4K20ME1001_N2_LTEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/DISN147_H4K20ME1001_N2_LTEMB_mean.bw"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "__Histone Modifications (H4) ChIP-chip arrays, DISN147_H4K20ME1001_N2_LTEMB peaks",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-chip arrays_ DISN147_H4K20ME1001_N2_LTEMB w peaks_bigbed_peaks",
+ "description" : "Peak calls for Histone Modifications (H4) ChIP-chip arrays, DISN147_H4K20ME1001_N2_LTEMB w peaks",
"displays" : [
{
- "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ DISN147_H4K20ME1001_N2_LTEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
"type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ DISN147_H4K20ME1001_N2_LTEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
}
],
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7940_details.gff.bb",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7940_details.gff.bb"
},
"type" : "BigBedAdapter"
- },
- "name" : "__Histone Modifications (H4) ChIP-chip arrays, DISN147_H4K20ME1001_N2_LTEMB peaks",
- "description" : "Peak calls for Histone Modifications (H4) ChIP-chip arrays, DISN147_H4K20ME1001_N2_LTEMB w peaks"
+ }
},
{
"description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"name" : "Histone Modifications (H4) ChIP-chip arrays, AB9051_H4K20ME1104513_N2_L3",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-chip arrays_ AB9051_H4K20ME1104513_N2_L3",
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB9051_H4K20ME1104513_N2_L3_mean_WS220.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB9051_H4K20ME1104513_N2_L3_mean_WS220.bw",
+ "locationType" : "UriLocation"
}
},
- "type" : "QuantitativeTrack",
"displays" : [
{
- "type" : "LinearWiggleDisplay",
"maxScore" : 3.53792439674434,
+ "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ AB9051_H4K20ME1104513_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"minScore" : 1.26131505092563,
- "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ AB9051_H4K20ME1104513_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
+ }
+ ]
+ },
+ {
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/DISN147_H4K20ME1_001_N2_EEMB_mean.bw"
+ }
+ },
+ "displays" : [
+ {
+ "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ DISN147_H4K20ME1_001_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 3.78842567835061,
+ "type" : "LinearWiggleDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-chip arrays_ AB9051_H4K20ME1104513_N2_L3",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-chip arrays_ DISN147_H4K20ME1_001_N2_EEMB w peaks",
+ "name" : "Histone Modifications (H4) ChIP-chip arrays, DISN147_H4K20ME1_001_N2_EEMB w peaks",
+ "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -17467,6 +16887,9 @@
]
},
{
+ "description" : "Peak calls for Histone Modifications (H4) ChIP-chip arrays, DISN147_H4K20ME1_001_N2_EEMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-chip arrays_ DISN147_H4K20ME1_001_N2_EEMB w peaks_bigbed_peaks",
+ "name" : "__Histone Modifications (H4) ChIP-chip arrays, DISN147_H4K20ME1_001_N2_EEMB peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -17475,154 +16898,129 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-chip arrays_ DISN147_H4K20ME1_001_N2_EEMB w peaks",
- "displays" : [
- {
- "minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 3.78842567835061,
- "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ DISN147_H4K20ME1_001_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
- }
- ],
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/DISN147_H4K20ME1_001_N2_EEMB_mean.bw"
- }
- },
- "type" : "QuantitativeTrack",
- "name" : "Histone Modifications (H4) ChIP-chip arrays, DISN147_H4K20ME1_001_N2_EEMB w peaks",
- "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
- "name" : "__Histone Modifications (H4) ChIP-chip arrays, DISN147_H4K20ME1_001_N2_EEMB peaks",
+ "type" : "FeatureTrack",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8615_details.gff.bb",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "description" : "Peak calls for Histone Modifications (H4) ChIP-chip arrays, DISN147_H4K20ME1_001_N2_EEMB w peaks",
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-chip arrays_ DISN147_H4K20ME1_001_N2_EEMB w peaks_bigbed_peaks",
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
- "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ DISN147_H4K20ME1_001_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"type" : "LinearBasicDisplay",
+ "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ DISN147_H4K20ME1_001_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
"renderer" : {
- "color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
"height" : 6,
- "showDescriptions" : false
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
}
}
]
},
{
- "displays" : [
- {
- "maxScore" : 2.37341248248639,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0.79662611922051,
- "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ AB9051_H4K20ME1104513_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
- }
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-chip arrays_ AB9051_H4K20ME1104513_N2_EEMB",
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-chip arrays_ AB9051_H4K20ME1104513_N2_EEMB",
"name" : "Histone Modifications (H4) ChIP-chip arrays, AB9051_H4K20ME1104513_N2_EEMB",
+ "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "minScore" : 0.79662611922051,
+ "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ AB9051_H4K20ME1104513_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "maxScore" : 2.37341248248639
+ }
+ ],
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB9051_H4K20ME1104513_N2_EEMB_mean_WS220.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB9051_H4K20ME1104513_N2_EEMB_mean_WS220.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack"
+ }
},
{
- "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Histone Modifications (H4) ChIP-chip arrays, AB15823_H4K8AC487128_N2_EEMB w peaks",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB15823_H4K8AC487128_N2_EEMB_mean.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "displays" : [
- {
- "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ AB15823_H4K8AC487128_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 1.833546,
- "minScore" : 0
- }
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-chip arrays_ AB15823_H4K8AC487128_N2_EEMB w peaks",
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ]
- },
- {
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-chip arrays_ AB15823_H4K8AC487128_N2_EEMB w peaks",
+ "name" : "Histone Modifications (H4) ChIP-chip arrays, AB15823_H4K8AC487128_N2_EEMB w peaks",
+ "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ AB15823_H4K8AC487128_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
+ "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ AB15823_H4K8AC487128_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 1.833546,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/AB15823_H4K8AC487128_N2_EEMB_mean.bw"
}
+ }
+ },
+ {
+ "name" : "__Histone Modifications (H4) ChIP-chip arrays, AB15823_H4K8AC487128_N2_EEMB peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-chip arrays_ AB15823_H4K8AC487128_N2_EEMB w peaks_bigbed_peaks",
+ "description" : "Peak calls for Histone Modifications (H4) ChIP-chip arrays, AB15823_H4K8AC487128_N2_EEMB w peaks",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-chip arrays_ AB15823_H4K8AC487128_N2_EEMB w peaks_bigbed_peaks",
- "description" : "Peak calls for Histone Modifications (H4) ChIP-chip arrays, AB15823_H4K8AC487128_N2_EEMB w peaks",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8668_details.gff.bb",
"locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ }
},
- "name" : "__Histone Modifications (H4) ChIP-chip arrays, AB15823_H4K8AC487128_N2_EEMB peaks"
+ "displays" : [
+ {
+ "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ AB15823_H4K8AC487128_N2_EEMB w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
+ "height" : 6,
+ "showDescriptions" : false,
+ "showLabels" : false
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 3.41224753746218,
+ "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ LPAR109_H4TETRAAC109_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 1.20644168736252
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -17630,36 +17028,23 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/LPAR109_H4TETRAAC109_N2_EEMB_mean_WS220.bw"
}
},
- "name" : "Histone Modifications (H4) ChIP-chip arrays, LPAR109_H4TETRAAC109_N2_EEMB",
- "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-chip arrays_ LPAR109_H4TETRAAC109_N2_EEMB",
- "displays" : [
- {
- "maxScore" : 3.41224753746218,
- "type" : "LinearWiggleDisplay",
- "minScore" : 1.20644168736252,
- "displayId" : "Histone Modifications (H4) ChIP-chip arrays_ LPAR109_H4TETRAAC109_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
- }
- ]
+ "name" : "Histone Modifications (H4) ChIP-chip arrays, LPAR109_H4TETRAAC109_N2_EEMB"
},
{
- "displays" : [
- {
- "displayId" : "Histone Variants ChIP-chip arrays w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 2.52165401298128
- }
- ],
+ "description" : "Histone Variants. Chromatin was prepared from C. elegans embryos and cross-linked with formaldehyde. Sonicated chromatin was immunoprecipitated with an affinity-purified polyclonal anti-HTZ-1 antibody. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. The median of four normalized log2(ratios) are shown in this track. Ref: PMID 18787694
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Variants ChIP-chip arrays w peaks",
+ "name" : "Histone Variants ChIP-chip arrays w peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -17668,133 +17053,129 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : "Histone Variants. Chromatin was prepared from C. elegans embryos and cross-linked with formaldehyde. Sonicated chromatin was immunoprecipitated with an affinity-purified polyclonal anti-HTZ-1 antibody. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. The median of four normalized log2(ratios) are shown in this track. Ref: PMID 18787694
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Histone Variants ChIP-chip arrays w peaks",
"type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HTZIPmean_WS220.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- }
- },
- {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/HTZIPmean_WS220.bw"
+ }
+ },
"displays" : [
{
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "Histone Variants ChIP-chip arrays w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
+ "type" : "LinearWiggleDisplay",
+ "minScore" : 0,
+ "displayId" : "Histone Variants ChIP-chip arrays w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "maxScore" : 2.52165401298128
}
- ],
+ ]
+ },
+ {
+ "description" : "Peak calls for Histone Variants ChIP-chip arrays w peaks",
+ "name" : "__Histone Variants ChIP-chip arrays peaks",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Variants ChIP-chip arrays w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "description" : "Peak calls for Histone Variants ChIP-chip arrays w peaks",
- "name" : "__Histone Variants ChIP-chip arrays peaks",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4490_details.gff.bb"
- }
- }
- },
- {
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Lin-15B ChIP-chip arrays w peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Transcription and Chromatin"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
- "displayId" : "Lin-15B ChIP-chip arrays w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "minScore" : 0,
- "maxScore" : 3.96715371225033,
- "type" : "LinearWiggleDisplay"
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "height" : 6,
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "color1" : "deeppink"
+ },
+ "displayId" : "Histone Variants ChIP-chip arrays w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
- ],
- "name" : "Lin-15B ChIP-chip arrays w peaks",
- "type" : "QuantitativeTrack",
+ ]
+ },
+ {
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SDQ2330_LIN15B_N2_LTEMB_mean.bw"
- }
+ },
+ "type" : "BigWigAdapter"
},
- "description" : "Lin-15B Late Embryo. Synchronized C. elegans late embryos from strain N2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Lin-15B ChIP-chip arrays w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 3.96715371225033,
+ "displayId" : "Lin-15B ChIP-chip arrays w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 0
+ }
],
+ "description" : "Lin-15B Late Embryo. Synchronized C. elegans late embryos from strain N2. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Lin-15B ChIP-chip arrays w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Lin-15B ChIP-chip arrays w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ]
+ },
+ {
"displays" : [
{
- "displayId" : "Lin-15B ChIP-chip arrays w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
- }
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false
+ },
+ "displayId" : "Lin-15B ChIP-chip arrays w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
- "name" : "__Lin-15B ChIP-chip arrays peaks",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9582_details.gff.bb",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "description" : "Peak calls for Lin-15B ChIP-chip arrays w peaks"
- },
- {
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
- "PolII Isoforms ChIP"
+ "Transcription and Chromatin"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII Isoforms ChIP_Polymerase II Isoforms ChIP-chip arrays_ AMA1_N2_MXEMB",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Peak calls for Lin-15B ChIP-chip arrays w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Lin-15B ChIP-chip arrays w peaks_bigbed_peaks",
+ "name" : "__Lin-15B ChIP-chip arrays peaks"
+ },
+ {
"displays" : [
{
"displayId" : "Polymerase II Isoforms ChIP-chip arrays_ AMA1_N2_MXEMB_Transcription Factors_PolII Isoforms ChIP-LinearWiggleDisplay",
+ "minScore" : 1.12418005,
"maxScore" : 3.392924,
- "type" : "LinearWiggleDisplay",
- "minScore" : 1.12418005
+ "type" : "LinearWiggleDisplay"
}
],
- "type" : "QuantitativeTrack",
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
@@ -17802,40 +17183,49 @@
},
"type" : "BigWigAdapter"
},
- "name" : "Polymerase II Isoforms ChIP-chip arrays, AMA1_N2_MXEMB",
- "description" : "RNA Polymerase II Isoforms. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with either an affinity-purified polyclonal antibody that recognizes the largest sub-unit of RNA polymerase II or monoclonal antibody recognizing subunit 8WG16 of PolII. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "PolII Isoforms ChIP"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "description" : "RNA Polymerase II Isoforms. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with either an affinity-purified polyclonal antibody that recognizes the largest sub-unit of RNA polymerase II or monoclonal antibody recognizing subunit 8WG16 of PolII. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII Isoforms ChIP_Polymerase II Isoforms ChIP-chip arrays_ AMA1_N2_MXEMB",
+ "name" : "Polymerase II Isoforms ChIP-chip arrays, AMA1_N2_MXEMB"
},
{
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/ABAB817_8WG16_N2_LTEMB_mean.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "type" : "LinearWiggleDisplay",
"maxScore" : 4.600618,
+ "displayId" : "Polymerase II Isoforms ChIP-chip arrays_ 8WG16_N2_LTEMB_ABAB817 w peaks_Transcription Factors_PolII Isoforms ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "displayId" : "Polymerase II Isoforms ChIP-chip arrays_ 8WG16_N2_LTEMB_ABAB817 w peaks_Transcription Factors_PolII Isoforms ChIP-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII Isoforms ChIP_Polymerase II Isoforms ChIP-chip arrays_ 8WG16_N2_LTEMB_ABAB817 w peaks",
+ "name" : "Polymerase II Isoforms ChIP-chip arrays, 8WG16_N2_LTEMB_ABAB817 w peaks",
+ "description" : "RNA Polymerase II Isoforms. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with either an affinity-purified polyclonal antibody that recognizes the largest sub-unit of RNA polymerase II or monoclonal antibody recognizing subunit 8WG16 of PolII. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"PolII Isoforms ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII Isoforms ChIP_Polymerase II Isoforms ChIP-chip arrays_ 8WG16_N2_LTEMB_ABAB817 w peaks",
- "description" : "RNA Polymerase II Isoforms. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with either an affinity-purified polyclonal antibody that recognizes the largest sub-unit of RNA polymerase II or monoclonal antibody recognizing subunit 8WG16 of PolII. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/ABAB817_8WG16_N2_LTEMB_mean.bw"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "Polymerase II Isoforms ChIP-chip arrays, 8WG16_N2_LTEMB_ABAB817 w peaks"
+ ]
},
{
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9559_details.gff.bb",
@@ -17843,41 +17233,22 @@
},
"type" : "BigBedAdapter"
},
- "name" : "__Polymerase II Isoforms ChIP-chip arrays, 8WG16_N2_LTEMB_ABAB817 peaks",
- "description" : "Peak calls for Polymerase II Isoforms ChIP-chip arrays, 8WG16_N2_LTEMB_ABAB817 w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "PolII Isoforms ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII Isoforms ChIP_Polymerase II Isoforms ChIP-chip arrays_ 8WG16_N2_LTEMB_ABAB817 w peaks_bigbed_peaks",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
"type" : "SvgFeatureRenderer",
"showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false,
"color1" : "deeppink"
},
- "type" : "LinearBasicDisplay",
"displayId" : "Polymerase II Isoforms ChIP-chip arrays_ 8WG16_N2_LTEMB_ABAB817 w peaks_Transcription Factors_PolII Isoforms ChIP_bigbed_peaks"
}
- ]
- },
- {
- "displays" : [
- {
- "type" : "LinearWiggleDisplay",
- "maxScore" : 4.13,
- "minScore" : 0,
- "displayId" : "Polymerase II Isoforms ChIP-chip arrays_ 8WG16_N2_EEMB_ABAB817 w peaks_Transcription Factors_PolII Isoforms ChIP-LinearWiggleDisplay"
- }
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII Isoforms ChIP_Polymerase II Isoforms ChIP-chip arrays_ 8WG16_N2_EEMB_ABAB817 w peaks",
+ "description" : "Peak calls for Polymerase II Isoforms ChIP-chip arrays, 8WG16_N2_LTEMB_ABAB817 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII Isoforms ChIP_Polymerase II Isoforms ChIP-chip arrays_ 8WG16_N2_LTEMB_ABAB817 w peaks_bigbed_peaks",
+ "name" : "__Polymerase II Isoforms ChIP-chip arrays, 8WG16_N2_LTEMB_ABAB817 peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -17886,31 +17257,59 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : "RNA Polymerase II Isoforms. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with either an affinity-purified polyclonal antibody that recognizes the largest sub-unit of RNA polymerase II or monoclonal antibody recognizing subunit 8WG16 of PolII. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Polymerase II Isoforms ChIP-chip arrays, 8WG16_N2_EEMB_ABAB817 w peaks",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/ABAB817_8WG16_N2_EEMB_mean.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack"
+ "type" : "FeatureTrack"
+ },
+ {
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "PolII Isoforms ChIP"
+ ],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "RNA Polymerase II Isoforms. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with either an affinity-purified polyclonal antibody that recognizes the largest sub-unit of RNA polymerase II or monoclonal antibody recognizing subunit 8WG16 of PolII. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Polymerase II Isoforms ChIP-chip arrays, 8WG16_N2_EEMB_ABAB817 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII Isoforms ChIP_Polymerase II Isoforms ChIP-chip arrays_ 8WG16_N2_EEMB_ABAB817 w peaks",
+ "displays" : [
+ {
+ "displayId" : "Polymerase II Isoforms ChIP-chip arrays_ 8WG16_N2_EEMB_ABAB817 w peaks_Transcription Factors_PolII Isoforms ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 4.13,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/ABAB817_8WG16_N2_EEMB_mean.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
"displays" : [
{
- "displayId" : "Polymerase II Isoforms ChIP-chip arrays_ 8WG16_N2_EEMB_ABAB817 w peaks_Transcription Factors_PolII Isoforms ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
- }
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false
+ },
+ "displayId" : "Polymerase II Isoforms ChIP-chip arrays_ 8WG16_N2_EEMB_ABAB817 w peaks_Transcription Factors_PolII Isoforms ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9542_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -17919,29 +17318,11 @@
"Transcription Factors",
"PolII Isoforms ChIP"
],
+ "name" : "__Polymerase II Isoforms ChIP-chip arrays, 8WG16_N2_EEMB_ABAB817 peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII Isoforms ChIP_Polymerase II Isoforms ChIP-chip arrays_ 8WG16_N2_EEMB_ABAB817 w peaks_bigbed_peaks",
- "description" : "Peak calls for Polymerase II Isoforms ChIP-chip arrays, 8WG16_N2_EEMB_ABAB817 w peaks",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9542_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "__Polymerase II Isoforms ChIP-chip arrays, 8WG16_N2_EEMB_ABAB817 peaks"
+ "description" : "Peak calls for Polymerase II Isoforms ChIP-chip arrays, 8WG16_N2_EEMB_ABAB817 w peaks"
},
{
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/RNAPIIIPmean_WS220.bw"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "Polymerase II Isoforms ChIP-chip arrays, 8WG16_N2_MXEMB",
- "description" : "RNA Polymerase II Isoforms. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with either an affinity-purified polyclonal antibody that recognizes the largest sub-unit of RNA polymerase II or monoclonal antibody recognizing subunit 8WG16 of PolII. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -17950,18 +17331,39 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
+ "description" : "RNA Polymerase II Isoforms. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with either an affinity-purified polyclonal antibody that recognizes the largest sub-unit of RNA polymerase II or monoclonal antibody recognizing subunit 8WG16 of PolII. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII Isoforms ChIP_Polymerase II Isoforms ChIP-chip arrays_ 8WG16_N2_MXEMB",
+ "name" : "Polymerase II Isoforms ChIP-chip arrays, 8WG16_N2_MXEMB",
"displays" : [
{
- "displayId" : "Polymerase II Isoforms ChIP-chip arrays_ 8WG16_N2_MXEMB_Transcription Factors_PolII Isoforms ChIP-LinearWiggleDisplay",
- "minScore" : 0.890608610956476,
"type" : "LinearWiggleDisplay",
- "maxScore" : 2.61760185138326
+ "maxScore" : 2.61760185138326,
+ "displayId" : "Polymerase II Isoforms ChIP-chip arrays_ 8WG16_N2_MXEMB_Transcription Factors_PolII Isoforms ChIP-LinearWiggleDisplay",
+ "minScore" : 0.890608610956476
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/RNAPIIIPmean_WS220.bw",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
+ "name" : "Polymerase II Isoforms ChIP-chip arrays, POLII4H8_N2_MXEMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII Isoforms ChIP_Polymerase II Isoforms ChIP-chip arrays_ POLII4H8_N2_MXEMB w peaks",
"description" : "RNA Polymerase II Isoforms. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with either an affinity-purified polyclonal antibody that recognizes the largest sub-unit of RNA polymerase II or monoclonal antibody recognizing subunit 8WG16 of PolII. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "PolII Isoforms ChIP"
+ ],
"adapter" : {
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/ABAB5408_4H8_N2_MXEMB_mean_WS220.bw",
@@ -17969,8 +17371,6 @@
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "name" : "Polymerase II Isoforms ChIP-chip arrays, POLII4H8_N2_MXEMB w peaks",
"displays" : [
{
"displayId" : "Polymerase II Isoforms ChIP-chip arrays_ POLII4H8_N2_MXEMB w peaks_Transcription Factors_PolII Isoforms ChIP-LinearWiggleDisplay",
@@ -17978,111 +17378,116 @@
"maxScore" : 4.58572140182186,
"type" : "LinearWiggleDisplay"
}
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "PolII Isoforms ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII Isoforms ChIP_Polymerase II Isoforms ChIP-chip arrays_ POLII4H8_N2_MXEMB w peaks"
+ ]
},
{
"displays" : [
{
"displayId" : "Polymerase II Isoforms ChIP-chip arrays_ POLII4H8_N2_MXEMB w peaks_Transcription Factors_PolII Isoforms ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
"height" : 6,
- "showDescriptions" : false
- }
+ "showLabels" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "PolII Isoforms ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII Isoforms ChIP_Polymerase II Isoforms ChIP-chip arrays_ POLII4H8_N2_MXEMB w peaks_bigbed_peaks",
- "description" : "Peak calls for Polymerase II Isoforms ChIP-chip arrays, POLII4H8_N2_MXEMB w peaks",
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4508_details.gff.bb"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4508_details.gff.bb",
+ "locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
- "name" : "__Polymerase II Isoforms ChIP-chip arrays, POLII4H8_N2_MXEMB peaks"
- },
- {
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII Isoforms ChIP_Polymerase II Isoforms ChIP-chip arrays_ 8WG16_N2_EEMB",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"PolII Isoforms ChIP"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "Peak calls for Polymerase II Isoforms ChIP-chip arrays, POLII4H8_N2_MXEMB w peaks",
+ "name" : "__Polymerase II Isoforms ChIP-chip arrays, POLII4H8_N2_MXEMB peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII Isoforms ChIP_Polymerase II Isoforms ChIP-chip arrays_ POLII4H8_N2_MXEMB w peaks_bigbed_peaks"
+ },
+ {
"displays" : [
{
+ "type" : "LinearWiggleDisplay",
"displayId" : "Polymerase II Isoforms ChIP-chip arrays_ 8WG16_N2_EEMB_Transcription Factors_PolII Isoforms ChIP-LinearWiggleDisplay",
"minScore" : 1.66942014219794,
- "type" : "LinearWiggleDisplay",
"maxScore" : 4.75430346120587
}
],
- "name" : "Polymerase II Isoforms ChIP-chip arrays, 8WG16_N2_EEMB",
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/ABAB817_8WG16_N2_EEMB_mean_WS220.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
"type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "PolII Isoforms ChIP"
+ ],
+ "name" : "Polymerase II Isoforms ChIP-chip arrays, 8WG16_N2_EEMB",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII Isoforms ChIP_Polymerase II Isoforms ChIP-chip arrays_ 8WG16_N2_EEMB",
+ "description" : "RNA Polymerase II Isoforms. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with either an affinity-purified polyclonal antibody that recognizes the largest sub-unit of RNA polymerase II or monoclonal antibody recognizing subunit 8WG16 of PolII. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ },
+ {
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/ABAB817_8WG16_N2_EEMB_mean_WS220.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/CVMMS126R_8WG16_N2_L4_mean.wig_mean_WS220.bw",
"locationType" : "UriLocation"
}
},
- "description" : "RNA Polymerase II Isoforms. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with either an affinity-purified polyclonal antibody that recognizes the largest sub-unit of RNA polymerase II or monoclonal antibody recognizing subunit 8WG16 of PolII. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "displayId" : "Polymerase II Isoforms ChIP-chip arrays_ 8WG16_N2_L4_Transcription Factors_PolII Isoforms ChIP-LinearWiggleDisplay",
+ "minScore" : 1.4143368608912,
+ "maxScore" : 4.28586927542787
+ }
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII Isoforms ChIP_Polymerase II Isoforms ChIP-chip arrays_ 8WG16_N2_L4",
+ "name" : "Polymerase II Isoforms ChIP-chip arrays, 8WG16_N2_L4",
+ "description" : "RNA Polymerase II Isoforms. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with either an affinity-purified polyclonal antibody that recognizes the largest sub-unit of RNA polymerase II or monoclonal antibody recognizing subunit 8WG16 of PolII. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"PolII Isoforms ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII Isoforms ChIP_Polymerase II Isoforms ChIP-chip arrays_ 8WG16_N2_L4",
+ ]
+ },
+ {
"displays" : [
{
- "displayId" : "Polymerase II Isoforms ChIP-chip arrays_ 8WG16_N2_L4_Transcription Factors_PolII Isoforms ChIP-LinearWiggleDisplay",
- "maxScore" : 4.28586927542787,
- "type" : "LinearWiggleDisplay",
- "minScore" : 1.4143368608912
+ "maxScore" : 561.98278945308,
+ "displayId" : "Core Histones ChIP-Seq w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
}
],
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/CVMMS126R_8WG16_N2_L4_mean.wig_mean_WS220.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-AB1791_H3_N2_L3_merged.bw"
}
},
- "name" : "Polymerase II Isoforms ChIP-chip arrays, 8WG16_N2_L4",
- "description" : "RNA Polymerase II Isoforms. Synchronized C. elegans embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with either an affinity-purified polyclonal antibody that recognizes the largest sub-unit of RNA polymerase II or monoclonal antibody recognizing subunit 8WG16 of PolII. After whole genome amplification, NimbleGen genomic tiling microarrays were used in two-color hybridization experiments to compare the signal from the input DNA versus the fragments pulled-down in the ChIP. Normalized log2(ratios) are shown in this track.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Core Histones ChIP-Seq w peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -18091,46 +17496,35 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "displays" : [
- {
- "minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 561.98278945308,
- "displayId" : "Core Histones ChIP-Seq w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
- }
- ],
- "name" : "Core Histones ChIP-Seq w peaks",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-AB1791_H3_N2_L3_merged.bw"
- },
- "type" : "BigWigAdapter"
- },
"type" : "QuantitativeTrack",
- "description" : "Core Histones ChIP-Seq. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes core histone H3. ChIP-seq analysis of elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "description" : "Core Histones ChIP-Seq. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes core histone H3. ChIP-seq analysis of elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Core Histones ChIP-Seq w peaks",
+ "name" : "Core Histones ChIP-Seq w peaks"
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Peak calls for Core Histones ChIP-Seq w peaks",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Core Histones ChIP-Seq w peaks_bigbed_peaks",
+ "name" : "__Core Histones ChIP-Seq peaks",
"displays" : [
{
- "displayId" : "Core Histones ChIP-Seq w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink",
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
- }
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "Core Histones ChIP-Seq w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
"adapter" : {
@@ -18139,55 +17533,41 @@
"locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "__Core Histones ChIP-Seq peaks",
- "description" : "Peak calls for Core Histones ChIP-Seq w peaks"
+ }
},
{
- "displays" : [
- {
- "displayId" : "Dosage Compensation ChIP-Seq w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 197.815659251644
- }
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-Seq w peaks",
"description" : "Dosage Compensation ChIP-Seq. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes dpy-27. ChIP-seq analysis of elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
+ "name" : "Dosage Compensation ChIP-Seq w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-Seq w peaks",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "minScore" : 0,
+ "displayId" : "Dosage Compensation ChIP-Seq w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 197.815659251644
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-JL00001_DPY27_N2_L3_merged.bw"
}
- },
- "name" : "Dosage Compensation ChIP-Seq w peaks"
+ }
},
{
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
- },
- "displayId" : "Dosage Compensation ChIP-Seq w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks"
- }
- ],
+ "description" : "Peak calls for Dosage Compensation ChIP-Seq w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Dosage Compensation ChIP-Seq w peaks_bigbed_peaks",
+ "name" : "__Dosage Compensation ChIP-Seq peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -18196,91 +17576,93 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : "Peak calls for Dosage Compensation ChIP-Seq w peaks",
- "name" : "__Dosage Compensation ChIP-Seq peaks",
"type" : "FeatureTrack",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10048_details.gff.bb",
- "locationType" : "UriLocation"
- }
- }
- },
- {
- "description" : "H3K4 modifications. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. ChIP-seq analysis of elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Histone Modifications (H3K4) ChIP-Seq, WA30534819_H3K4me3_N2_L3 w peaks",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-WA30534819_H3K4me3_N2_L3_merged.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10048_details.gff.bb"
},
- "type" : "BigWigAdapter"
+ "type" : "BigBedAdapter"
},
- "type" : "QuantitativeTrack",
"displays" : [
{
- "minScore" : 0,
- "maxScore" : 414.125234294639,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Histone Modifications (H3K4) ChIP-Seq_ WA30534819_H3K4me3_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "Dosage Compensation ChIP-Seq w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks"
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-Seq_ WA30534819_H3K4me3_N2_L3 w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
]
},
{
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
+ "name" : "Histone Modifications (H3K4) ChIP-Seq, WA30534819_H3K4me3_N2_L3 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-Seq_ WA30534819_H3K4me3_N2_L3 w peaks",
+ "description" : "H3K4 modifications. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 trimethylated on lysine 4. ChIP-seq analysis of elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 414.125234294639,
+ "minScore" : 0,
+ "displayId" : "Histone Modifications (H3K4) ChIP-Seq_ WA30534819_H3K4me3_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ }
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-Seq_ WA30534819_H3K4me3_N2_L3 w peaks_bigbed_peaks",
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-WA30534819_H3K4me3_N2_L3_merged.bw"
+ }
+ }
+ },
+ {
"displays" : [
{
"renderer" : {
"type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "deeppink",
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
+ "color1" : "deeppink"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "Histone Modifications (H3K4) ChIP-Seq_ WA30534819_H3K4me3_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks"
+ "displayId" : "Histone Modifications (H3K4) ChIP-Seq_ WA30534819_H3K4me3_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10681_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10681_details.gff.bb"
+ }
},
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Peak calls for Histone Modifications (H3K4) ChIP-Seq, WA30534819_H3K4me3_N2_L3 w peaks",
"name" : "__Histone Modifications (H3K4) ChIP-Seq, WA30534819_H3K4me3_N2_L3 peaks",
- "description" : "Peak calls for Histone Modifications (H3K4) ChIP-Seq, WA30534819_H3K4me3_N2_L3 w peaks"
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K4) ChIP-Seq_ WA30534819_H3K4me3_N2_L3 w peaks_bigbed_peaks"
},
{
"type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-LPAR109_H4tetraac_109_N2_L3_merged.bw"
- }
- },
- "name" : "Histone Modifications (H4) ChIP-Seq w peaks",
- "description" : "H4 modifications. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes tetra-acetylated histone H4. ChIP-seq analysis of elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-seq analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -18289,28 +17671,46 @@
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "name" : "Histone Modifications (H4) ChIP-Seq w peaks",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-Seq w peaks",
+ "description" : "H4 modifications. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes tetra-acetylated histone H4. ChIP-seq analysis of elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents. We will integrate information generated with existing knowledge on the biology of the targets, perform ChIP-seq analysis on mutant and RNAi extracts lacking selected target proteins, use extrachromosomal arrays to assess the ability of candidate identified sequence motifs to recruit targets in vivo, identify tissue-specific patterns of selected targets, and create integrated, quantitative models of transcription and whole-chromosome functions.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "displayId" : "Histone Modifications (H4) ChIP-Seq w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 496.363933305558
+ "displayId" : "Histone Modifications (H4) ChIP-Seq w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "maxScore" : 496.363933305558,
+ "type" : "LinearWiggleDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-LPAR109_H4tetraac_109_N2_L3_merged.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
- "name" : "__Histone Modifications (H4) ChIP-Seq peaks",
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
+ "showDescriptions" : false,
+ "height" : 6,
+ "showLabels" : false
+ },
+ "displayId" : "Histone Modifications (H4) ChIP-Seq w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10745_details.gff.bb"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10745_details.gff.bb",
+ "locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "description" : "Peak calls for Histone Modifications (H4) ChIP-Seq w peaks",
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-Seq w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -18319,32 +17719,30 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "displays" : [
- {
- "displayId" : "Histone Modifications (H4) ChIP-Seq w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink"
- }
- }
- ]
+ "type" : "FeatureTrack",
+ "description" : "Peak calls for Histone Modifications (H4) ChIP-Seq w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4) ChIP-Seq w peaks_bigbed_peaks",
+ "name" : "__Histone Modifications (H4) ChIP-Seq peaks"
},
{
- "name" : "Polycomb Proteins ChIP-Seq w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-SDQ0820_EPC1_N2_L3_merged.bw"
- },
- "type" : "BigWigAdapter"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-SDQ0820_EPC1_N2_L3_merged.bw",
+ "locationType" : "UriLocation"
+ }
},
+ "displays" : [
+ {
+ "minScore" : 0,
+ "displayId" : "Polycomb Proteins ChIP-Seq w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 315.471166056582,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"description" : "Dosage Compensation ChIP-Seq. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes dpy-27. ChIP-seq analysis of elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Polycomb Proteins ChIP-Seq w peaks",
+ "name" : "Polycomb Proteins ChIP-Seq w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -18353,90 +17751,73 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "displays" : [
- {
- "displayId" : "Polycomb Proteins ChIP-Seq w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "minScore" : 0,
- "maxScore" : 315.471166056582,
- "type" : "LinearWiggleDisplay"
- }
- ]
+ "type" : "QuantitativeTrack"
},
{
- "name" : "__Polycomb Proteins ChIP-Seq peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10332_details.gff.bb"
- }
- },
- "description" : "Peak calls for Polycomb Proteins ChIP-Seq w peaks",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Polycomb Proteins ChIP-Seq w peaks_bigbed_peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Polycomb Proteins ChIP-Seq w peaks_bigbed_peaks",
+ "name" : "__Polycomb Proteins ChIP-Seq peaks",
+ "description" : "Peak calls for Polycomb Proteins ChIP-Seq w peaks",
"displays" : [
{
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
"color1" : "deeppink",
"showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6,
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "Polycomb Proteins ChIP-Seq w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks"
+ "displayId" : "Polycomb Proteins ChIP-Seq w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10332_details.gff.bb"
+ }
+ }
},
{
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ3599_DPL1_N2_L3 w peaks",
"name" : "Transcription Factors ChIP-Seq L3, SDQ3599_DPL1_N2_L3 w peaks",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-SDQ3599_DPL1_N2_L3_merged.bw",
- "locationType" : "UriLocation"
- }
- },
"description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ3599_DPL1_N2_L3 w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-SDQ3599_DPL1_N2_L3_merged.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "type" : "LinearWiggleDisplay",
"maxScore" : 228.612058772144,
"minScore" : 0,
- "displayId" : "Transcription Factors ChIP-Seq L3_ SDQ3599_DPL1_N2_L3 w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "displayId" : "Transcription Factors ChIP-Seq L3_ SDQ3599_DPL1_N2_L3 w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
]
},
{
- "name" : "__Transcription Factors ChIP-Seq L3, SDQ3599_DPL1_N2_L3 peaks",
"type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10534_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "description" : "Peak calls for Transcription Factors ChIP-Seq L3, SDQ3599_DPL1_N2_L3 w peaks",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ3599_DPL1_N2_L3 w peaks_bigbed_peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -18445,23 +17826,31 @@
"Transcription Factors",
"Transcription and Chromatin"
],
+ "name" : "__Transcription Factors ChIP-Seq L3, SDQ3599_DPL1_N2_L3 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ3599_DPL1_N2_L3 w peaks_bigbed_peaks",
+ "description" : "Peak calls for Transcription Factors ChIP-Seq L3, SDQ3599_DPL1_N2_L3 w peaks",
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq L3_ SDQ3599_DPL1_N2_L3 w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
"renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
+ "showLabels" : false,
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
+ "type" : "SvgFeatureRenderer"
},
+ "displayId" : "Transcription Factors ChIP-Seq L3_ SDQ3599_DPL1_N2_L3 w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
"type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10534_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
- "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Transcription Factors ChIP-Seq L3, JA00011_LIN35_N2_L3 w peaks",
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
@@ -18469,27 +17858,29 @@
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq L3_ JA00011_LIN35_N2_L3 w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 231.61418169361
+ "displayId" : "Transcription Factors ChIP-Seq L3_ JA00011_LIN35_N2_L3 w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 231.61418169361,
+ "type" : "LinearWiggleDisplay"
}
],
+ "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ JA00011_LIN35_N2_L3 w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "Transcription Factors ChIP-Seq L3, JA00011_LIN35_N2_L3 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
- ]
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack"
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ JA00011_LIN35_N2_L3 w peaks_bigbed_peaks",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -18498,78 +17889,60 @@
"Transcription Factors",
"Transcription and Chromatin"
],
+ "name" : "__Transcription Factors ChIP-Seq L3, JA00011_LIN35_N2_L3 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ JA00011_LIN35_N2_L3 w peaks_bigbed_peaks",
+ "description" : "Peak calls for Transcription Factors ChIP-Seq L3, JA00011_LIN35_N2_L3 w peaks",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "Transcription Factors ChIP-Seq L3_ JA00011_LIN35_N2_L3 w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
"renderer" : {
- "color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
"height" : 6,
- "showDescriptions" : false
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "Transcription Factors ChIP-Seq L3_ JA00011_LIN35_N2_L3 w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks"
+ "showLabels" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "name" : "__Transcription Factors ChIP-Seq L3, JA00011_LIN35_N2_L3 peaks",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10485_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Peak calls for Transcription Factors ChIP-Seq L3, JA00011_LIN35_N2_L3 w peaks"
+ }
+ }
},
{
- "displays" : [
- {
- "minScore" : 94.8860813454422,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 221.975094986189,
- "displayId" : "Transcription Factors ChIP-Seq L3_ JA00001_HTZ1_N2_L3_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
- }
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ JA00001_HTZ1_N2_L3",
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ JA00001_HTZ1_N2_L3",
"name" : "Transcription Factors ChIP-Seq L3, JA00001_HTZ1_N2_L3",
- "type" : "QuantitativeTrack",
+ "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "maxScore" : 221.975094986189,
+ "minScore" : 94.8860813454422,
+ "displayId" : "Transcription Factors ChIP-Seq L3_ JA00001_HTZ1_N2_L3_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_3569.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_3569.bw"
},
"type" : "BigWigAdapter"
}
},
{
- "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5976.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "name" : "Transcription Factors ChIP-Seq L3, SDQ2340_HPL2_N2_L3",
- "displays" : [
- {
- "maxScore" : 744.41201764654,
- "type" : "LinearWiggleDisplay",
- "minScore" : 266.854765823358,
- "displayId" : "Transcription Factors ChIP-Seq L3_ SDQ2340_HPL2_N2_L3_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
- }
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -18578,17 +17951,42 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ2340_HPL2_N2_L3"
+ "type" : "QuantitativeTrack",
+ "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ2340_HPL2_N2_L3",
+ "name" : "Transcription Factors ChIP-Seq L3, SDQ2340_HPL2_N2_L3",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 744.41201764654,
+ "displayId" : "Transcription Factors ChIP-Seq L3_ SDQ2340_HPL2_N2_L3_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 266.854765823358
+ }
+ ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5976.bw"
+ }
+ }
},
{
"displays" : [
{
"displayId" : "Transcription Factors ChIP-Seq L3_ BH00004_LIN54_N2_L3 w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 159.109099944408
+ "maxScore" : 159.109099944408,
+ "type" : "LinearWiggleDisplay"
}
],
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-BH00004_LIN54_N2_L3_merged.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -18597,125 +17995,128 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ BH00004_LIN54_N2_L3 w peaks",
- "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-BH00004_LIN54_N2_L3_merged.bw"
- },
- "type" : "BigWigAdapter"
- },
"type" : "QuantitativeTrack",
+ "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ BH00004_LIN54_N2_L3 w peaks",
"name" : "Transcription Factors ChIP-Seq L3, BH00004_LIN54_N2_L3 w peaks"
},
{
- "description" : "Peak calls for Transcription Factors ChIP-Seq L3, BH00004_LIN54_N2_L3 w peaks",
"name" : "__Transcription Factors ChIP-Seq L3, BH00004_LIN54_N2_L3 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ BH00004_LIN54_N2_L3 w peaks_bigbed_peaks",
+ "description" : "Peak calls for Transcription Factors ChIP-Seq L3, BH00004_LIN54_N2_L3 w peaks",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Transcription and Chromatin"
+ ],
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10431_details.gff.bb"
- }
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10431_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq L3_ BH00004_LIN54_N2_L3 w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
"type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
+ "color1" : "deeppink",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
- }
+ "height" : 6,
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "Transcription Factors ChIP-Seq L3_ BH00004_LIN54_N2_L3 w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks"
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ BH00004_LIN54_N2_L3 w peaks_bigbed_peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Transcription and Chromatin"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
]
},
{
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-BH00001_LIN52_N2_L3_merged.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "maxScore" : 215.656054691891,
"type" : "LinearWiggleDisplay",
+ "displayId" : "Transcription Factors ChIP-Seq L3_ BH00001_LIN52_N2_L3 w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
"minScore" : 0,
- "displayId" : "Transcription Factors ChIP-Seq L3_ BH00001_LIN52_N2_L3 w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "maxScore" : 215.656054691891
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ BH00001_LIN52_N2_L3 w peaks",
+ "name" : "Transcription Factors ChIP-Seq L3, BH00001_LIN52_N2_L3 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ BH00001_LIN52_N2_L3 w peaks",
- "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-BH00001_LIN52_N2_L3_merged.bw"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "Transcription Factors ChIP-Seq L3, BH00001_LIN52_N2_L3 w peaks"
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack"
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ BH00001_LIN52_N2_L3 w peaks_bigbed_peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ BH00001_LIN52_N2_L3 w peaks_bigbed_peaks",
+ "name" : "__Transcription Factors ChIP-Seq L3, BH00001_LIN52_N2_L3 peaks",
+ "description" : "Peak calls for Transcription Factors ChIP-Seq L3, BH00001_LIN52_N2_L3 w peaks",
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq L3_ BH00001_LIN52_N2_L3 w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "deeppink",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"height" : 6,
- "showDescriptions" : false
- }
+ "showDescriptions" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "Transcription Factors ChIP-Seq L3_ BH00001_LIN52_N2_L3 w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
- "name" : "__Transcription Factors ChIP-Seq L3, BH00001_LIN52_N2_L3 peaks",
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10709_details.gff.bb",
"locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
- },
- "description" : "Peak calls for Transcription Factors ChIP-Seq L3, BH00001_LIN52_N2_L3 w peaks"
+ }
},
{
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ BH00003_LIN37_N2_L3 w peaks",
+ "name" : "Transcription Factors ChIP-Seq L3, BH00003_LIN37_N2_L3 w peaks",
+ "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ BH00003_LIN37_N2_L3 w peaks",
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-BH00003_LIN37_N2_L3_merged.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
"displayId" : "Transcription Factors ChIP-Seq L3_ BH00003_LIN37_N2_L3 w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
@@ -18723,43 +18124,21 @@
"maxScore" : 168.140787257841,
"type" : "LinearWiggleDisplay"
}
- ],
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-BH00003_LIN37_N2_L3_merged.bw"
- }
- },
- "name" : "Transcription Factors ChIP-Seq L3, BH00003_LIN37_N2_L3 w peaks",
- "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ ]
},
{
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ BH00003_LIN37_N2_L3 w peaks_bigbed_peaks",
+ "name" : "__Transcription Factors ChIP-Seq L3, BH00003_LIN37_N2_L3 peaks",
+ "description" : "Peak calls for Transcription Factors ChIP-Seq L3, BH00003_LIN37_N2_L3 w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "displays" : [
- {
- "displayId" : "Transcription Factors ChIP-Seq L3_ BH00003_LIN37_N2_L3 w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
- }
- }
- ],
- "name" : "__Transcription Factors ChIP-Seq L3, BH00003_LIN37_N2_L3 peaks",
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
@@ -18767,84 +18146,91 @@
},
"type" : "BigBedAdapter"
},
- "description" : "Peak calls for Transcription Factors ChIP-Seq L3, BH00003_LIN37_N2_L3 w peaks"
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false
+ },
+ "displayId" : "Transcription Factors ChIP-Seq L3_ BH00003_LIN37_N2_L3 w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ3528_NURF1_N2_L3",
+ "name" : "Transcription Factors ChIP-Seq L3, SDQ3528_NURF1_N2_L3",
+ "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ3528_NURF1_N2_L3",
- "displays" : [
- {
- "displayId" : "Transcription Factors ChIP-Seq L3_ SDQ3528_NURF1_N2_L3_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 593.045783812995,
- "minScore" : 219.496808658288
- }
- ],
- "type" : "QuantitativeTrack",
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5987.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5987.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
- "name" : "Transcription Factors ChIP-Seq L3, SDQ3528_NURF1_N2_L3",
- "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "minScore" : 219.496808658288,
+ "displayId" : "Transcription Factors ChIP-Seq L3_ SDQ3528_NURF1_N2_L3_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 593.045783812995
+ }
+ ]
},
{
- "name" : "Transcription Factors ChIP-Seq L3, SDQ2354_HDA1_N2_L3",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5973.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ2354_HDA1_N2_L3",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ2354_HDA1_N2_L3",
+ "name" : "Transcription Factors ChIP-Seq L3, SDQ2354_HDA1_N2_L3",
+ "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
"type" : "LinearWiggleDisplay",
- "maxScore" : 653.48501337985,
"minScore" : 240.70805441535,
- "displayId" : "Transcription Factors ChIP-Seq L3_ SDQ2354_HDA1_N2_L3_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "displayId" : "Transcription Factors ChIP-Seq L3_ SDQ2354_HDA1_N2_L3_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 653.48501337985
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5973.bw"
+ }
+ }
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ4663_RPC1_N2_L3",
+ "name" : "Transcription Factors ChIP-Seq L3, SDQ4663_RPC1_N2_L3",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ4663_RPC1_N2_L3",
- "displays" : [
- {
- "maxScore" : 63.518614892249,
- "type" : "LinearWiggleDisplay",
- "minScore" : 25.3228429144422,
- "displayId" : "Transcription Factors ChIP-Seq L3_ SDQ4663_RPC1_N2_L3_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
- }
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"adapter" : {
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6300.bw",
@@ -18852,30 +18238,28 @@
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "name" : "Transcription Factors ChIP-Seq L3, SDQ4663_RPC1_N2_L3",
- "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
"displays" : [
{
"type" : "LinearWiggleDisplay",
- "maxScore" : 767.703295735295,
- "minScore" : 290.714687592647,
- "displayId" : "Transcription Factors ChIP-Seq L3_ SDQ3861_LET418_N2_L3_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "displayId" : "Transcription Factors ChIP-Seq L3_ SDQ4663_RPC1_N2_L3_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 25.3228429144422,
+ "maxScore" : 63.518614892249
}
- ],
+ ]
+ },
+ {
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ3861_LET418_N2_L3",
+ "name" : "Transcription Factors ChIP-Seq L3, SDQ3861_LET418_N2_L3",
+ "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ3861_LET418_N2_L3",
- "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
"adapter" : {
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5974.bw",
@@ -18883,38 +18267,52 @@
},
"type" : "BigWigAdapter"
},
- "name" : "Transcription Factors ChIP-Seq L3, SDQ3861_LET418_N2_L3"
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 767.703295735295,
+ "minScore" : 290.714687592647,
+ "displayId" : "Transcription Factors ChIP-Seq L3_ SDQ3861_LET418_N2_L3_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ }
+ ]
},
{
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5980.bw"
+ }
+ },
"displays" : [
{
+ "maxScore" : 314.997760088093,
"displayId" : "Transcription Factors ChIP-Seq L3_ HM4077_LIN61_N2_L3_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
"minScore" : 126.916860829071,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 314.997760088093
+ "type" : "LinearWiggleDisplay"
}
],
+ "name" : "Transcription Factors ChIP-Seq L3, HM4077_LIN61_N2_L3",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ HM4077_LIN61_N2_L3",
+ "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ HM4077_LIN61_N2_L3",
- "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ ]
+ },
+ {
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5980.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5975.bw"
}
},
- "type" : "QuantitativeTrack",
- "name" : "Transcription Factors ChIP-Seq L3, HM4077_LIN61_N2_L3"
- },
- {
"displays" : [
{
"displayId" : "Transcription Factors ChIP-Seq L3_ SDQ2342_LET418_N2_L3_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
@@ -18923,38 +18321,20 @@
"type" : "LinearWiggleDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ2342_LET418_N2_L3",
+ "name" : "Transcription Factors ChIP-Seq L3, SDQ2342_LET418_N2_L3",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ2342_LET418_N2_L3",
- "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5975.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "name" : "Transcription Factors ChIP-Seq L3, SDQ2342_LET418_N2_L3"
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack"
},
{
- "name" : "Transcription Factors ChIP-Seq L3, BH00005_LIN9_N2_L3 w peaks",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-BH00005_LIN9_N2_L3_merged.bw"
- }
- },
- "type" : "QuantitativeTrack",
- "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ BH00005_LIN9_N2_L3 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -18963,27 +18343,48 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
+ "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ BH00005_LIN9_N2_L3 w peaks",
+ "name" : "Transcription Factors ChIP-Seq L3, BH00005_LIN9_N2_L3 w peaks",
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq L3_ BH00005_LIN9_N2_L3 w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay",
"maxScore" : 170.851137105502,
+ "displayId" : "Transcription Factors ChIP-Seq L3_ BH00005_LIN9_N2_L3 w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
"minScore" : 0
}
- ]
+ ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-BH00005_LIN9_N2_L3_merged.bw"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
- "name" : "__Transcription Factors ChIP-Seq L3, BH00005_LIN9_N2_L3 peaks",
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "renderer" : {
+ "showDescriptions" : false,
+ "height" : 6,
+ "showLabels" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "Transcription Factors ChIP-Seq L3_ BH00005_LIN9_N2_L3 w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10459_details.gff.bb",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10459_details.gff.bb"
}
},
- "description" : "Peak calls for Transcription Factors ChIP-Seq L3, BH00005_LIN9_N2_L3 w peaks",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ BH00005_LIN9_N2_L3 w peaks_bigbed_peaks",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -18992,31 +18393,11 @@
"Transcription Factors",
"Transcription and Chromatin"
],
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink"
- },
- "displayId" : "Transcription Factors ChIP-Seq L3_ BH00005_LIN9_N2_L3 w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks"
- }
- ]
+ "name" : "__Transcription Factors ChIP-Seq L3, BH00005_LIN9_N2_L3 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ BH00005_LIN9_N2_L3 w peaks_bigbed_peaks",
+ "description" : "Peak calls for Transcription Factors ChIP-Seq L3, BH00005_LIN9_N2_L3 w peaks"
},
{
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_3574.bw"
- }
- },
- "name" : "Transcription Factors ChIP-Seq L3, SDQ2370_LIN53_N2_L3",
- "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -19025,112 +18406,117 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
+ "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ2370_LIN53_N2_L3",
+ "name" : "Transcription Factors ChIP-Seq L3, SDQ2370_LIN53_N2_L3",
"displays" : [
{
"displayId" : "Transcription Factors ChIP-Seq L3_ SDQ2370_LIN53_N2_L3_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 119.039747979395,
"maxScore" : 302.822266604227,
- "type" : "LinearWiggleDisplay",
- "minScore" : 119.039747979395
+ "type" : "LinearWiggleDisplay"
}
- ]
- },
- {
- "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
+ ],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5986.bw"
- }
- },
- "name" : "Transcription Factors ChIP-Seq L3, SDQ3525_NURF1_N2_L3",
- "displays" : [
- {
- "maxScore" : 274.281081653404,
- "type" : "LinearWiggleDisplay",
- "minScore" : 105.279556945623,
- "displayId" : "Transcription Factors ChIP-Seq L3_ SDQ3525_NURF1_N2_L3_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
- }
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Transcription and Chromatin"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ3525_NURF1_N2_L3"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_3574.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ3520_LIN61_N2_L3",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Transcription Factors ChIP-Seq L3, SDQ3525_NURF1_N2_L3",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ3525_NURF1_N2_L3",
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq L3_ SDQ3520_LIN61_N2_L3_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "minScore" : 156.233240034001,
"type" : "LinearWiggleDisplay",
- "maxScore" : 394.841030406062
+ "maxScore" : 274.281081653404,
+ "displayId" : "Transcription Factors ChIP-Seq L3_ SDQ3525_NURF1_N2_L3_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 105.279556945623
}
],
- "name" : "Transcription Factors ChIP-Seq L3, SDQ3520_LIN61_N2_L3",
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5979.bw"
- },
- "type" : "BigWigAdapter"
- },
- "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5986.bw",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
- "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5985.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5979.bw"
}
},
- "type" : "QuantitativeTrack",
- "name" : "Transcription Factors ChIP-Seq L3, SDQ2940_NURF1_N2_L3",
"displays" : [
{
- "minScore" : 137.166996325145,
- "maxScore" : 377.18332219741,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Transcription Factors ChIP-Seq L3_ SDQ2940_NURF1_N2_L3_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "displayId" : "Transcription Factors ChIP-Seq L3_ SDQ3520_LIN61_N2_L3_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 156.233240034001,
+ "maxScore" : 394.841030406062,
+ "type" : "LinearWiggleDisplay"
}
],
- "assemblyNames" : [
+ "name" : "Transcription Factors ChIP-Seq L3, SDQ3520_LIN61_N2_L3",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ3520_LIN61_N2_L3",
+ "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ2940_NURF1_N2_L3"
+ ]
},
{
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq L3_ SDQ3590_EFL1_N2_L3 w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay",
- "maxScore" : 318.009069603423,
- "minScore" : 0
+ "displayId" : "Transcription Factors ChIP-Seq L3_ SDQ2940_NURF1_N2_L3_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 137.166996325145,
+ "maxScore" : 377.18332219741
+ }
+ ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5985.bw"
}
+ },
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Transcription and Chromatin"
],
+ "name" : "Transcription Factors ChIP-Seq L3, SDQ2940_NURF1_N2_L3",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ2940_NURF1_N2_L3",
+ "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ },
+ {
+ "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ3590_EFL1_N2_L3 w peaks",
+ "name" : "Transcription Factors ChIP-Seq L3, SDQ3590_EFL1_N2_L3 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -19139,84 +18525,98 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ3590_EFL1_N2_L3 w peaks",
- "description" : "seq-SDQ2370_LIN53_N2_L3. Synchronized C. elegans L3 larvae from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-SDQ3590_EFL1_N2_L3_merged.bw"
- }
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-SDQ3590_EFL1_N2_L3_merged.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "name" : "Transcription Factors ChIP-Seq L3, SDQ3590_EFL1_N2_L3 w peaks"
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 318.009069603423,
+ "minScore" : 0,
+ "displayId" : "Transcription Factors ChIP-Seq L3_ SDQ3590_EFL1_N2_L3 w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ }
+ ]
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ3590_EFL1_N2_L3 w peaks_bigbed_peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq L3_ SDQ3590_EFL1_N2_L3 w peaks_bigbed_peaks",
+ "name" : "__Transcription Factors ChIP-Seq L3, SDQ3590_EFL1_N2_L3 peaks",
+ "description" : "Peak calls for Transcription Factors ChIP-Seq L3, SDQ3590_EFL1_N2_L3 w peaks",
"displays" : [
{
"displayId" : "Transcription Factors ChIP-Seq L3_ SDQ3590_EFL1_N2_L3 w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
+ "showLabels" : false,
"showDescriptions" : false,
"height" : 6
},
"type" : "LinearBasicDisplay"
}
],
- "name" : "__Transcription Factors ChIP-Seq L3, SDQ3590_EFL1_N2_L3 peaks",
"adapter" : {
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10535_details.gff.bb",
"locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Peak calls for Transcription Factors ChIP-Seq L3, SDQ3590_EFL1_N2_L3 w peaks"
+ }
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Transcription and Chromatin"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ BH00003_LIN37_N2_LEMB w peaks",
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-BH00003_LIN37_N2_LTemb_mean.bw",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
"minScore" : 0,
+ "displayId" : "Transcription Factors ChIP-Seq Late Embryo_ BH00003_LIN37_N2_LEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
"maxScore" : 140.358900609624,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Transcription Factors ChIP-Seq Late Embryo_ BH00003_LIN37_N2_LEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
],
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-BH00003_LIN37_N2_LTemb_mean.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ BH00003_LIN37_N2_LEMB w peaks",
"name" : "Transcription Factors ChIP-Seq Late Embryo, BH00003_LIN37_N2_LEMB w peaks",
- "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Transcription and Chromatin"
+ ]
},
{
"description" : "Peak calls for Transcription Factors ChIP-Seq Late Embryo, BH00003_LIN37_N2_LEMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ BH00003_LIN37_N2_LEMB w peaks_bigbed_peaks",
"name" : "__Transcription Factors ChIP-Seq Late Embryo, BH00003_LIN37_N2_LEMB peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Transcription and Chromatin"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
@@ -19227,101 +18627,82 @@
},
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "Transcription Factors ChIP-Seq Late Embryo_ BH00003_LIN37_N2_LEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks"
}
+ ]
+ },
+ {
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ SDQ3590_EFL1_N2_LEMB w peaks",
+ "name" : "Transcription Factors ChIP-Seq Late Embryo, SDQ3590_EFL1_N2_LEMB w peaks",
+ "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ BH00003_LIN37_N2_LEMB w peaks_bigbed_peaks",
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ]
- },
- {
- "name" : "Transcription Factors ChIP-Seq Late Embryo, SDQ3590_EFL1_N2_LEMB w peaks",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-SDQ3590_EFL1_N2_LTemb_mean.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-SDQ3590_EFL1_N2_LTemb_mean.bw",
+ "locationType" : "UriLocation"
}
},
- "type" : "QuantitativeTrack",
- "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ SDQ3590_EFL1_N2_LEMB w peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Transcription and Chromatin"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
- "maxScore" : 120.221684096231,
"type" : "LinearWiggleDisplay",
+ "displayId" : "Transcription Factors ChIP-Seq Late Embryo_ SDQ3590_EFL1_N2_LEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
"minScore" : 0,
- "displayId" : "Transcription Factors ChIP-Seq Late Embryo_ SDQ3590_EFL1_N2_LEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "maxScore" : 120.221684096231
}
]
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ SDQ3590_EFL1_N2_LEMB w peaks_bigbed_peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ SDQ3590_EFL1_N2_LEMB w peaks_bigbed_peaks",
+ "name" : "__Transcription Factors ChIP-Seq Late Embryo, SDQ3590_EFL1_N2_LEMB peaks",
+ "description" : "Peak calls for Transcription Factors ChIP-Seq Late Embryo, SDQ3590_EFL1_N2_LEMB w peaks",
"displays" : [
{
"displayId" : "Transcription Factors ChIP-Seq Late Embryo_ SDQ3590_EFL1_N2_LEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
"color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
},
"type" : "LinearBasicDisplay"
}
],
- "name" : "__Transcription Factors ChIP-Seq Late Embryo, SDQ3590_EFL1_N2_LEMB peaks",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/12218_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Peak calls for Transcription Factors ChIP-Seq Late Embryo, SDQ3590_EFL1_N2_LEMB w peaks"
+ }
+ }
},
{
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_3929.bw",
- "locationType" : "UriLocation"
- }
- },
- "type" : "QuantitativeTrack",
- "name" : "Transcription Factors ChIP-Seq Late Embryo, SDQ3166_LIN37_N2_LEMB",
- "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -19330,36 +18711,45 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
+ "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ SDQ3166_LIN37_N2_LEMB",
+ "name" : "Transcription Factors ChIP-Seq Late Embryo, SDQ3166_LIN37_N2_LEMB",
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq Late Embryo_ SDQ3166_LIN37_N2_LEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "maxScore" : 110.984904361756,
"type" : "LinearWiggleDisplay",
- "minScore" : 50.6347184393796
+ "minScore" : 50.6347184393796,
+ "displayId" : "Transcription Factors ChIP-Seq Late Embryo_ SDQ3166_LIN37_N2_LEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 110.984904361756
}
- ]
+ ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_3929.bw"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
- "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Transcription Factors ChIP-Seq Late Embryo, BH00004_LIN54_N2_LEMB w peaks",
"adapter" : {
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-BH00004_LIN54_N2_LTemb_mean.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-BH00004_LIN54_N2_LTemb_mean.bw"
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
"displays" : [
{
- "minScore" : 0,
"type" : "LinearWiggleDisplay",
- "maxScore" : 148.495009165449,
- "displayId" : "Transcription Factors ChIP-Seq Late Embryo_ BH00004_LIN54_N2_LEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "displayId" : "Transcription Factors ChIP-Seq Late Embryo_ BH00004_LIN54_N2_LEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 148.495009165449
}
],
+ "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ BH00004_LIN54_N2_LEMB w peaks",
+ "name" : "Transcription Factors ChIP-Seq Late Embryo, BH00004_LIN54_N2_LEMB w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -19367,62 +18757,63 @@
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
+ ],
+ "type" : "QuantitativeTrack"
},
{
"description" : "Peak calls for Transcription Factors ChIP-Seq Late Embryo, BH00004_LIN54_N2_LEMB w peaks",
"name" : "__Transcription Factors ChIP-Seq Late Embryo, BH00004_LIN54_N2_LEMB peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ BH00004_LIN54_N2_LEMB w peaks_bigbed_peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Transcription and Chromatin"
+ ],
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/12350_details.gff.bb"
- },
- "type" : "BigBedAdapter"
+ }
},
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "Transcription Factors ChIP-Seq Late Embryo_ BH00004_LIN54_N2_LEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
"renderer" : {
- "showDescriptions" : false,
"height" : 6,
- "type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
"showLabels" : false,
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay"
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ }
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ BH00004_LIN54_N2_LEMB w peaks_bigbed_peaks",
+ ]
+ },
+ {
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ BH00005_LIN9_N2_LEMB w peaks",
+ "name" : "Transcription Factors ChIP-Seq Late Embryo, BH00005_LIN9_N2_LEMB w peaks",
+ "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
- ]
- },
- {
- "name" : "Transcription Factors ChIP-Seq Late Embryo, BH00005_LIN9_N2_LEMB w peaks",
- "type" : "QuantitativeTrack",
+ ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-BH00005_LIN9_N2_LTemb_mean.bw"
- },
- "type" : "BigWigAdapter"
+ }
},
- "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ BH00005_LIN9_N2_LEMB w peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Transcription and Chromatin"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
"displayId" : "Transcription Factors ChIP-Seq Late Embryo_ BH00005_LIN9_N2_LEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
@@ -19433,59 +18824,48 @@
]
},
{
- "displays" : [
- {
- "renderer" : {
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "height" : 6,
- "showDescriptions" : false
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "Transcription Factors ChIP-Seq Late Embryo_ BH00005_LIN9_N2_LEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks"
- }
- ],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ BH00005_LIN9_N2_LEMB w peaks_bigbed_peaks",
+ "name" : "__Transcription Factors ChIP-Seq Late Embryo, BH00005_LIN9_N2_LEMB peaks",
+ "description" : "Peak calls for Transcription Factors ChIP-Seq Late Embryo, BH00005_LIN9_N2_LEMB w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : "Peak calls for Transcription Factors ChIP-Seq Late Embryo, BH00005_LIN9_N2_LEMB w peaks",
- "name" : "__Transcription Factors ChIP-Seq Late Embryo, BH00005_LIN9_N2_LEMB peaks",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/12362_details.gff.bb",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/12362_details.gff.bb"
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack"
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6
+ },
+ "displayId" : "Transcription Factors ChIP-Seq Late Embryo_ BH00005_LIN9_N2_LEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ BH00001_LIN52_N2_LEMB w peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Transcription and Chromatin"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq Late Embryo_ BH00001_LIN52_N2_LEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "minScore" : 0,
"type" : "LinearWiggleDisplay",
- "maxScore" : 148.065183442545
+ "maxScore" : 148.065183442545,
+ "displayId" : "Transcription Factors ChIP-Seq Late Embryo_ BH00001_LIN52_N2_LEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 0
}
],
- "name" : "Transcription Factors ChIP-Seq Late Embryo, BH00001_LIN52_N2_LEMB w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -19493,9 +18873,7 @@
"locationType" : "UriLocation"
}
},
- "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -19504,20 +18882,23 @@
"Transcription Factors",
"Transcription and Chromatin"
],
+ "name" : "Transcription Factors ChIP-Seq Late Embryo, BH00001_LIN52_N2_LEMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ BH00001_LIN52_N2_LEMB w peaks",
+ "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ },
+ {
+ "description" : "Peak calls for Transcription Factors ChIP-Seq Late Embryo, BH00001_LIN52_N2_LEMB w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ BH00001_LIN52_N2_LEMB w peaks_bigbed_peaks",
- "displays" : [
- {
- "displayId" : "Transcription Factors ChIP-Seq Late Embryo_ BH00001_LIN52_N2_LEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
- "renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay"
- }
+ "name" : "__Transcription Factors ChIP-Seq Late Embryo, BH00001_LIN52_N2_LEMB peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Transcription and Chromatin"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
@@ -19525,21 +18906,25 @@
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "name" : "__Transcription Factors ChIP-Seq Late Embryo, BH00001_LIN52_N2_LEMB peaks",
- "description" : "Peak calls for Transcription Factors ChIP-Seq Late Embryo, BH00001_LIN52_N2_LEMB w peaks"
+ "displays" : [
+ {
+ "displayId" : "Transcription Factors ChIP-Seq Late Embryo_ BH00001_LIN52_N2_LEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_3931.bw",
- "locationType" : "UriLocation"
- }
- },
- "type" : "QuantitativeTrack",
"name" : "Transcription Factors ChIP-Seq Late Embryo, SDQ2370_LIN53_N2_LEMB",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ SDQ2370_LIN53_N2_LEMB",
"description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -19548,19 +18933,31 @@
"Transcription Factors",
"Transcription and Chromatin"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ SDQ2370_LIN53_N2_LEMB",
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_3931.bw"
+ }
+ },
"displays" : [
{
- "maxScore" : 110.984731830151,
"type" : "LinearWiggleDisplay",
- "minScore" : 50.6346615039498,
- "displayId" : "Transcription Factors ChIP-Seq Late Embryo_ SDQ2370_LIN53_N2_LEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "maxScore" : 110.984731830151,
+ "displayId" : "Transcription Factors ChIP-Seq Late Embryo_ SDQ2370_LIN53_N2_LEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 50.6346615039498
}
]
},
{
- "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Transcription Factors ChIP-Seq Late Embryo, SDQ3599_DPL1_N2_LEMB w peaks",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 115.130762148693,
+ "minScore" : 0,
+ "displayId" : "Transcription Factors ChIP-Seq Late Embryo_ SDQ3599_DPL1_N2_LEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -19568,162 +18965,147 @@
"locationType" : "UriLocation"
}
},
- "type" : "QuantitativeTrack",
- "displays" : [
- {
- "displayId" : "Transcription Factors ChIP-Seq Late Embryo_ SDQ3599_DPL1_N2_LEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "maxScore" : 115.130762148693,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
- }
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ SDQ3599_DPL1_N2_LEMB w peaks",
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ]
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ SDQ3599_DPL1_N2_LEMB w peaks",
+ "name" : "Transcription Factors ChIP-Seq Late Embryo, SDQ3599_DPL1_N2_LEMB w peaks",
+ "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "description" : "Peak calls for Transcription Factors ChIP-Seq Late Embryo, SDQ3599_DPL1_N2_LEMB w peaks",
- "name" : "__Transcription Factors ChIP-Seq Late Embryo, SDQ3599_DPL1_N2_LEMB peaks",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/12280_details.gff.bb",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq Late Embryo_ SDQ3599_DPL1_N2_LEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
"type" : "LinearBasicDisplay",
+ "displayId" : "Transcription Factors ChIP-Seq Late Embryo_ SDQ3599_DPL1_N2_LEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
"renderer" : {
- "color1" : "deeppink",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
+ "showLabels" : false,
"height" : 6,
- "showDescriptions" : false
+ "showDescriptions" : false,
+ "color1" : "deeppink"
}
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ SDQ3599_DPL1_N2_LEMB w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/12280_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
- ]
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Peak calls for Transcription Factors ChIP-Seq Late Embryo, SDQ3599_DPL1_N2_LEMB w peaks",
+ "name" : "__Transcription Factors ChIP-Seq Late Embryo, SDQ3599_DPL1_N2_LEMB peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ SDQ3599_DPL1_N2_LEMB w peaks_bigbed_peaks"
},
{
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-JA00011_LIN35_N2_LTemb_mean.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
"minScore" : 0,
+ "displayId" : "Transcription Factors ChIP-Seq Late Embryo_ JA00011_LIN35_N2_LEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
"maxScore" : 160.249526643697,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Transcription Factors ChIP-Seq Late Embryo_ JA00011_LIN35_N2_LEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ JA00011_LIN35_N2_LEMB w peaks",
+ "name" : "Transcription Factors ChIP-Seq Late Embryo, JA00011_LIN35_N2_LEMB w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ JA00011_LIN35_N2_LEMB w peaks",
- "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-JA00011_LIN35_N2_LTemb_mean.bw"
- }
- },
- "type" : "QuantitativeTrack",
- "name" : "Transcription Factors ChIP-Seq Late Embryo, JA00011_LIN35_N2_LEMB w peaks"
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack"
},
{
+ "name" : "__Transcription Factors ChIP-Seq Late Embryo, JA00011_LIN35_N2_LEMB peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ JA00011_LIN35_N2_LEMB w peaks_bigbed_peaks",
"description" : "Peak calls for Transcription Factors ChIP-Seq Late Embryo, JA00011_LIN35_N2_LEMB w peaks",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Transcription and Chromatin"
+ ],
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/12368_details.gff.bb",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/12368_details.gff.bb"
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "name" : "__Transcription Factors ChIP-Seq Late Embryo, JA00011_LIN35_N2_LEMB peaks",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "height" : 6,
+ "showDescriptions" : false
},
- "type" : "LinearBasicDisplay",
"displayId" : "Transcription Factors ChIP-Seq Late Embryo_ JA00011_LIN35_N2_LEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks"
}
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Transcription and Chromatin"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Late Embryo_ JA00011_LIN35_N2_LEMB w peaks_bigbed_peaks"
+ ]
},
{
- "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6227.bw",
"locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ }
},
- "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ2357Q2358_AMA1_N2_MXEMB_EE",
"displays" : [
{
"displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ2357Q2358_AMA1_N2_MXEMB_EE_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 83.9640420796966,
"maxScore" : 205.364066908172,
- "type" : "LinearWiggleDisplay",
- "minScore" : 83.9640420796966
+ "type" : "LinearWiggleDisplay"
}
],
+ "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ2357Q2358_AMA1_N2_MXEMB_EE",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ2357Q2358_AMA1_N2_MXEMB_EE",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ2357Q2358_AMA1_N2_MXEMB_EE"
+ ]
},
{
"type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-SDQ4663_RPC1_N2_MXemb_merged.bw",
- "locationType" : "UriLocation"
- }
- },
- "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ4663_RPC1_N2_MXEMB w peaks",
- "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -19732,41 +19114,46 @@
"Transcription Factors",
"Transcription and Chromatin"
],
+ "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ4663_RPC1_N2_MXEMB w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4663_RPC1_N2_MXEMB w peaks",
+ "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4663_RPC1_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
"maxScore" : 182.343421334315,
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4663_RPC1_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-SDQ4663_RPC1_N2_MXemb_merged.bw",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
- "description" : "Peak calls for Transcription Factors ChIP-Seq Mixed embryo, SDQ4663_RPC1_N2_MXEMB w peaks",
- "name" : "__Transcription Factors ChIP-Seq Mixed embryo, SDQ4663_RPC1_N2_MXEMB peaks",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10307_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4663_RPC1_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
"showDescriptions" : false,
"height" : 6,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
+ "showLabels" : false
},
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4663_RPC1_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4663_RPC1_N2_MXEMB w peaks_bigbed_peaks",
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10307_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -19774,20 +19161,13 @@
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Peak calls for Transcription Factors ChIP-Seq Mixed embryo, SDQ4663_RPC1_N2_MXEMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4663_RPC1_N2_MXEMB w peaks_bigbed_peaks",
+ "name" : "__Transcription Factors ChIP-Seq Mixed embryo, SDQ4663_RPC1_N2_MXEMB peaks"
},
{
- "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ4526_TF3C_N2_MXEMB w peaks",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-SDQ4526_SFC1_N2_MXemb_merged.bw",
- "locationType" : "UriLocation"
- }
- },
- "type" : "QuantitativeTrack",
- "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4526_TF3C_N2_MXEMB w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -19796,30 +19176,51 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
+ "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4526_TF3C_N2_MXEMB w peaks",
+ "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ4526_TF3C_N2_MXEMB w peaks",
"displays" : [
{
"type" : "LinearWiggleDisplay",
"maxScore" : 86.0678665668335,
- "minScore" : 0,
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4526_TF3C_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4526_TF3C_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 0
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-SDQ4526_SFC1_N2_MXemb_merged.bw"
+ }
+ }
},
{
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10244_details.gff.bb"
+ }
+ },
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4526_TF3C_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4526_TF3C_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks"
}
],
+ "name" : "__Transcription Factors ChIP-Seq Mixed embryo, SDQ4526_TF3C_N2_MXEMB peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4526_TF3C_N2_MXEMB w peaks_bigbed_peaks",
+ "description" : "Peak calls for Transcription Factors ChIP-Seq Mixed embryo, SDQ4526_TF3C_N2_MXEMB w peaks",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -19827,22 +19228,9 @@
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
- ],
- "description" : "Peak calls for Transcription Factors ChIP-Seq Mixed embryo, SDQ4526_TF3C_N2_MXEMB w peaks",
- "name" : "__Transcription Factors ChIP-Seq Mixed embryo, SDQ4526_TF3C_N2_MXEMB peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10244_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- }
+ ]
},
{
- "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ4470_TAG315_N2_MXEMB w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq_SDQ4470_TAG315_N2_MXemb_merged.bw",
@@ -19852,213 +19240,223 @@
},
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4470_TAG315_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 45.8285700407547
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4470_TAG315_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 45.8285700407547,
+ "type" : "LinearWiggleDisplay"
}
],
+ "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ4470_TAG315_N2_MXEMB w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4470_TAG315_N2_MXEMB w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Transcription and Chromatin"
- ]
- },
- {
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4470_TAG315_N2_MXEMB w peaks_bigbed_peaks",
+ ]
+ },
+ {
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10309_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4470_TAG315_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "showDescriptions" : false,
+ "height" : 6,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4470_TAG315_N2_MXEMB w peaks_Transcription Factors_Transcription and Chromatin_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10309_details.gff.bb",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
+ "description" : "Peak calls for Transcription Factors ChIP-Seq Mixed embryo, SDQ4470_TAG315_N2_MXEMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4470_TAG315_N2_MXEMB w peaks_bigbed_peaks",
"name" : "__Transcription Factors ChIP-Seq Mixed embryo, SDQ4470_TAG315_N2_MXEMB peaks",
- "description" : "Peak calls for Transcription Factors ChIP-Seq Mixed embryo, SDQ4470_TAG315_N2_MXEMB w peaks"
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Transcription and Chromatin"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack"
},
{
- "name" : "Transcription Factors ChIP-Seq Mixed embryo, AB46540_NIgG_N2_MXEMB",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6208.bw",
- "locationType" : "UriLocation"
- }
- },
"description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Transcription Factors ChIP-Seq Mixed embryo, AB46540_NIgG_N2_MXEMB",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ AB46540_NIgG_N2_MXEMB",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6208.bw"
+ }
+ },
"displays" : [
{
"type" : "LinearWiggleDisplay",
"maxScore" : 22.1603870355924,
- "minScore" : 10.2743277217455,
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ AB46540_NIgG_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ AB46540_NIgG_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 10.2743277217455
}
]
},
{
"description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ4585_ASH2_N2_MXEMB",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4585_ASH2_N2_MXEMB",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Transcription and Chromatin"
+ ],
"type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6291.bw"
- }
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6291.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
},
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4585_ASH2_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "minScore" : 5.55468892349661,
"type" : "LinearWiggleDisplay",
+ "minScore" : 5.55468892349661,
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4585_ASH2_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
"maxScore" : 12.8326937075655
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4585_ASH2_N2_MXEMB",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Transcription and Chromatin"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
]
},
{
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4481_PQN85_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
"minScore" : 7.12659566914409,
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4481_PQN85_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
"maxScore" : 15.8093808155882,
"type" : "LinearWiggleDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4481_PQN85_N2_MXEMB",
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6265.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4481_PQN85_N2_MXEMB",
"name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ4481_PQN85_N2_MXEMB",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6265.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- }
+ "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "name" : "Transcription Factors ChIP-Seq Mixed embryo, NBP170893_HTZ1_N2_MXEMB",
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 150.284472804388,
+ "minScore" : 61.0776760254482,
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ NBP170893_HTZ1_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6218.bw"
- }
+ },
+ "type" : "BigWigAdapter"
},
- "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ NBP170893_HTZ1_N2_MXEMB",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Transcription Factors ChIP-Seq Mixed embryo, NBP170893_HTZ1_N2_MXEMB",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ NBP170893_HTZ1_N2_MXEMB"
+ },
+ {
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ NBP170893_HTZ1_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "minScore" : 61.0776760254482,
- "maxScore" : 150.284472804388,
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ3856_SDC1_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 11.2818146327517,
+ "maxScore" : 24.4621655537929,
"type" : "LinearWiggleDisplay"
}
- ]
- },
- {
- "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
+ ],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6235.bw",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigWigAdapter"
},
- "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ3856_SDC1_N2_MXEMB",
- "displays" : [
- {
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ3856_SDC1_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "maxScore" : 24.4621655537929,
- "type" : "LinearWiggleDisplay",
- "minScore" : 11.2818146327517
- }
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ3856_SDC1_N2_MXEMB"
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ3856_SDC1_N2_MXEMB",
+ "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ3856_SDC1_N2_MXEMB"
},
{
- "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ2966_MIS12_N2_MXEMB",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6021.bw"
- },
- "type" : "BigWigAdapter"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6021.bw",
+ "locationType" : "UriLocation"
+ }
},
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "minScore" : 6.57237140540609,
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ2966_MIS12_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 14.7796103194124
+ }
+ ],
"description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ2966_MIS12_N2_MXEMB",
+ "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ2966_MIS12_N2_MXEMB",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -20067,48 +19465,46 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "displays" : [
- {
- "minScore" : 6.57237140540609,
- "maxScore" : 14.7796103194124,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ2966_MIS12_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
- }
- ]
+ "type" : "QuantitativeTrack"
},
{
- "displays" : [
- {
- "minScore" : 8.83646031473484,
- "maxScore" : 19.0416979234389,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ OD0039_SMC4_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
- }
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ OD0039_SMC4_N2_MXEMB",
"description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Transcription Factors ChIP-Seq Mixed embryo, OD0039_SMC4_N2_MXEMB",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ OD0039_SMC4_N2_MXEMB",
+ "displays" : [
+ {
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ OD0039_SMC4_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 8.83646031473484,
+ "maxScore" : 19.0416979234389,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6219.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6219.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "Transcription Factors ChIP-Seq Mixed embryo, OD0039_SMC4_N2_MXEMB"
+ }
},
{
- "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ2357Q2358_AMA1_N2_MXEMB_RiIMB1",
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "maxScore" : 139.285524394249,
+ "minScore" : 56.9857230501022,
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ2357Q2358_AMA1_N2_MXEMB_RiIMB1_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -20116,15 +19512,6 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6230.bw"
}
},
- "displays" : [
- {
- "type" : "LinearWiggleDisplay",
- "maxScore" : 139.285524394249,
- "minScore" : 56.9857230501022,
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ2357Q2358_AMA1_N2_MXEMB_RiIMB1_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
- }
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ2357Q2358_AMA1_N2_MXEMB_RiIMB1",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -20132,11 +19519,21 @@
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
+ ],
+ "type" : "QuantitativeTrack",
+ "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ2357Q2358_AMA1_N2_MXEMB_RiIMB1",
+ "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ2357Q2358_AMA1_N2_MXEMB_RiIMB1"
},
{
- "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ4564_DPY28_N2_MXEMB",
+ "displays" : [
+ {
+ "minScore" : 10.1574895283019,
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4564_DPY28_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 23.4711803887937,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -20145,207 +19542,269 @@
}
},
"type" : "QuantitativeTrack",
- "displays" : [
- {
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4564_DPY28_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 23.4711803887937,
- "minScore" : 10.1574895283019
- }
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4564_DPY28_N2_MXEMB",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ]
+ "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ4564_DPY28_N2_MXEMB",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4564_DPY28_N2_MXEMB",
+ "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4109_TAF1_N2_MXEMB",
"name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ4109_TAF1_N2_MXEMB",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6251.bw"
- }
- },
- "type" : "QuantitativeTrack",
"description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4109_TAF1_N2_MXEMB",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6251.bw",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "minScore" : 36.2116956944842,
- "maxScore" : 85.246956649952,
"type" : "LinearWiggleDisplay",
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4109_TAF1_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "minScore" : 36.2116956944842,
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4109_TAF1_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 85.246956649952
}
]
},
{
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6297.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4640_SWD3_N2_MXEMB",
"name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ4640_SWD3_N2_MXEMB",
"description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4640_SWD3_N2_MXEMB",
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6297.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "minScore" : 11.1460279366295,
"maxScore" : 24.5176604140289,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4640_SWD3_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "minScore" : 11.1460279366295,
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4640_SWD3_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
]
},
{
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "minScore" : 6.73400911644787,
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4562_SMC6_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 15.3303306559026,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6283.bw"
- },
- "type" : "BigWigAdapter"
+ }
},
- "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ4562_SMC6_N2_MXEMB",
- "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4562_SMC6_N2_MXEMB",
+ "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ4562_SMC6_N2_MXEMB",
+ "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ },
+ {
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6281.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4562_SMC6_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "maxScore" : 15.3303306559026,
"type" : "LinearWiggleDisplay",
- "minScore" : 6.73400911644787
+ "maxScore" : 88.2867280414155,
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4561_DPY26_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 40.5849202536671
}
+ ],
+ "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ4561_DPY26_N2_MXEMB",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4561_DPY26_N2_MXEMB",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Transcription and Chromatin"
+ ],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
]
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ3582_CBP1_N2_MXEMB",
+ "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ3582_CBP1_N2_MXEMB",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4561_DPY26_N2_MXEMB",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6234.bw"
+ }
+ },
"displays" : [
{
- "maxScore" : 88.2867280414155,
"type" : "LinearWiggleDisplay",
- "minScore" : 40.5849202536671,
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4561_DPY26_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "minScore" : 6.46665638001253,
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ3582_CBP1_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "maxScore" : 14.2968375151895
}
- ],
+ ]
+ },
+ {
+ "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ4496_DPY26_N2_MXEMB",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4496_DPY26_N2_MXEMB",
+ "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Transcription and Chromatin"
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6281.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6269.bw"
}
},
- "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ4561_DPY26_N2_MXEMB",
- "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "displays" : [
+ {
+ "maxScore" : 62.248617644546,
+ "minScore" : 28.3877438227002,
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4496_DPY26_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
+ }
+ ]
},
{
- "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6234.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6232.bw",
"locationType" : "UriLocation"
}
},
- "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ3582_CBP1_N2_MXEMB",
"displays" : [
{
- "type" : "LinearWiggleDisplay",
- "maxScore" : 14.2968375151895,
- "minScore" : 6.46665638001253,
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ3582_CBP1_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "maxScore" : 15.2546681713766,
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ3499_DPY30_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 6.69564049655428,
+ "type" : "LinearWiggleDisplay"
}
],
+ "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ3499_DPY30_N2_MXEMB",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ3499_DPY30_N2_MXEMB",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ3582_CBP1_N2_MXEMB"
+ ]
},
{
- "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6269.bw"
- },
- "type" : "BigWigAdapter"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6267.bw"
+ }
},
- "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ4496_DPY26_N2_MXEMB",
"displays" : [
{
- "minScore" : 28.3877438227002,
"type" : "LinearWiggleDisplay",
- "maxScore" : 62.248617644546,
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4496_DPY26_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "maxScore" : 17.3786317103895,
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4493_MAU2_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 7.73824846442854
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4493_MAU2_N2_MXEMB",
+ "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ4493_MAU2_N2_MXEMB",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4496_DPY26_N2_MXEMB"
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack"
},
{
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6257.bw",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ3499_DPY30_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "minScore" : 6.69564049655428,
"type" : "LinearWiggleDisplay",
- "maxScore" : 15.2546681713766
+ "maxScore" : 14.8321846781902,
+ "minScore" : 6.60312094380278,
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4154_IMB1_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
}
],
+ "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4154_IMB1_N2_MXEMB",
+ "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ4154_IMB1_N2_MXEMB",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -20354,38 +19813,25 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ3499_DPY30_N2_MXEMB",
- "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6232.bw"
- }
- },
- "type" : "QuantitativeTrack",
- "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ3499_DPY30_N2_MXEMB"
+ "type" : "QuantitativeTrack"
},
{
- "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ4493_MAU2_N2_MXEMB",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ3892_MIX1_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 7.86645990422369,
+ "maxScore" : 17.584423952193
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6267.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6237.bw",
"locationType" : "UriLocation"
}
},
"type" : "QuantitativeTrack",
- "displays" : [
- {
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4493_MAU2_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
- "minScore" : 7.73824846442854,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 17.3786317103895
- }
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4493_MAU2_N2_MXEMB",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -20393,10 +19839,13 @@
"modENCODE data (2014)",
"Transcription Factors",
"Transcription and Chromatin"
- ]
+ ],
+ "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ3892_MIX1_N2_MXEMB",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ3892_MIX1_N2_MXEMB",
+ "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ4154_IMB1_N2_MXEMB",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -20405,85 +19854,44 @@
"Transcription Factors",
"Transcription and Chromatin"
],
+ "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ2946_HCP4_N2_MXEMB",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ2946_HCP4_N2_MXEMB",
+ "description" : "seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ4154_IMB1_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay",
- "maxScore" : 14.8321846781902,
- "minScore" : 6.60312094380278
+ "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ2946_HCP4_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay",
+ "minScore" : 5.51084238076003,
+ "maxScore" : 12.4155829720001
}
],
- "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ4154_IMB1_N2_MXEMB",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6257.bw"
- }
- },
- "type" : "QuantitativeTrack",
- "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
- "displays" : [
- {
- "type" : "LinearWiggleDisplay",
- "maxScore" : 17.584423952193,
- "minScore" : 7.86645990422369,
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ3892_MIX1_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
- }
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Transcription and Chromatin"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ3892_MIX1_N2_MXEMB",
- "description" : " seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6237.bw",
- "locationType" : "UriLocation"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6023.bw"
}
- },
- "type" : "QuantitativeTrack",
- "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ3892_MIX1_N2_MXEMB"
+ }
},
{
- "type" : "QuantitativeTrack",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6023.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SDQ4051_LEM2_SP646_MXEMB_2_A_SP646_KI1802_MA2Cscore.bw",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigWigAdapter"
},
- "name" : "Transcription Factors ChIP-Seq Mixed embryo, SDQ2946_HCP4_N2_MXEMB",
- "description" : "seq-SDQ2370_LIN53_N2_LTemb. Synchronized C. elegans late embryos from strain N2 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes lin-53. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. Our 126 strategically selected targets include RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Transcription and Chromatin"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Transcription and Chromatin_Transcription Factors ChIP-Seq Mixed embryo_ SDQ2946_HCP4_N2_MXEMB",
"displays" : [
{
- "type" : "LinearWiggleDisplay",
- "maxScore" : 12.4155829720001,
- "minScore" : 5.51084238076003,
- "displayId" : "Transcription Factors ChIP-Seq Mixed embryo_ SDQ2946_HCP4_N2_MXEMB_Transcription Factors_Transcription and Chromatin-LinearWiggleDisplay"
+ "minScore" : 0,
+ "displayId" : "Chromosome-Nuclear Envelope Interaction_ SDQ4051_LEM2_SP646_MXEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay",
+ "maxScore" : 3.2595,
+ "type" : "LinearWiggleDisplay"
}
- ]
- },
- {
+ ],
+ "description" : " Chromosome-Nuclear Envelope Interaction proteins. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Chromosome-Nuclear Envelope Interaction_ SDQ4051_LEM2_SP646_MXEMB w peaks",
+ "name" : "Chromosome-Nuclear Envelope Interaction, SDQ4051_LEM2_SP646_MXEMB w peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -20492,27 +19900,22 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack"
+ },
+ {
"displays" : [
{
- "displayId" : "Chromosome-Nuclear Envelope Interaction_ SDQ4051_LEM2_SP646_MXEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 3.2595,
- "minScore" : 0
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6
+ },
+ "displayId" : "Chromosome-Nuclear Envelope Interaction_ SDQ4051_LEM2_SP646_MXEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
- "name" : "Chromosome-Nuclear Envelope Interaction, SDQ4051_LEM2_SP646_MXEMB w peaks",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SDQ4051_LEM2_SP646_MXEMB_2_A_SP646_KI1802_MA2Cscore.bw",
- "locationType" : "UriLocation"
- }
- },
- "description" : " Chromosome-Nuclear Envelope Interaction proteins. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
@@ -20520,133 +19923,131 @@
"locationType" : "UriLocation"
}
},
- "name" : "__Chromosome-Nuclear Envelope Interaction, SDQ4051_LEM2_SP646_MXEMB peaks",
- "description" : "Peak calls for Chromosome-Nuclear Envelope Interaction, SDQ4051_LEM2_SP646_MXEMB w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Chromatin Modifying Enzymes"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Chromosome-Nuclear Envelope Interaction_ SDQ4051_LEM2_SP646_MXEMB w peaks_bigbed_peaks",
- "displays" : [
- {
- "displayId" : "Chromosome-Nuclear Envelope Interaction_ SDQ4051_LEM2_SP646_MXEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes_bigbed_peaks",
- "renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "type" : "LinearBasicDisplay"
- }
- ]
+ "name" : "__Chromosome-Nuclear Envelope Interaction, SDQ4051_LEM2_SP646_MXEMB peaks",
+ "description" : "Peak calls for Chromosome-Nuclear Envelope Interaction, SDQ4051_LEM2_SP646_MXEMB w peaks"
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Chromatin Modifying Enzymes"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "description" : " Chromosome-Nuclear Envelope Interaction proteins. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Chromosome-Nuclear Envelope Interaction_ SDQ4051_LEM2_N2_MXEMB w peaks",
+ "name" : "Chromosome-Nuclear Envelope Interaction, SDQ4051_LEM2_N2_MXEMB w peaks",
"displays" : [
{
- "minScore" : 0,
"maxScore" : 3.63908271924183,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Chromosome-Nuclear Envelope Interaction_ SDQ4051_LEM2_N2_MXEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay"
+ "displayId" : "Chromosome-Nuclear Envelope Interaction_ SDQ4051_LEM2_N2_MXEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
}
],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/7823.bw",
"locationType" : "UriLocation"
- }
- },
- "type" : "QuantitativeTrack",
- "name" : "Chromosome-Nuclear Envelope Interaction, SDQ4051_LEM2_N2_MXEMB w peaks",
- "description" : " Chromosome-Nuclear Envelope Interaction proteins. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
- "name" : "__Chromosome-Nuclear Envelope Interaction, SDQ4051_LEM2_N2_MXEMB peaks",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7824_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
"description" : "Peak calls for Chromosome-Nuclear Envelope Interaction, SDQ4051_LEM2_N2_MXEMB w peaks",
+ "name" : "__Chromosome-Nuclear Envelope Interaction, SDQ4051_LEM2_N2_MXEMB peaks",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Chromosome-Nuclear Envelope Interaction_ SDQ4051_LEM2_N2_MXEMB w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Chromatin Modifying Enzymes"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7824_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
+ "displayId" : "Chromosome-Nuclear Envelope Interaction_ SDQ4051_LEM2_N2_MXEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes_bigbed_peaks",
"renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "Chromosome-Nuclear Envelope Interaction_ SDQ4051_LEM2_N2_MXEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
]
},
{
- "name" : "Chromosome-Nuclear Envelope Interaction, SDQ3891_LEM2_N2_MXEMB",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SDQ3891_LEM2_N2_MXEMB_mean_WS220.bw"
- },
- "type" : "BigWigAdapter"
- },
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
- "description" : " Chromosome-Nuclear Envelope Interaction proteins. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Chromosome-Nuclear Envelope Interaction_ SDQ3891_LEM2_N2_MXEMB",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Chromatin Modifying Enzymes"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Chromosome-Nuclear Envelope Interaction_ SDQ3891_LEM2_N2_MXEMB",
+ "name" : "Chromosome-Nuclear Envelope Interaction, SDQ3891_LEM2_N2_MXEMB",
+ "description" : " Chromosome-Nuclear Envelope Interaction proteins. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "displayId" : "Chromosome-Nuclear Envelope Interaction_ SDQ3891_LEM2_N2_MXEMB_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay",
- "maxScore" : 3.32,
- "minScore" : 1.29660570293988
+ "displayId" : "Chromosome-Nuclear Envelope Interaction_ SDQ3891_LEM2_N2_MXEMB_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay",
+ "minScore" : 1.29660570293988,
+ "maxScore" : 3.32
}
- ]
+ ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SDQ3891_LEM2_N2_MXEMB_mean_WS220.bw"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Chromosome-Nuclear Envelope Interaction_ SDQ3891_LEM2_SP646_MXEMB w peaks",
+ "name" : "Chromosome-Nuclear Envelope Interaction, SDQ3891_LEM2_SP646_MXEMB w peaks",
+ "description" : " Chromosome-Nuclear Envelope Interaction proteins. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Chromatin Modifying Enzymes"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Chromosome-Nuclear Envelope Interaction_ SDQ3891_LEM2_SP646_MXEMB w peaks",
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SDQ3891_LEM2_SP646_MXEMB_1_A_SP646_KI1777_MA2Cscore.bw",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
"displayId" : "Chromosome-Nuclear Envelope Interaction_ SDQ3891_LEM2_SP646_MXEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay",
@@ -20654,54 +20055,51 @@
"maxScore" : 2.792887,
"type" : "LinearWiggleDisplay"
}
- ],
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SDQ3891_LEM2_SP646_MXEMB_1_A_SP646_KI1777_MA2Cscore.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "Chromosome-Nuclear Envelope Interaction, SDQ3891_LEM2_SP646_MXEMB w peaks",
- "description" : " Chromosome-Nuclear Envelope Interaction proteins. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ ]
},
{
- "name" : "__Chromosome-Nuclear Envelope Interaction, SDQ3891_LEM2_SP646_MXEMB peaks",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7945_details.gff.bb",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigBedAdapter"
},
+ "displays" : [
+ {
+ "displayId" : "Chromosome-Nuclear Envelope Interaction_ SDQ3891_LEM2_SP646_MXEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes_bigbed_peaks",
+ "renderer" : {
+ "height" : 6,
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"description" : "Peak calls for Chromosome-Nuclear Envelope Interaction, SDQ3891_LEM2_SP646_MXEMB w peaks",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Chromosome-Nuclear Envelope Interaction_ SDQ3891_LEM2_SP646_MXEMB w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "__Chromosome-Nuclear Envelope Interaction, SDQ3891_LEM2_SP646_MXEMB peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Chromatin Modifying Enzymes"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack"
+ },
+ {
"displays" : [
{
- "renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "Chromosome-Nuclear Envelope Interaction_ SDQ3891_LEM2_SP646_MXEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes_bigbed_peaks"
+ "displayId" : "Chromosome-Nuclear Envelope Interaction_ SDQ3891_LEM2_VC1317_MXEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 3.00370802101397,
+ "type" : "LinearWiggleDisplay"
}
- ]
- },
- {
- "name" : "Chromosome-Nuclear Envelope Interaction, SDQ3891_LEM2_VC1317_MXEMB w peaks",
+ ],
"adapter" : {
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SDQ3891_LEM2_VC1317_MXEMB_1_A_VC1317_KI1761_MA2Cscore.bw",
@@ -20709,28 +20107,32 @@
},
"type" : "BigWigAdapter"
},
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Chromatin Modifying Enzymes"
+ ],
"type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"description" : "Chromosome-Nuclear Envelope Interaction proteins. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Chromosome-Nuclear Envelope Interaction_ SDQ3891_LEM2_VC1317_MXEMB w peaks",
+ "name" : "Chromosome-Nuclear Envelope Interaction, SDQ3891_LEM2_VC1317_MXEMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Chromosome-Nuclear Envelope Interaction_ SDQ3891_LEM2_VC1317_MXEMB w peaks"
+ },
+ {
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Chromosome-Nuclear Envelope Interaction_ SDQ3891_LEM2_VC1317_MXEMB w peaks_bigbed_peaks",
+ "name" : "__Chromosome-Nuclear Envelope Interaction, SDQ3891_LEM2_VC1317_MXEMB peaks",
+ "description" : "Peak calls for Chromosome-Nuclear Envelope Interaction, SDQ3891_LEM2_VC1317_MXEMB w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Chromatin Modifying Enzymes"
],
- "displays" : [
- {
- "minScore" : 0,
- "maxScore" : 3.00370802101397,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Chromosome-Nuclear Envelope Interaction_ SDQ3891_LEM2_VC1317_MXEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay"
- }
- ]
- },
- {
- "name" : "__Chromosome-Nuclear Envelope Interaction, SDQ3891_LEM2_VC1317_MXEMB peaks",
"adapter" : {
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7837_details.gff.bb",
@@ -20738,69 +20140,53 @@
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "description" : "Peak calls for Chromosome-Nuclear Envelope Interaction, SDQ3891_LEM2_VC1317_MXEMB w peaks",
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Chromosome-Nuclear Envelope Interaction_ SDQ3891_LEM2_VC1317_MXEMB w peaks_bigbed_peaks",
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Chromatin Modifying Enzymes"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
- "displayId" : "Chromosome-Nuclear Envelope Interaction_ SDQ3891_LEM2_VC1317_MXEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes_bigbed_peaks",
"type" : "LinearBasicDisplay",
"renderer" : {
+ "showLabels" : false,
"height" : 6,
"showDescriptions" : false,
"color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "Chromosome-Nuclear Envelope Interaction_ SDQ3891_LEM2_VC1317_MXEMB w peaks_Chromatin Structure_Chromatin Modifying Enzymes_bigbed_peaks"
}
]
},
{
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SDQ3897_NPP13_N2_MXEMB_mean_WS220.bw"
+ }
+ },
"displays" : [
{
- "minScore" : 0.936169142594296,
- "maxScore" : 2.87748225028575,
"type" : "LinearWiggleDisplay",
- "displayId" : "Chromosome-Nuclear Envelope Interaction_ SDQ3897_NPP13_N2_MXEMB_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay"
+ "displayId" : "Chromosome-Nuclear Envelope Interaction_ SDQ3897_NPP13_N2_MXEMB_Chromatin Structure_Chromatin Modifying Enzymes-LinearWiggleDisplay",
+ "minScore" : 0.936169142594296,
+ "maxScore" : 2.87748225028575
}
],
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Chromatin Modifying Enzymes_Chromosome-Nuclear Envelope Interaction_ SDQ3897_NPP13_N2_MXEMB",
+ "name" : "Chromosome-Nuclear Envelope Interaction, SDQ3897_NPP13_N2_MXEMB",
+ "description" : " Chromosome-Nuclear Envelope Interaction proteins. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Chromatin Modifying Enzymes"
- ],
- "description" : " Chromosome-Nuclear Envelope Interaction proteins. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Chromosome-Nuclear Envelope Interaction, SDQ3897_NPP13_N2_MXEMB",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/SDQ3897_NPP13_N2_MXEMB_mean_WS220.bw"
- }
- },
- "type" : "QuantitativeTrack"
+ ]
},
{
- "displays" : [
- {
- "displayId" : "Histone Modifications in H3K14 (ChIP-Seq)_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 59.0920013496473,
- "minScore" : 29.1952604453836
- }
- ],
+ "description" : "Histone Modifications in H3K14 (ChIP-seq). Synchronized C. elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K14 (ChIP-Seq)",
+ "name" : "Histone Modifications in H3K14 (ChIP-Seq)",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -20809,8 +20195,7 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K14 (ChIP-Seq)",
- "description" : "Histone Modifications in H3K14 (ChIP-seq). Synchronized C. elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -20818,47 +20203,34 @@
"locationType" : "UriLocation"
}
},
- "type" : "QuantitativeTrack",
- "name" : "Histone Modifications in H3K14 (ChIP-Seq)"
- },
- {
"displays" : [
{
- "displayId" : "Histone Modifications in H3K36 (ChIP-Seq)_ H3K36me1_AD_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "maxScore" : 87.7001255513025,
- "type" : "LinearWiggleDisplay",
- "minScore" : 42.2874414319298
+ "minScore" : 29.1952604453836,
+ "displayId" : "Histone Modifications in H3K14 (ChIP-Seq)_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "maxScore" : 59.0920013496473,
+ "type" : "LinearWiggleDisplay"
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K36 (ChIP-Seq)_ H3K36me1_AD",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
- "description" : "Histone Modifications in H3K36 (ChIP-seq). Synchronized C. elegans early embryos from strain N2 and synchronized C.elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Histone Modifications in H3K36 (ChIP-Seq), H3K36me1_AD",
+ ]
+ },
+ {
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6244.bw"
- },
- "type" : "BigWigAdapter"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6244.bw",
+ "locationType" : "UriLocation"
+ }
},
- "type" : "QuantitativeTrack"
- },
- {
"displays" : [
{
- "displayId" : "Histone Modifications in H3K36 (ChIP-Seq)_ H3K36me1_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "minScore" : 36.8275092558389,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 84.7376038055725
+ "displayId" : "Histone Modifications in H3K36 (ChIP-Seq)_ H3K36me1_AD_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 42.2874414319298,
+ "maxScore" : 87.7001255513025,
+ "type" : "LinearWiggleDisplay"
}
],
+ "description" : "Histone Modifications in H3K36 (ChIP-seq). Synchronized C. elegans early embryos from strain N2 and synchronized C.elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K36 (ChIP-Seq)_ H3K36me1_AD",
+ "name" : "Histone Modifications in H3K36 (ChIP-Seq), H3K36me1_AD",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -20867,124 +20239,126 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K36 (ChIP-Seq)_ H3K36me1_Eemb",
- "description" : "Histone Modifications in H3K36 (ChIP-seq). Synchronized C. elegans early embryos from strain N2 and synchronized C.elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5167.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "Histone Modifications in H3K36 (ChIP-Seq), H3K36me1_Eemb"
+ "type" : "QuantitativeTrack"
},
{
- "displays" : [
- {
- "displayId" : "Histone Modifications in H3K36 (ChIP-Seq)_ H3K36me2 N2 Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "maxScore" : 240.422730192315,
- "type" : "LinearWiggleDisplay",
- "minScore" : 101.121200963464
- }
- ],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K36 (ChIP-Seq)_ H3K36me2 N2 Eemb",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K36 (ChIP-Seq)_ H3K36me1_Eemb",
+ "name" : "Histone Modifications in H3K36 (ChIP-Seq), H3K36me1_Eemb",
"description" : "Histone Modifications in H3K36 (ChIP-seq). Synchronized C. elegans early embryos from strain N2 and synchronized C.elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "minScore" : 36.8275092558389,
+ "displayId" : "Histone Modifications in H3K36 (ChIP-Seq)_ H3K36me1_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "maxScore" : 84.7376038055725,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5164.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5167.bw"
}
- },
- "type" : "QuantitativeTrack",
- "name" : "Histone Modifications in H3K36 (ChIP-Seq), H3K36me2 N2 Eemb"
+ }
},
{
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K36 (ChIP-Seq)_ H3K36me3_N2_Eemb",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "Histone Modifications in H3K36 (ChIP-seq). Synchronized C. elegans early embryos from strain N2 and synchronized C.elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications in H3K36 (ChIP-Seq), H3K36me2 N2 Eemb",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K36 (ChIP-Seq)_ H3K36me2 N2 Eemb",
"displays" : [
{
- "minScore" : 67.9105172864549,
"type" : "LinearWiggleDisplay",
- "maxScore" : 162.807931171075,
- "displayId" : "Histone Modifications in H3K36 (ChIP-Seq)_ H3K36me3_N2_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "maxScore" : 240.422730192315,
+ "minScore" : 101.121200963464,
+ "displayId" : "Histone Modifications in H3K36 (ChIP-Seq)_ H3K36me2 N2 Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
}
],
- "name" : "Histone Modifications in H3K36 (ChIP-Seq), H3K36me3_N2_Eemb",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5165.bw",
- "locationType" : "UriLocation"
- }
- },
- "type" : "QuantitativeTrack",
- "description" : "Histone Modifications in H3K36 (ChIP-seq). Synchronized C. elegans early embryos from strain N2 and synchronized C.elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5164.bw"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
- "displays" : [
- {
- "displayId" : "Histone Modifications in H3K36 (ChIP-Seq)_ H3K36me3_AD_F_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "minScore" : 43.5098238638733,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 100.175223829919
- }
- ],
+ "description" : "Histone Modifications in H3K36 (ChIP-seq). Synchronized C. elegans early embryos from strain N2 and synchronized C.elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications in H3K36 (ChIP-Seq), H3K36me3_N2_Eemb",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K36 (ChIP-Seq)_ H3K36me3_N2_Eemb",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K36 (ChIP-Seq)_ H3K36me3_AD_F",
- "description" : "Histone Modifications in H3K36 (ChIP-seq). Synchronized C. elegans early embryos from strain N2 and synchronized C.elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"adapter" : {
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6256.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5165.bw",
"locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "name" : "Histone Modifications in H3K36 (ChIP-Seq), H3K36me3_AD_F"
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 162.807931171075,
+ "minScore" : 67.9105172864549,
+ "displayId" : "Histone Modifications in H3K36 (ChIP-Seq)_ H3K36me3_N2_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ }
+ ]
},
{
- "description" : "Histone Modifications in H3K23 (ChIP-seq). Synchronized C. elegans early embryos from strain N2.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K36 (ChIP-Seq)_ H3K36me3_AD_F",
+ "name" : "Histone Modifications in H3K36 (ChIP-Seq), H3K36me3_AD_F",
+ "description" : "Histone Modifications in H3K36 (ChIP-seq). Synchronized C. elegans early embryos from strain N2 and synchronized C.elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5151.bw"
- }
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6256.bw"
+ },
+ "type" : "BigWigAdapter"
},
- "name" : "Histone Modifications in H3K23 (ChIP-Seq)",
"displays" : [
{
- "maxScore" : 134.760423737605,
- "type" : "LinearWiggleDisplay",
- "minScore" : 64.0885398334098,
- "displayId" : "Histone Modifications in H3K23 (ChIP-Seq)_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "displayId" : "Histone Modifications in H3K36 (ChIP-Seq)_ H3K36me3_AD_F_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 43.5098238638733,
+ "maxScore" : 100.175223829919,
+ "type" : "LinearWiggleDisplay"
}
- ],
+ ]
+ },
+ {
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -20993,157 +20367,179 @@
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K23 (ChIP-Seq)"
- },
- {
- "description" : "Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 phosphorylated on serine 10. The recovered DNA fragments (as well as a sample of input DNA) were sequenced on the Illumina GA-II platform. The signal graph data track shows the coverage of short reads in each sample. The alignment files were used to call binding peaks with the MACS algorithm to generate the track showing sequence features.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Histone Modifications in H3Ser10",
- "type" : "QuantitativeTrack",
+ "name" : "Histone Modifications in H3K23 (ChIP-Seq)",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K23 (ChIP-Seq)",
+ "description" : "Histone Modifications in H3K23 (ChIP-seq). Synchronized C. elegans early embryos from strain N2.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "displayId" : "Histone Modifications in H3K23 (ChIP-Seq)_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 64.0885398334098,
+ "maxScore" : 134.760423737605,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5244.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5151.bw",
"locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
- },
+ }
+ },
+ {
"displays" : [
{
- "displayId" : "Histone Modifications in H3Ser10_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "maxScore" : 233.977591630043,
"type" : "LinearWiggleDisplay",
- "minScore" : 103.469905237914
+ "displayId" : "Histone Modifications in H3Ser10_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 103.469905237914,
+ "maxScore" : 233.977591630043
}
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3Ser10",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5244.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
- ]
+ ],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Synchronized C. elegans adult females from strain DH245 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 phosphorylated on serine 10. The recovered DNA fragments (as well as a sample of input DNA) were sequenced on the Illumina GA-II platform. The signal graph data track shows the coverage of short reads in each sample. The alignment files were used to call binding peaks with the MACS algorithm to generate the track showing sequence features.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications in H3Ser10",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3Ser10"
},
{
"displays" : [
{
- "displayId" : "Histone Modifications in H3K27 (ChIP-Seq)_ H3K27me3_AD_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
"maxScore" : 37.4757915173666,
- "minScore" : 16.326711200731
+ "minScore" : 16.326711200731,
+ "displayId" : "Histone Modifications in H3K27 (ChIP-Seq)_ H3K27me3_AD_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K27 (ChIP-Seq)_ H3K27me3_AD",
- "description" : "Histone Modifications in H3K27 (ChIP-seq). Synchronized C. elegans adult females from strain DH245 and synchronized C.elegans eraly embryos form strain N2.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6254.bw",
"locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ }
},
- "name" : "Histone Modifications in H3K27 (ChIP-Seq), H3K27me3_AD"
- },
- {
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K27 (ChIP-Seq)_ H3K27me1_Eemb",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Histone Modifications in H3K27 (ChIP-seq). Synchronized C. elegans adult females from strain DH245 and synchronized C.elegans eraly embryos form strain N2.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications in H3K27 (ChIP-Seq), H3K27me3_AD",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K27 (ChIP-Seq)_ H3K27me3_AD"
+ },
+ {
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K27 (ChIP-Seq)_ H3K27me1_Eemb",
+ "name" : "Histone Modifications in H3K27 (ChIP-Seq), H3K27me1_Eemb",
+ "description" : "Histone Modifications in H3K27 (ChIP-seq). Synchronized C. elegans adult females from strain DH245 and synchronized C.elegans eraly embryos form strain N2.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
"maxScore" : 172.764670427679,
- "type" : "LinearWiggleDisplay",
"minScore" : 72.5496412411341,
- "displayId" : "Histone Modifications in H3K27 (ChIP-Seq)_ H3K27me1_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "displayId" : "Histone Modifications in H3K27 (ChIP-Seq)_ H3K27me1_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
],
- "name" : "Histone Modifications in H3K27 (ChIP-Seq), H3K27me1_Eemb",
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5160.bw"
}
- },
- "description" : "Histone Modifications in H3K27 (ChIP-seq). Synchronized C. elegans adult females from strain DH245 and synchronized C.elegans eraly embryos form strain N2.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
},
{
- "displays" : [
- {
- "displayId" : "Histone Modifications in H3K27 (ChIP-Seq)_ H3K27me3_N2_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 222.757303101851,
- "minScore" : 90.3068100236108
- }
- ],
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K27 (ChIP-Seq)_ H3K27me3_N2_Eemb",
+ "name" : "Histone Modifications in H3K27 (ChIP-Seq), H3K27me3_N2_Eemb",
+ "description" : " Histone Modifications in H3K27 (ChIP-seq). Synchronized C. elegans adult females from strain DH245 and synchronized C.elegans eraly embryos form strain N2.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : " Histone Modifications in H3K27 (ChIP-seq). Synchronized C. elegans adult females from strain DH245 and synchronized C.elegans eraly embryos form strain N2.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Histone Modifications in H3K27 (ChIP-Seq), H3K27me3_N2_Eemb",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5163.bw",
"locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ }
},
- "type" : "QuantitativeTrack"
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 222.757303101851,
+ "displayId" : "Histone Modifications in H3K27 (ChIP-Seq)_ H3K27me3_N2_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 90.3068100236108
+ }
+ ]
},
{
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5159.bw"
+ }
+ },
"displays" : [
{
+ "minScore" : 120.976899457107,
"displayId" : "Histone Modifications in H3K27 (ChIP-Seq)_ H3K27ac_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
"maxScore" : 306.51999835487,
- "minScore" : 120.976899457107
+ "type" : "LinearWiggleDisplay"
}
],
+ "description" : " Histone Modifications in H3K27 (ChIP-seq). Synchronized C. elegans adult females from strain DH245 and synchronized C.elegans eraly embryos form strain N2.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K27 (ChIP-Seq)_ H3K27ac_Eemb",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "Histone Modifications in H3K27 (ChIP-Seq), H3K27ac_Eemb",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "description" : " Histone Modifications in H3K27 (ChIP-seq). Synchronized C. elegans adult females from strain DH245 and synchronized C.elegans eraly embryos form strain N2.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Histone Modifications in H3K27 (ChIP-Seq), H3K27ac_Eemb",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5159.bw",
- "locationType" : "UriLocation"
- }
- },
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack"
},
{
- "description" : " Histone Modifications in H3K27 (ChIP-seq). Synchronized C. elegans adult females from strain DH245 and synchronized C.elegans eraly embryos form strain N2.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Histone Modifications in H3K27 (ChIP-Seq), H3K27ac_AD",
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 327.693780937475,
+ "displayId" : "Histone Modifications in H3K27 (ChIP-Seq)_ H3K27ac_AD_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 142.885147709367
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -21151,26 +20547,21 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_3921.bw"
}
},
- "displays" : [
- {
- "minScore" : 142.885147709367,
- "maxScore" : 327.693780937475,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Histone Modifications in H3K27 (ChIP-Seq)_ H3K27ac_AD_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
- }
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K27 (ChIP-Seq)_ H3K27ac_AD",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
+ ],
+ "description" : " Histone Modifications in H3K27 (ChIP-seq). Synchronized C. elegans adult females from strain DH245 and synchronized C.elegans eraly embryos form strain N2.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications in H3K27 (ChIP-Seq), H3K27ac_AD",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K27 (ChIP-Seq)_ H3K27ac_AD"
},
{
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K4 (ChIP-Seq)_ H3K4me2_YA",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -21179,66 +20570,73 @@
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "name" : "Histone Modifications in H3K4 (ChIP-Seq), H3K4me2_YA",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K4 (ChIP-Seq)_ H3K4me2_YA",
+ "description" : "Histone Modifications in H3K4 (ChIP-seq). Synchronized C. elegans early embryos from strain N2, synchronized C.elegans adult females from strain DH245, synchronized C.elegans young adults from strain DH424 fem-2(b245ts), and synchronized C.elegans youg adults from strain WH223.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "minScore" : 66.811976489147,
"type" : "LinearWiggleDisplay",
"maxScore" : 127.014474209536,
- "displayId" : "Histone Modifications in H3K4 (ChIP-Seq)_ H3K4me2_YA_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "displayId" : "Histone Modifications in H3K4 (ChIP-Seq)_ H3K4me2_YA_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 66.811976489147
}
],
- "name" : "Histone Modifications in H3K4 (ChIP-Seq), H3K4me2_YA",
- "type" : "QuantitativeTrack",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5253.bw"
- }
- },
- "description" : "Histone Modifications in H3K4 (ChIP-seq). Synchronized C. elegans early embryos from strain N2, synchronized C.elegans adult females from strain DH245, synchronized C.elegans young adults from strain DH424 fem-2(b245ts), and synchronized C.elegans youg adults from strain WH223.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5157.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
+ "displays" : [
+ {
+ "displayId" : "Histone Modifications in H3K4 (ChIP-Seq)_ H3K4ME2 Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 56.5974124747429,
+ "maxScore" : 139.469128711342,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K4 (ChIP-Seq)_ H3K4ME2 Eemb",
+ "name" : "Histone Modifications in H3K4 (ChIP-Seq), H3K4ME2 Eemb",
+ "description" : "Histone Modifications in H3K4 (ChIP-seq). Synchronized C. elegans early embryos from strain N2, synchronized C.elegans adult females from strain DH245, synchronized C.elegans young adults from strain DH424 fem-2(b245ts), and synchronized C.elegans youg adults from strain WH223.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
- ],
- "displays" : [
- {
- "type" : "LinearWiggleDisplay",
- "maxScore" : 139.469128711342,
- "minScore" : 56.5974124747429,
- "displayId" : "Histone Modifications in H3K4 (ChIP-Seq)_ H3K4ME2 Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
- }
- ],
- "name" : "Histone Modifications in H3K4 (ChIP-Seq), H3K4ME2 Eemb",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5157.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "description" : "Histone Modifications in H3K4 (ChIP-seq). Synchronized C. elegans early embryos from strain N2, synchronized C.elegans adult females from strain DH245, synchronized C.elegans young adults from strain DH424 fem-2(b245ts), and synchronized C.elegans youg adults from strain WH223.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ ]
},
{
- "name" : "Histone Modifications in H3K4 (ChIP-Seq), H3K4me1_Eemb",
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5158.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5158.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "maxScore" : 144.256782991399,
+ "displayId" : "Histone Modifications in H3K4 (ChIP-Seq)_ H3K4me1_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 62.7467383871617,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"description" : "Histone Modifications in H3K4 (ChIP-seq). Synchronized C. elegans early embryos from strain N2, synchronized C.elegans adult females from strain DH245, synchronized C.elegans young adults from strain DH424 fem-2(b245ts), and synchronized C.elegans youg adults from strain WH223.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K4 (ChIP-Seq)_ H3K4me1_Eemb",
+ "name" : "Histone Modifications in H3K4 (ChIP-Seq), H3K4me1_Eemb",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -21247,25 +20645,9 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "displays" : [
- {
- "displayId" : "Histone Modifications in H3K4 (ChIP-Seq)_ H3K4me1_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "minScore" : 62.7467383871617,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 144.256782991399
- }
- ]
+ "type" : "QuantitativeTrack"
},
{
- "displays" : [
- {
- "displayId" : "Histone Modifications in H3K4 (ChIP-Seq)_ H3K4me1_YA_F_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "minScore" : 50.6796560194347,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 100.827442483135
- }
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K4 (ChIP-Seq)_ H3K4me1_YA_F",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -21274,37 +20656,45 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"description" : "Histone Modifications in H3K4 (ChIP-seq). Synchronized C. elegans early embryos from strain N2, synchronized C.elegans adult females from strain DH245, synchronized C.elegans young adults from strain DH424 fem-2(b245ts), and synchronized C.elegans youg adults from strain WH223.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K4 (ChIP-Seq)_ H3K4me1_YA_F",
"name" : "Histone Modifications in H3K4 (ChIP-Seq), H3K4me1_YA_F",
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "maxScore" : 100.827442483135,
+ "minScore" : 50.6796560194347,
+ "displayId" : "Histone Modifications in H3K4 (ChIP-Seq)_ H3K4me1_YA_F_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5245.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5245.bw"
+ }
}
},
{
- "description" : "Histone Modifications in H3K4 (ChIP-seq). Synchronized C. elegans early embryos from strain N2, synchronized C.elegans adult females from strain DH245, synchronized C.elegans young adults from strain DH424 fem-2(b245ts), and synchronized C.elegans youg adults from strain WH223.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Histone Modifications in H3K4 (ChIP-Seq), H3K4me3_Eemb",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5166.bw",
"locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ }
},
- "type" : "QuantitativeTrack",
"displays" : [
{
+ "displayId" : "Histone Modifications in H3K4 (ChIP-Seq)_ H3K4me3_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"minScore" : 59.1048327103382,
- "type" : "LinearWiggleDisplay",
"maxScore" : 152.914644576783,
- "displayId" : "Histone Modifications in H3K4 (ChIP-Seq)_ H3K4me3_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
],
+ "description" : "Histone Modifications in H3K4 (ChIP-seq). Synchronized C. elegans early embryos from strain N2, synchronized C.elegans adult females from strain DH245, synchronized C.elegans young adults from strain DH424 fem-2(b245ts), and synchronized C.elegans youg adults from strain WH223.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K4 (ChIP-Seq)_ H3K4me3_Eemb",
+ "name" : "Histone Modifications in H3K4 (ChIP-Seq), H3K4me3_Eemb",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -21312,10 +20702,18 @@
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
+ ],
+ "type" : "QuantitativeTrack"
},
{
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "minScore" : 85.3487012958274,
+ "displayId" : "Histone Modifications in H3K4 (ChIP-Seq)_ H3K4me1_AD_F_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "maxScore" : 182.374246350992,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -21323,28 +20721,28 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6246.bw"
}
},
- "name" : "Histone Modifications in H3K4 (ChIP-Seq), H3K4me1_AD_F",
- "description" : "Histone Modifications in H3K4 (ChIP-seq). Synchronized C. elegans early embryos from strain N2, synchronized C.elegans adult females from strain DH245, synchronized C.elegans young adults from strain DH424 fem-2(b245ts), and synchronized C.elegans youg adults from strain WH223.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K4 (ChIP-Seq)_ H3K4me1_AD_F",
+ "name" : "Histone Modifications in H3K4 (ChIP-Seq), H3K4me1_AD_F",
+ "description" : "Histone Modifications in H3K4 (ChIP-seq). Synchronized C. elegans early embryos from strain N2, synchronized C.elegans adult females from strain DH245, synchronized C.elegans young adults from strain DH424 fem-2(b245ts), and synchronized C.elegans youg adults from strain WH223.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ },
+ {
"displays" : [
{
- "type" : "LinearWiggleDisplay",
- "maxScore" : 182.374246350992,
- "minScore" : 85.3487012958274,
- "displayId" : "Histone Modifications in H3K4 (ChIP-Seq)_ H3K4me1_AD_F_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "maxScore" : 396.712345184297,
+ "minScore" : 150.237873910818,
+ "displayId" : "Histone Modifications in H3K9 (ChIP-Seq)_ H3K9me3_UP07442_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
- ]
- },
- {
- "description" : "Histone Modifications in H3K9 (ChIP-seq). Synchronized C. elegans L3 larvae from strain N2, synchronized C.elegans early embryos from strain N2, and synchronized C.elegans young adults from strain WH223.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -21352,28 +20750,6 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5154.bw"
}
},
- "type" : "QuantitativeTrack",
- "name" : "Histone Modifications in H3K9 (ChIP-Seq), H3K9me3_UP07442_Eemb",
- "displays" : [
- {
- "displayId" : "Histone Modifications in H3K9 (ChIP-Seq)_ H3K9me3_UP07442_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "minScore" : 150.237873910818,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 396.712345184297
- }
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K9 (ChIP-Seq)_ H3K9me3_UP07442_Eemb"
- },
- {
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K9 (ChIP-Seq)_ H3K9me1_Eemb",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -21382,16 +20758,20 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
+ "description" : "Histone Modifications in H3K9 (ChIP-seq). Synchronized C. elegans L3 larvae from strain N2, synchronized C.elegans early embryos from strain N2, and synchronized C.elegans young adults from strain WH223.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K9 (ChIP-Seq)_ H3K9me3_UP07442_Eemb",
+ "name" : "Histone Modifications in H3K9 (ChIP-Seq), H3K9me3_UP07442_Eemb"
+ },
+ {
"displays" : [
{
- "minScore" : 63.8272664941266,
"type" : "LinearWiggleDisplay",
"maxScore" : 153.906262103414,
- "displayId" : "Histone Modifications in H3K9 (ChIP-Seq)_ H3K9me1_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "displayId" : "Histone Modifications in H3K9 (ChIP-Seq)_ H3K9me1_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 63.8272664941266
}
],
- "name" : "Histone Modifications in H3K9 (ChIP-Seq), H3K9me1_Eemb",
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -21399,213 +20779,224 @@
"locationType" : "UriLocation"
}
},
- "description" : "Histone Modifications in H3K9 (ChIP-seq). Synchronized C. elegans L3 larvae from strain N2, synchronized C.elegans early embryos from strain N2, and synchronized C.elegans young adults from strain WH223.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5153.bw",
- "locationType" : "UriLocation"
- }
- },
- "name" : "Histone Modifications in H3K9 (ChIP-Seq), H3K9me3_HK00009_Eemb",
- "description" : "Histone Modifications in H3K9 (ChIP-seq). Synchronized C. elegans L3 larvae from strain N2, synchronized C.elegans early embryos from strain N2, and synchronized C.elegans young adults from strain WH223.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K9 (ChIP-Seq)_ H3K9me3_HK00009_Eemb",
- "displays" : [
- {
- "type" : "LinearWiggleDisplay",
- "maxScore" : 169.233819673682,
- "minScore" : 63.9876604923151,
- "displayId" : "Histone Modifications in H3K9 (ChIP-Seq)_ H3K9me3_HK00009_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
- }
- ]
+ "description" : "Histone Modifications in H3K9 (ChIP-seq). Synchronized C. elegans L3 larvae from strain N2, synchronized C.elegans early embryos from strain N2, and synchronized C.elegans young adults from strain WH223.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications in H3K9 (ChIP-Seq), H3K9me1_Eemb",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K9 (ChIP-Seq)_ H3K9me1_Eemb"
},
{
- "description" : "Histone Modifications in H3K9 (ChIP-seq). Synchronized C. elegans L3 larvae from strain N2, synchronized C.elegans early embryos from strain N2, and synchronized C.elegans young adults from strain WH223.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5149.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5153.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
- "name" : "Histone Modifications in H3K9 (ChIP-Seq), H3K9acS10ph_Eemb",
"displays" : [
{
- "displayId" : "Histone Modifications in H3K9 (ChIP-Seq)_ H3K9acS10ph_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "minScore" : 45.6116041820306,
- "maxScore" : 102.199406612214,
- "type" : "LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay",
+ "minScore" : 63.9876604923151,
+ "displayId" : "Histone Modifications in H3K9 (ChIP-Seq)_ H3K9me3_HK00009_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "maxScore" : 169.233819673682
}
],
+ "description" : "Histone Modifications in H3K9 (ChIP-seq). Synchronized C. elegans L3 larvae from strain N2, synchronized C.elegans early embryos from strain N2, and synchronized C.elegans young adults from strain WH223.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications in H3K9 (ChIP-Seq), H3K9me3_HK00009_Eemb",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K9 (ChIP-Seq)_ H3K9me3_HK00009_Eemb",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K9 (ChIP-Seq)_ H3K9acS10ph_Eemb"
+ ]
},
{
"displays" : [
{
- "minScore" : 123.373825410011,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 323.447652757611,
- "displayId" : "Histone Modifications in H3K9 (ChIP-Seq)_ H3K9me2_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "maxScore" : 102.199406612214,
+ "displayId" : "Histone Modifications in H3K9 (ChIP-Seq)_ H3K9acS10ph_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 45.6116041820306,
+ "type" : "LinearWiggleDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K9 (ChIP-Seq)_ H3K9me2_N2_EEMB",
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5149.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
+ "name" : "Histone Modifications in H3K9 (ChIP-Seq), H3K9acS10ph_Eemb",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K9 (ChIP-Seq)_ H3K9acS10ph_Eemb",
+ "description" : "Histone Modifications in H3K9 (ChIP-seq). Synchronized C. elegans L3 larvae from strain N2, synchronized C.elegans early embryos from strain N2, and synchronized C.elegans young adults from strain WH223.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ },
+ {
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"description" : "Histone Modifications in H3K9 (ChIP-seq). Synchronized C. elegans L3 larvae from strain N2, synchronized C.elegans early embryos from strain N2, and synchronized C.elegans young adults from strain WH223.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"name" : "Histone Modifications in H3K9 (ChIP-Seq), H3K9me2_N2_EEMB",
- "type" : "QuantitativeTrack",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K9 (ChIP-Seq)_ H3K9me2_N2_EEMB",
+ "displays" : [
+ {
+ "maxScore" : 323.447652757611,
+ "minScore" : 123.373825410011,
+ "displayId" : "Histone Modifications in H3K9 (ChIP-Seq)_ H3K9me2_N2_EEMB_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5161.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5161.bw"
+ }
}
},
{
- "displays" : [
- {
- "minScore" : 87.1794578698883,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 196.611690514813,
- "displayId" : "Histone Modifications in H3K9 (ChIP-Seq)_ H3K9ac L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
- }
- ],
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K9 (ChIP-Seq)_ H3K9ac L3",
+ "name" : "Histone Modifications in H3K9 (ChIP-Seq), H3K9ac L3",
+ "description" : "Histone Modifications in H3K9 (ChIP-seq). Synchronized C. elegans L3 larvae from strain N2, synchronized C.elegans early embryos from strain N2, and synchronized C.elegans young adults from strain WH223.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K9 (ChIP-Seq)_ H3K9ac L3",
- "description" : "Histone Modifications in H3K9 (ChIP-seq). Synchronized C. elegans L3 larvae from strain N2, synchronized C.elegans early embryos from strain N2, and synchronized C.elegans young adults from strain WH223.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_3578.bw",
- "locationType" : "UriLocation"
- }
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_3578.bw"
+ },
+ "type" : "BigWigAdapter"
},
- "name" : "Histone Modifications in H3K9 (ChIP-Seq), H3K9ac L3"
- },
- {
"displays" : [
{
- "displayId" : "Histone Modifications in H3K9 (ChIP-Seq)_ H3K9me3_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "minScore" : 82.3841360374424,
"type" : "LinearWiggleDisplay",
- "maxScore" : 212.961321325583
+ "maxScore" : 196.611690514813,
+ "displayId" : "Histone Modifications in H3K9 (ChIP-Seq)_ H3K9ac L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 87.1794578698883
}
- ],
+ ]
+ },
+ {
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K9 (ChIP-Seq)_ H3K9me3_Eemb",
"description" : "Histone Modifications in H3K9 (ChIP-seq). Synchronized C. elegans L3 larvae from strain N2, synchronized C.elegans early embryos from strain N2, and synchronized C.elegans young adults from strain WH223.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
+ "name" : "Histone Modifications in H3K9 (ChIP-Seq), H3K9me3_Eemb",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K9 (ChIP-Seq)_ H3K9me3_Eemb",
+ "displays" : [
+ {
+ "maxScore" : 212.961321325583,
+ "displayId" : "Histone Modifications in H3K9 (ChIP-Seq)_ H3K9me3_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 82.3841360374424,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5155.bw",
"locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "name" : "Histone Modifications in H3K9 (ChIP-Seq), H3K9me3_Eemb"
+ }
+ }
},
{
- "name" : "Histone Modifications in H3K9 (ChIP-Seq), H3K9me2_YA",
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6325.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6325.bw"
}
},
+ "displays" : [
+ {
+ "minScore" : 44.7411618175145,
+ "displayId" : "Histone Modifications in H3K9 (ChIP-Seq)_ H3K9me2_YA_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "maxScore" : 88.496550962165,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"description" : "Histone Modifications in H3K9 (ChIP-seq). Synchronized C. elegans L3 larvae from strain N2, synchronized C.elegans early embryos from strain N2, and synchronized C.elegans young adults from strain WH223.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications in H3K9 (ChIP-Seq), H3K9me2_YA",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K9 (ChIP-Seq)_ H3K9me2_YA",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "displays" : [
- {
- "displayId" : "Histone Modifications in H3K9 (ChIP-Seq)_ H3K9me2_YA_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "minScore" : 44.7411618175145,
- "maxScore" : 88.496550962165,
- "type" : "LinearWiggleDisplay"
- }
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
]
},
{
- "description" : "Histone Modifications in H3K9 (ChIP-seq). Synchronized C. elegans L3 larvae from strain N2, synchronized C.elegans early embryos from strain N2, and synchronized C.elegans young adults from strain WH223.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Histone Modifications in H3K9 (ChIP-Seq), H3K9acS10_L3",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5988.bw"
- }
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5988.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
"displays" : [
{
- "displayId" : "Histone Modifications in H3K9 (ChIP-Seq)_ H3K9acS10_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "minScore" : 77.6285503918399,
+ "type" : "LinearWiggleDisplay",
"maxScore" : 172.339243611636,
- "type" : "LinearWiggleDisplay"
+ "minScore" : 77.6285503918399,
+ "displayId" : "Histone Modifications in H3K9 (ChIP-Seq)_ H3K9acS10_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
}
],
+ "description" : "Histone Modifications in H3K9 (ChIP-seq). Synchronized C. elegans L3 larvae from strain N2, synchronized C.elegans early embryos from strain N2, and synchronized C.elegans young adults from strain WH223.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications in H3K9 (ChIP-Seq), H3K9acS10_L3",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K9 (ChIP-Seq)_ H3K9acS10_L3",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
+ ],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
]
},
{
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K18 (ChIP-Seq)",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -21614,103 +21005,103 @@
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "name" : "Histone Modifications in H3K18 (ChIP-Seq)",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K18 (ChIP-Seq)",
+ "description" : "Histone Modifications in H3K18 (ChIP-seq). Synchronized C. elegans early embryos from strain N2.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "minScore" : 64.3452119335747,
"type" : "LinearWiggleDisplay",
"maxScore" : 144.573066465378,
- "displayId" : "Histone Modifications in H3K18 (ChIP-Seq)_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "displayId" : "Histone Modifications in H3K18 (ChIP-Seq)_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 64.3452119335747
}
],
- "name" : "Histone Modifications in H3K18 (ChIP-Seq)",
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5152.bw"
- },
- "type" : "BigWigAdapter"
- },
- "description" : "Histone Modifications in H3K18 (ChIP-seq). Synchronized C. elegans early embryos from strain N2.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
+ }
},
{
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H4K8 (ChIP-Seq)_ L3",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
"displays" : [
{
- "displayId" : "Histone Modifications in H4K8 (ChIP-Seq)_ L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "maxScore" : 261.79341,
"type" : "LinearWiggleDisplay",
+ "maxScore" : 261.79341,
+ "displayId" : "Histone Modifications in H4K8 (ChIP-Seq)_ L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"minScore" : 123.2342878
}
],
- "name" : "Histone Modifications in H4K8 (ChIP-Seq), L3",
- "type" : "QuantitativeTrack",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6002.bw",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigWigAdapter"
},
- "description" : "Histone Modifications in H4K8 (ChIP-seq). Synchronized C. elegans L3 larvae from strain N2, synchronized C.elegans early embryos from strain N2, and synchronized C.elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
- "name" : "Histone Modifications in H4K8 (ChIP-Seq), Adult",
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
"type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6009.bw"
- }
- },
- "description" : "Histone Modifications in H4K8 (ChIP-seq). Synchronized C. elegans L3 larvae from strain N2, synchronized C.elegans early embryos from strain N2, and synchronized C.elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H4K8 (ChIP-Seq)_ Adult",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "Histone Modifications in H4K8 (ChIP-seq). Synchronized C. elegans L3 larvae from strain N2, synchronized C.elegans early embryos from strain N2, and synchronized C.elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications in H4K8 (ChIP-Seq), L3",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H4K8 (ChIP-Seq)_ L3"
+ },
+ {
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "description" : "Histone Modifications in H4K8 (ChIP-seq). Synchronized C. elegans L3 larvae from strain N2, synchronized C.elegans early embryos from strain N2, and synchronized C.elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H4K8 (ChIP-Seq)_ Adult",
+ "name" : "Histone Modifications in H4K8 (ChIP-Seq), Adult",
"displays" : [
{
- "displayId" : "Histone Modifications in H4K8 (ChIP-Seq)_ Adult_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "maxScore" : 204.712529,
"type" : "LinearWiggleDisplay",
- "minScore" : 92.69767115
+ "displayId" : "Histone Modifications in H4K8 (ChIP-Seq)_ Adult_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 92.69767115,
+ "maxScore" : 204.712529
}
- ]
+ ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6009.bw"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
- "description" : "Histone Modifications in H4K8 (ChIP-seq). Synchronized C. elegans L3 larvae from strain N2, synchronized C.elegans early embryos from strain N2, and synchronized C.elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Histone Modifications in H4K8 (ChIP-Seq), Embryo",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5162.bw",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
"displays" : [
{
- "displayId" : "Histone Modifications in H4K8 (ChIP-Seq)_ Embryo_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"minScore" : 77.58437595,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 174.871937
+ "displayId" : "Histone Modifications in H4K8 (ChIP-Seq)_ Embryo_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "maxScore" : 174.871937,
+ "type" : "LinearWiggleDisplay"
}
],
+ "name" : "Histone Modifications in H4K8 (ChIP-Seq), Embryo",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H4K8 (ChIP-Seq)_ Embryo",
+ "description" : "Histone Modifications in H4K8 (ChIP-seq). Synchronized C. elegans L3 larvae from strain N2, synchronized C.elegans early embryos from strain N2, and synchronized C.elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -21721,189 +21112,184 @@
]
},
{
- "displays" : [
- {
- "displayId" : "Histone Modifications in H3K79 (ChIP-Seq)_ H3K79me3_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 258.834749192124,
- "minScore" : 104.972767233401
- }
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K79 (ChIP-Seq)_ H3K79me3_Eemb",
+ "name" : "Histone Modifications in H3K79 (ChIP-Seq), H3K79me3_Eemb",
"description" : "Histone Modifications in H3K79 (ChIP-seq). Synchronized C. elegans early embryos from strain N2 and synchronized C.elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "maxScore" : 258.834749192124,
+ "displayId" : "Histone Modifications in H3K79 (ChIP-Seq)_ H3K79me3_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 104.972767233401,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5170.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ }
+ },
+ {
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5170.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5173.bw",
+ "locationType" : "UriLocation"
}
},
- "name" : "Histone Modifications in H3K79 (ChIP-Seq), H3K79me3_Eemb"
- },
- {
"displays" : [
{
"minScore" : 70.401799738725,
- "type" : "LinearWiggleDisplay",
+ "displayId" : "Histone Modifications in H3K79 (ChIP-Seq)_ H3K79me3_AD_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"maxScore" : 165.159696177954,
- "displayId" : "Histone Modifications in H3K79 (ChIP-Seq)_ H3K79me3_AD_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
],
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K79 (ChIP-Seq)_ H3K79me3_AD",
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
+ "name" : "Histone Modifications in H3K79 (ChIP-Seq), H3K79me3_AD",
+ "description" : "Histone Modifications in H3K79 (ChIP-seq). Synchronized C. elegans early embryos from strain N2 and synchronized C.elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : "Histone Modifications in H3K79 (ChIP-seq). Synchronized C. elegans early embryos from strain N2 and synchronized C.elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Histone Modifications in H3K79 (ChIP-Seq), H3K79me3_AD",
"type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5173.bw"
- },
- "type" : "BigWigAdapter"
- }
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ]
},
{
- "name" : "Histone Modifications in H3K79 (ChIP-Seq), H3K79me1_Eemb",
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5168.bw"
- },
- "type" : "BigWigAdapter"
+ }
},
- "description" : "Histone Modifications in H3K79 (ChIP-seq). Synchronized C. elegans early embryos from strain N2 and synchronized C.elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K79 (ChIP-Seq)_ H3K79me1_Eemb",
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
- "displayId" : "Histone Modifications in H3K79 (ChIP-Seq)_ H3K79me1_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "maxScore" : 116.556013480922,
"type" : "LinearWiggleDisplay",
+ "maxScore" : 116.556013480922,
+ "displayId" : "Histone Modifications in H3K79 (ChIP-Seq)_ H3K79me1_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"minScore" : 51.2202844487043
}
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K79 (ChIP-Seq)_ H3K79me1_Eemb",
+ "name" : "Histone Modifications in H3K79 (ChIP-Seq), H3K79me1_Eemb",
+ "description" : "Histone Modifications in H3K79 (ChIP-seq). Synchronized C. elegans early embryos from strain N2 and synchronized C.elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
]
},
{
"description" : "Histone Modifications in H3K79 (ChIP-seq). Synchronized C. elegans early embryos from strain N2 and synchronized C.elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5169.bw"
- },
- "type" : "BigWigAdapter"
- },
"name" : "Histone Modifications in H3K79 (ChIP-Seq), H3K79me2_Eemb",
- "displays" : [
- {
- "minScore" : 87.178420803106,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 216.404002433655,
- "displayId" : "Histone Modifications in H3K79 (ChIP-Seq)_ H3K79me2_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
- }
- ],
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K79 (ChIP-Seq)_ H3K79me2_Eemb",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H3K79 (ChIP-Seq)_ H3K79me2_Eemb"
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5169.bw",
+ "locationType" : "UriLocation"
+ }
+ },
+ "displays" : [
+ {
+ "maxScore" : 216.404002433655,
+ "displayId" : "Histone Modifications in H3K79 (ChIP-Seq)_ H3K79me2_Eemb_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 87.178420803106,
+ "type" : "LinearWiggleDisplay"
+ }
+ ]
},
{
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H2AK5 (ChIP-Seq)_ H2AK5ac_YA_germline",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "Histone Modifications in H2AK5 (ChIP-seq). Synchronized C. elegans young adults from strain WH223 and synchronized C.elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications in H2AK5 (ChIP-Seq), H2AK5ac_YA_germline",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H2AK5 (ChIP-Seq)_ H2AK5ac_YA_germline",
"displays" : [
{
"maxScore" : 127.596646271622,
- "type" : "LinearWiggleDisplay",
"minScore" : 66.9102932696353,
- "displayId" : "Histone Modifications in H2AK5 (ChIP-Seq)_ H2AK5ac_YA_germline_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "displayId" : "Histone Modifications in H2AK5 (ChIP-Seq)_ H2AK5ac_YA_germline_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
],
- "name" : "Histone Modifications in H2AK5 (ChIP-Seq), H2AK5ac_YA_germline",
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5251.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5251.bw"
}
- },
- "description" : "Histone Modifications in H2AK5 (ChIP-seq). Synchronized C. elegans young adults from strain WH223 and synchronized C.elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
},
{
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H2AK5 (ChIP-Seq)_ H2AK5ac_YA_F",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H2AK5 (ChIP-Seq)_ H2AK5ac_YA_F",
+ "name" : "Histone Modifications in H2AK5 (ChIP-Seq), H2AK5ac_YA_F",
+ "description" : "Histone Modifications in H2AK5 (ChIP-seq). Synchronized C. elegans young adults from strain WH223 and synchronized C.elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "minScore" : 78.3226994091829,
"type" : "LinearWiggleDisplay",
"maxScore" : 190.23848305813,
+ "minScore" : 78.3226994091829,
"displayId" : "Histone Modifications in H2AK5 (ChIP-Seq)_ H2AK5ac_YA_F_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
}
],
- "name" : "Histone Modifications in H2AK5 (ChIP-Seq), H2AK5ac_YA_F",
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5252.bw"
- },
- "type" : "BigWigAdapter"
- },
- "description" : "Histone Modifications in H2AK5 (ChIP-seq). Synchronized C. elegans young adults from strain WH223 and synchronized C.elegans adult females from strain DH245.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5252.bw",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
- "displays" : [
- {
- "displayId" : "Mononucleosomes_ GermlinelessAdults_Chromatin Structure_Nucleosome Structure-LinearWiggleDisplay",
- "maxScore" : 4,
- "type" : "LinearWiggleDisplay",
- "minScore" : -4
- }
- ],
+ "name" : "Mononucleosomes, GermlinelessAdults",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Nucleosome Structure_Mononucleosomes_ GermlinelessAdults",
+ "description" : "Chromosome-Nuclear Envelope Interaction proteins. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -21912,36 +21298,31 @@
"Chromatin Structure",
"Nucleosome Structure"
],
- "description" : "Chromosome-Nuclear Envelope Interaction proteins. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page",
- "name" : "Mononucleosomes, GermlinelessAdults",
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/GermlinelessAdults_NormalizedAveraged_WS220.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/GermlinelessAdults_NormalizedAveraged_WS220.bw",
+ "locationType" : "UriLocation"
}
- }
+ },
+ "displays" : [
+ {
+ "maxScore" : 4,
+ "minScore" : -4,
+ "displayId" : "Mononucleosomes_ GermlinelessAdults_Chromatin Structure_Nucleosome Structure-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
+ }
+ ]
},
{
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Nucleosome Structure_Mononucleosomes_ GermlinecontainingAdults",
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Nucleosome Structure"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
- "maxScore" : 4,
"type" : "LinearWiggleDisplay",
"minScore" : -4,
- "displayId" : "Mononucleosomes_ GermlinecontainingAdults_Chromatin Structure_Nucleosome Structure-LinearWiggleDisplay"
+ "displayId" : "Mononucleosomes_ GermlinecontainingAdults_Chromatin Structure_Nucleosome Structure-LinearWiggleDisplay",
+ "maxScore" : 4
}
],
- "name" : "Mononucleosomes, GermlinecontainingAdults",
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
@@ -21949,58 +21330,57 @@
},
"type" : "BigWigAdapter"
},
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Nucleosome Structure"
+ ],
"type" : "QuantitativeTrack",
- "description" : " Chromosome-Nuclear Envelope Interaction proteins. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page"
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : " Chromosome-Nuclear Envelope Interaction proteins. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page",
+ "name" : "Mononucleosomes, GermlinecontainingAdults",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Nucleosome Structure_Mononucleosomes_ GermlinecontainingAdults"
},
{
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/Embryos_NormalizedAveraged_WS220.bw"
- }
- },
- "name" : "Mononucleosomes, Mixed Embryos",
- "description" : " Chromosome-Nuclear Envelope Interaction proteins. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Nucleosome Structure"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Nucleosome Structure_Mononucleosomes_ Mixed Embryos",
+ "name" : "Mononucleosomes, Mixed Embryos",
+ "description" : " Chromosome-Nuclear Envelope Interaction proteins. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page",
"displays" : [
{
- "displayId" : "Mononucleosomes_ Mixed Embryos_Chromatin Structure_Nucleosome Structure-LinearWiggleDisplay",
"maxScore" : 4,
- "type" : "LinearWiggleDisplay",
- "minScore" : -4
+ "displayId" : "Mononucleosomes_ Mixed Embryos_Chromatin Structure_Nucleosome Structure-LinearWiggleDisplay",
+ "minScore" : -4,
+ "type" : "LinearWiggleDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/Embryos_NormalizedAveraged_WS220.bw"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
"displays" : [
{
- "type" : "LinearWiggleDisplay",
"maxScore" : 74.304448578503,
+ "displayId" : "CEH-30 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
"minScore" : 0,
- "displayId" : "CEH-30 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_CEH-30 Combined (GFP ChIP) recalled peaks w peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP (Peak Recall)"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : "Identification of Transcription Factor CEH-30::GFP Binding Regions in Late Embyros. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "CEH-30 Combined (GFP ChIP) recalled peaks w peaks",
"adapter" : {
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_CEH-30_GFP_lemb_combined_WS220.bw",
@@ -22008,73 +21388,95 @@
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack"
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP (Peak Recall)"
+ ],
+ "name" : "CEH-30 Combined (GFP ChIP) recalled peaks w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_CEH-30 Combined (GFP ChIP) recalled peaks w peaks",
+ "description" : "Identification of Transcription Factor CEH-30::GFP Binding Regions in Late Embyros. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10179_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "__CEH-30 Combined (GFP ChIP) recalled peaks peaks",
- "description" : "Peak calls for CEH-30 Combined (GFP ChIP) recalled peaks w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_CEH-30 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
+ "name" : "__CEH-30 Combined (GFP ChIP) recalled peaks peaks",
+ "description" : "Peak calls for CEH-30 Combined (GFP ChIP) recalled peaks w peaks",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
+ "showDescriptions" : false,
"height" : 6,
- "showDescriptions" : false
+ "showLabels" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "CEH-30 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks"
}
- ]
+ ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10179_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ }
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "Identification of Transcription Factor ALY-2::GFP Binding Regions in L3. Synchronized L3 larvae from C. elegans strain OP217 (a transgenic strain engineered to express a gene fusion between aly-2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ALY-2 Combined (GFP ChIP)_ ALY-2_GFP_L3 w peaks",
+ "name" : "ALY-2 Combined (GFP ChIP), ALY-2_GFP_L3 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ALY-2 Combined (GFP ChIP)_ ALY-2_GFP_L3 w peaks",
- "displays" : [
- {
- "displayId" : "ALY-2 Combined (GFP ChIP)_ ALY-2_GFP_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 143.163767201053,
- "minScore" : 0
- }
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8240.bw",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "name" : "ALY-2 Combined (GFP ChIP), ALY-2_GFP_L3 w peaks",
- "description" : "Identification of Transcription Factor ALY-2::GFP Binding Regions in L3. Synchronized L3 larvae from C. elegans strain OP217 (a transgenic strain engineered to express a gene fusion between aly-2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "displays" : [
+ {
+ "displayId" : "ALY-2 Combined (GFP ChIP)_ ALY-2_GFP_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 143.163767201053,
+ "type" : "LinearWiggleDisplay"
+ }
+ ]
},
{
"name" : "__ALY-2 Combined (GFP ChIP), ALY-2_GFP_L3 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ALY-2 Combined (GFP ChIP)_ ALY-2_GFP_L3 w peaks_bigbed_peaks",
+ "description" : "Peak calls for ALY-2 Combined (GFP ChIP), ALY-2_GFP_L3 w peaks",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
@@ -22082,285 +21484,273 @@
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "description" : "Peak calls for ALY-2 Combined (GFP ChIP), ALY-2_GFP_L3 w peaks",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ALY-2 Combined (GFP ChIP)_ ALY-2_GFP_L3 w peaks_bigbed_peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
- "displayId" : "ALY-2 Combined (GFP ChIP)_ ALY-2_GFP_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
+ "type" : "SvgFeatureRenderer",
"showDescriptions" : false,
- "color1" : "deeppink",
+ "height" : 6,
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
- }
+ "color1" : "deeppink"
+ },
+ "displayId" : "ALY-2 Combined (GFP ChIP)_ ALY-2_GFP_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
]
},
{
- "displays" : [
- {
- "displayId" : "ALY-2 Combined (GFP ChIP)_ ALY-2_GFP_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 137.15747884158,
- "minScore" : 0
- }
- ],
+ "description" : "Identification of Transcription Factor ALY-2::GFP Binding Regions in L3. Synchronized L3 larvae from C. elegans strain OP217 (a transgenic strain engineered to express a gene fusion between aly-2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "ALY-2 Combined (GFP ChIP), ALY-2_GFP_L2 w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ALY-2 Combined (GFP ChIP)_ ALY-2_GFP_L2 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : "Identification of Transcription Factor ALY-2::GFP Binding Regions in L3. Synchronized L3 larvae from C. elegans strain OP217 (a transgenic strain engineered to express a gene fusion between aly-2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "ALY-2 Combined (GFP ChIP), ALY-2_GFP_L2 w peaks",
"adapter" : {
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/14857.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/14857.bw"
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack"
+ "displays" : [
+ {
+ "minScore" : 0,
+ "displayId" : "ALY-2 Combined (GFP ChIP)_ ALY-2_GFP_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 137.15747884158,
+ "type" : "LinearWiggleDisplay"
+ }
+ ]
},
{
"displays" : [
{
+ "displayId" : "ALY-2 Combined (GFP ChIP)_ ALY-2_GFP_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
"type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
"showLabels" : false,
- "color1" : "deeppink"
+ "height" : 6,
+ "showDescriptions" : false
},
- "type" : "LinearBasicDisplay",
- "displayId" : "ALY-2 Combined (GFP ChIP)_ ALY-2_GFP_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/14864_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ALY-2 Combined (GFP ChIP)_ ALY-2_GFP_L2 w peaks_bigbed_peaks",
- "description" : "Peak calls for ALY-2 Combined (GFP ChIP), ALY-2_GFP_L2 w peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/14864_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "__ALY-2 Combined (GFP ChIP), ALY-2_GFP_L2 peaks"
+ "name" : "__ALY-2 Combined (GFP ChIP), ALY-2_GFP_L2 peaks",
+ "description" : "Peak calls for ALY-2 Combined (GFP ChIP), ALY-2_GFP_L2 w peaks"
},
{
- "description" : "Identification of Transcription Factor ALY-2::GFP Binding Regions in L3. Synchronized L3 larvae from C. elegans strain OP217 (a transgenic strain engineered to express a gene fusion between aly-2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8102.bw"
- },
- "type" : "BigWigAdapter"
+ }
},
- "name" : "ALY-2 Combined (GFP ChIP), ALY-2_GFP_L1 w peaks",
"displays" : [
{
+ "minScore" : 0,
"displayId" : "ALY-2 Combined (GFP ChIP)_ ALY-2_GFP_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
"maxScore" : 158.568313496582,
- "minScore" : 0
+ "type" : "LinearWiggleDisplay"
}
],
+ "description" : "Identification of Transcription Factor ALY-2::GFP Binding Regions in L3. Synchronized L3 larvae from C. elegans strain OP217 (a transgenic strain engineered to express a gene fusion between aly-2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "ALY-2 Combined (GFP ChIP), ALY-2_GFP_L1 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ALY-2 Combined (GFP ChIP)_ ALY-2_GFP_L1 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ALY-2 Combined (GFP ChIP)_ ALY-2_GFP_L1 w peaks"
+ ]
},
{
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "name" : "__ALY-2 Combined (GFP ChIP), ALY-2_GFP_L1 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ALY-2 Combined (GFP ChIP)_ ALY-2_GFP_L1 w peaks_bigbed_peaks",
+ "description" : "Peak calls for ALY-2 Combined (GFP ChIP), ALY-2_GFP_L1 w peaks",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false,
"color1" : "deeppink"
},
- "type" : "LinearBasicDisplay",
"displayId" : "ALY-2 Combined (GFP ChIP)_ ALY-2_GFP_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ALY-2 Combined (GFP ChIP)_ ALY-2_GFP_L1 w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "description" : "Peak calls for ALY-2 Combined (GFP ChIP), ALY-2_GFP_L1 w peaks",
- "name" : "__ALY-2 Combined (GFP ChIP), ALY-2_GFP_L1 peaks",
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8109_details.gff.bb",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8109_details.gff.bb"
},
"type" : "BigBedAdapter"
}
},
{
- "description" : "Identification of Transcription Factor C01B12.2::GFP Binding Regions in L2. Synchronized L2 larvae from C. elegans strain OP343 (a transgenic strain engineered to express a gene fusion between C01B12.2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8172.bw",
- "locationType" : "UriLocation"
- }
- },
+ "description" : "Identification of Transcription Factor C01B12.2::GFP Binding Regions in L2. Synchronized L2 larvae from C. elegans strain OP343 (a transgenic strain engineered to express a gene fusion between C01B12.2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_C01B12.2 Combined (GFP ChIP) w peaks",
"name" : "C01B12.2 Combined (GFP ChIP) w peaks",
"displays" : [
{
+ "displayId" : "C01B12.2 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
"maxScore" : 143.537623346149,
- "displayId" : "C01B12.2 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_C01B12.2 Combined (GFP ChIP) w peaks"
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8172.bw"
+ }
+ }
},
{
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8179_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
- "displayId" : "C01B12.2 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink",
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
},
+ "displayId" : "C01B12.2 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay"
}
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_C01B12.2 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "name" : "__C01B12.2 Combined (GFP ChIP) peaks",
+ "description" : "Peak calls for C01B12.2 Combined (GFP ChIP) w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_C01B12.2 Combined (GFP ChIP) w peaks_bigbed_peaks",
- "description" : "Peak calls for C01B12.2 Combined (GFP ChIP) w peaks",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8179_details.gff.bb"
- }
- },
- "type" : "FeatureTrack",
- "name" : "__C01B12.2 Combined (GFP ChIP) peaks"
+ ]
},
{
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 44.4436012513859,
+ "minScore" : 0,
+ "displayId" : "CEH-26 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/9166.bw"
- },
- "type" : "BigWigAdapter"
+ }
},
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
- "name" : "CEH-26 Combined (GFP ChIP) w peaks",
- "description" : " Identification of Transcription Factor CEH-14::GFP Binding Regions in L2 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-26 Combined (GFP ChIP) w peaks",
- "displays" : [
- {
- "displayId" : "CEH-26 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
- "maxScore" : 44.4436012513859,
- "type" : "LinearWiggleDisplay"
- }
- ]
+ "name" : "CEH-26 Combined (GFP ChIP) w peaks",
+ "description" : " Identification of Transcription Factor CEH-14::GFP Binding Regions in L2 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "description" : "Peak calls for CEH-26 Combined (GFP ChIP) w peaks",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9172_details.gff.bb",
- "locationType" : "UriLocation"
- }
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9172_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "name" : "__CEH-26 Combined (GFP ChIP) peaks",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "CEH-26 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "CEH-26 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false
+ }
}
],
+ "description" : "Peak calls for CEH-26 Combined (GFP ChIP) w peaks",
+ "name" : "__CEH-26 Combined (GFP ChIP) peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-26 Combined (GFP ChIP) w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-26 Combined (GFP ChIP) w peaks_bigbed_peaks"
+ ]
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CES-1 Combined (GFP ChIP)_ CES-1_GFP_L4 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -22369,216 +21759,216 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
+ "description" : " Identification of Transcription Factor CES-1::GFP Binding Regions in EMB. Synchronized organisms from C. elegans strain OP174 (a transgenic strain engineered to express a gene fusion between ces-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CES-1 Combined (GFP ChIP)_ CES-1_GFP_L4 w peaks",
+ "name" : "CES-1 Combined (GFP ChIP), CES-1_GFP_L4 w peaks",
"displays" : [
{
- "type" : "LinearWiggleDisplay",
- "maxScore" : 50.237136832182,
"minScore" : 0,
- "displayId" : "CES-1 Combined (GFP ChIP)_ CES-1_GFP_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "displayId" : "CES-1 Combined (GFP ChIP)_ CES-1_GFP_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 50.237136832182,
+ "type" : "LinearWiggleDisplay"
}
],
- "name" : "CES-1 Combined (GFP ChIP), CES-1_GFP_L4 w peaks",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8115.bw",
"locationType" : "UriLocation"
}
- },
- "type" : "QuantitativeTrack",
- "description" : " Identification of Transcription Factor CES-1::GFP Binding Regions in EMB. Synchronized organisms from C. elegans strain OP174 (a transgenic strain engineered to express a gene fusion between ces-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
},
{
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8126_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "__CES-1 Combined (GFP ChIP), CES-1_GFP_L4 peaks",
- "description" : "Peak calls for CES-1 Combined (GFP ChIP), CES-1_GFP_L4 w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Peak calls for CES-1 Combined (GFP ChIP), CES-1_GFP_L4 w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CES-1 Combined (GFP ChIP)_ CES-1_GFP_L4 w peaks_bigbed_peaks",
+ "name" : "__CES-1 Combined (GFP ChIP), CES-1_GFP_L4 peaks",
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "deeppink",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
"height" : 6,
- "showDescriptions" : false
+ "showLabels" : false,
+ "color1" : "deeppink"
},
- "displayId" : "CES-1 Combined (GFP ChIP)_ CES-1_GFP_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "displayId" : "CES-1 Combined (GFP ChIP)_ CES-1_GFP_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8126_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ }
},
{
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CES-1 Combined (GFP ChIP)_ CES-1_GFP_L1 w peaks",
"name" : "CES-1 Combined (GFP ChIP), CES-1_GFP_L1 w peaks",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/9155.bw"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
"description" : " Identification of Transcription Factor CES-1::GFP Binding Regions in EMB. Synchronized organisms from C. elegans strain OP174 (a transgenic strain engineered to express a gene fusion between ces-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CES-1 Combined (GFP ChIP)_ CES-1_GFP_L1 w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/9155.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "type" : "LinearWiggleDisplay",
"maxScore" : 56.4058984607179,
+ "displayId" : "CES-1 Combined (GFP ChIP)_ CES-1_GFP_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "displayId" : "CES-1 Combined (GFP ChIP)_ CES-1_GFP_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
]
},
{
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "showDescriptions" : false,
+ "height" : 6
},
- "displayId" : "CES-1 Combined (GFP ChIP)_ CES-1_GFP_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "displayId" : "CES-1 Combined (GFP ChIP)_ CES-1_GFP_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9162_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "__CES-1 Combined (GFP ChIP), CES-1_GFP_L1 peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CES-1 Combined (GFP ChIP)_ CES-1_GFP_L1 w peaks_bigbed_peaks",
- "description" : "Peak calls for CES-1 Combined (GFP ChIP), CES-1_GFP_L1 w peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9162_details.gff.bb",
- "locationType" : "UriLocation"
- }
- },
- "name" : "__CES-1 Combined (GFP ChIP), CES-1_GFP_L1 peaks"
+ "description" : "Peak calls for CES-1 Combined (GFP ChIP), CES-1_GFP_L1 w peaks"
},
{
- "displays" : [
- {
- "minScore" : 0,
- "maxScore" : 44.0072521491075,
- "type" : "LinearWiggleDisplay",
- "displayId" : "CES-1 Combined (GFP ChIP)_ CES-1_GFP_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CES-1 Combined (GFP ChIP)_ CES-1_GFP_L3 w peaks",
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"description" : " Identification of Transcription Factor CES-1::GFP Binding Regions in EMB. Synchronized organisms from C. elegans strain OP174 (a transgenic strain engineered to express a gene fusion between ces-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "CES-1 Combined (GFP ChIP), CES-1_GFP_L3 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CES-1 Combined (GFP ChIP)_ CES-1_GFP_L3 w peaks",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "minScore" : 0,
+ "displayId" : "CES-1 Combined (GFP ChIP)_ CES-1_GFP_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 44.0072521491075
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/11327.bw",
"locationType" : "UriLocation"
}
- },
- "type" : "QuantitativeTrack",
- "name" : "CES-1 Combined (GFP ChIP), CES-1_GFP_L3 w peaks"
+ }
},
{
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "CES-1 Combined (GFP ChIP)_ CES-1_GFP_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
+ "height" : 6,
+ "showDescriptions" : false,
+ "showLabels" : false
+ }
+ }
+ ],
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/11333_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/11333_details.gff.bb"
+ }
},
- "type" : "FeatureTrack",
- "name" : "__CES-1 Combined (GFP ChIP), CES-1_GFP_L3 peaks",
- "description" : "Peak calls for CES-1 Combined (GFP ChIP), CES-1_GFP_L3 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CES-1 Combined (GFP ChIP)_ CES-1_GFP_L3 w peaks_bigbed_peaks",
- "displays" : [
- {
- "displayId" : "CES-1 Combined (GFP ChIP)_ CES-1_GFP_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "renderer" : {
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "height" : 6,
- "showDescriptions" : false
- },
- "type" : "LinearBasicDisplay"
- }
- ]
+ "description" : "Peak calls for CES-1 Combined (GFP ChIP), CES-1_GFP_L3 w peaks",
+ "name" : "__CES-1 Combined (GFP ChIP), CES-1_GFP_L3 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CES-1 Combined (GFP ChIP)_ CES-1_GFP_L3 w peaks_bigbed_peaks"
},
{
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DAF-12 Combined (GFP ChIP)_ DAF-12_GFP_L4 w peaks",
+ "name" : "DAF-12 Combined (GFP ChIP), DAF-12_GFP_L4 w peaks",
+ "description" : " Identification of Transcription Factor CES-1::GFP Binding Regions in EMB. Synchronized organisms from C. elegans strain OP174 (a transgenic strain engineered to express a gene fusion between ces-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DAF-12 Combined (GFP ChIP)_ DAF-12_GFP_L4 w peaks",
- "displays" : [
- {
- "displayId" : "DAF-12 Combined (GFP ChIP)_ DAF-12_GFP_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "maxScore" : 28.1126415614812,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
- }
- ],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8212.bw",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "name" : "DAF-12 Combined (GFP ChIP), DAF-12_GFP_L4 w peaks",
- "description" : " Identification of Transcription Factor CES-1::GFP Binding Regions in EMB. Synchronized organisms from C. elegans strain OP174 (a transgenic strain engineered to express a gene fusion between ces-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "displays" : [
+ {
+ "displayId" : "DAF-12 Combined (GFP ChIP)_ DAF-12_GFP_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 28.1126415614812,
+ "type" : "LinearWiggleDisplay"
+ }
+ ]
},
{
- "description" : "Peak calls for DAF-12 Combined (GFP ChIP), DAF-12_GFP_L4 w peaks",
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
@@ -22586,21 +21976,22 @@
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "name" : "__DAF-12 Combined (GFP ChIP), DAF-12_GFP_L4 peaks",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "DAF-12 Combined (GFP ChIP)_ DAF-12_GFP_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
"showDescriptions" : false,
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink"
+ "showLabels" : false
},
- "displayId" : "DAF-12 Combined (GFP ChIP)_ DAF-12_GFP_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
],
+ "description" : "Peak calls for DAF-12 Combined (GFP ChIP), DAF-12_GFP_L4 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DAF-12 Combined (GFP ChIP)_ DAF-12_GFP_L4 w peaks_bigbed_peaks",
+ "name" : "__DAF-12 Combined (GFP ChIP), DAF-12_GFP_L4 peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -22609,39 +22000,38 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DAF-12 Combined (GFP ChIP)_ DAF-12_GFP_L4 w peaks_bigbed_peaks"
+ "type" : "FeatureTrack"
},
{
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DAF-12 Combined (GFP ChIP)_ DAF-12_GFP_L3 OP222 w peaks",
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8225.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
+ "maxScore" : 83.859151988705,
"displayId" : "DAF-12 Combined (GFP ChIP)_ DAF-12_GFP_L3 OP222 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 83.859151988705
+ "type" : "LinearWiggleDisplay"
}
],
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8225.bw"
- }
- },
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DAF-12 Combined (GFP ChIP)_ DAF-12_GFP_L3 OP222 w peaks",
"name" : "DAF-12 Combined (GFP ChIP), DAF-12_GFP_L3 OP222 w peaks",
- "description" : " Identification of Transcription Factor CES-1::GFP Binding Regions in EMB. Synchronized organisms from C. elegans strain OP174 (a transgenic strain engineered to express a gene fusion between ces-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "description" : " Identification of Transcription Factor CES-1::GFP Binding Regions in EMB. Synchronized organisms from C. elegans strain OP174 (a transgenic strain engineered to express a gene fusion between ces-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ]
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DAF-12 Combined (GFP ChIP)_ DAF-12_GFP_L3 OP222 w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -22650,95 +22040,96 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "description" : "Peak calls for DAF-12 Combined (GFP ChIP), DAF-12_GFP_L3 OP222 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DAF-12 Combined (GFP ChIP)_ DAF-12_GFP_L3 OP222 w peaks_bigbed_peaks",
+ "name" : "__DAF-12 Combined (GFP ChIP), DAF-12_GFP_L3 OP222 peaks",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "DAF-12 Combined (GFP ChIP)_ DAF-12_GFP_L3 OP222 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
- },
- "displayId" : "DAF-12 Combined (GFP ChIP)_ DAF-12_GFP_L3 OP222 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false
+ }
}
],
- "name" : "__DAF-12 Combined (GFP ChIP), DAF-12_GFP_L3 OP222 peaks",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8233_details.gff.bb",
"locationType" : "UriLocation"
}
- },
- "type" : "FeatureTrack",
- "description" : "Peak calls for DAF-12 Combined (GFP ChIP), DAF-12_GFP_L3 OP222 w peaks"
+ }
},
{
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/9252.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "displayId" : "DAF-12 Combined (GFP ChIP)_ DAF-12 GFP L3 OP167 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 85.276681209373,
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 85.276681209373
+ "displayId" : "DAF-12 Combined (GFP ChIP)_ DAF-12 GFP L3 OP167 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DAF-12 Combined (GFP ChIP)_ DAF-12 GFP L3 OP167 w peaks",
+ "name" : "DAF-12 Combined (GFP ChIP), DAF-12 GFP L3 OP167 w peaks",
+ "description" : " Identification of Transcription Factor CES-1::GFP Binding Regions in EMB. Synchronized organisms from C. elegans strain OP174 (a transgenic strain engineered to express a gene fusion between ces-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DAF-12 Combined (GFP ChIP)_ DAF-12 GFP L3 OP167 w peaks",
- "description" : " Identification of Transcription Factor CES-1::GFP Binding Regions in EMB. Synchronized organisms from C. elegans strain OP174 (a transgenic strain engineered to express a gene fusion between ces-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/9252.bw"
- },
- "type" : "BigWigAdapter"
- },
- "name" : "DAF-12 Combined (GFP ChIP), DAF-12 GFP L3 OP167 w peaks"
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ]
},
{
- "description" : "Peak calls for DAF-12 Combined (GFP ChIP), DAF-12 GFP L3 OP167 w peaks",
"name" : "__DAF-12 Combined (GFP ChIP), DAF-12 GFP L3 OP167 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DAF-12 Combined (GFP ChIP)_ DAF-12 GFP L3 OP167 w peaks_bigbed_peaks",
+ "description" : "Peak calls for DAF-12 Combined (GFP ChIP), DAF-12 GFP L3 OP167 w peaks",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9266_details.gff.bb",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9266_details.gff.bb"
}
},
"displays" : [
{
+ "displayId" : "DAF-12 Combined (GFP ChIP)_ DAF-12 GFP L3 OP167 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 6,
"showDescriptions" : false,
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "showLabels" : false,
+ "color1" : "deeppink"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "DAF-12 Combined (GFP ChIP)_ DAF-12 GFP L3 OP167 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DAF-12 Combined (GFP ChIP)_ DAF-12 GFP L3 OP167 w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
]
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DPL-1 Combined (GFP ChIP)_ Pdpl1_DPL1_GFP_L1 w peaks",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -22747,24 +22138,24 @@
"Transcription Factors",
"GFP ChIP"
],
+ "name" : "DPL-1 Combined (GFP ChIP), Pdpl1_DPL1_GFP_L1 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DPL-1 Combined (GFP ChIP)_ Pdpl1_DPL1_GFP_L1 w peaks",
+ "description" : "Identification of Transcription Factor NHR-6::GFP Binding Regions in L2 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "displayId" : "DPL-1 Combined (GFP ChIP)_ Pdpl1_DPL1_GFP_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "maxScore" : 255.530494860916,
"type" : "LinearWiggleDisplay",
- "minScore" : 0
+ "displayId" : "DPL-1 Combined (GFP ChIP)_ Pdpl1_DPL1_GFP_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 255.530494860916
}
],
- "name" : "DPL-1 Combined (GFP ChIP), Pdpl1_DPL1_GFP_L1 w peaks",
"adapter" : {
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/9140.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/9140.bw"
},
"type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "description" : "Identification of Transcription Factor NHR-6::GFP Binding Regions in L2 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
},
{
"category" : [
@@ -22775,160 +22166,158 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "description" : "Peak calls for DPL-1 Combined (GFP ChIP), Pdpl1_DPL1_GFP_L1 w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DPL-1 Combined (GFP ChIP)_ Pdpl1_DPL1_GFP_L1 w peaks_bigbed_peaks",
+ "name" : "__DPL-1 Combined (GFP ChIP), Pdpl1_DPL1_GFP_L1 peaks",
"displays" : [
{
"displayId" : "DPL-1 Combined (GFP ChIP)_ Pdpl1_DPL1_GFP_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
"color1" : "deeppink",
"showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6,
"type" : "SvgFeatureRenderer"
- }
+ },
+ "type" : "LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9148_details.gff.bb",
"locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
- },
- "name" : "__DPL-1 Combined (GFP ChIP), Pdpl1_DPL1_GFP_L1 peaks",
- "description" : "Peak calls for DPL-1 Combined (GFP ChIP), Pdpl1_DPL1_GFP_L1 w peaks"
+ }
},
{
- "name" : "DPL-1 Combined (GFP ChIP), DPL1_GFP_L1 w peaks",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/15138.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
"description" : "Identification of Transcription Factor NHR-6::GFP Binding Regions in L2 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DPL-1 Combined (GFP ChIP)_ DPL1_GFP_L1 w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "DPL-1 Combined (GFP ChIP), DPL1_GFP_L1 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/15138.bw"
+ }
+ },
"displays" : [
{
- "maxScore" : 152.155401798281,
"type" : "LinearWiggleDisplay",
+ "displayId" : "DPL-1 Combined (GFP ChIP)_ DPL1_GFP_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "displayId" : "DPL-1 Combined (GFP ChIP)_ DPL1_GFP_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "maxScore" : 152.155401798281
}
]
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "Peak calls for DPL-1 Combined (GFP ChIP), DPL1_GFP_L1 w peaks",
+ "name" : "__DPL-1 Combined (GFP ChIP), DPL1_GFP_L1 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DPL-1 Combined (GFP ChIP)_ DPL1_GFP_L1 w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DPL-1 Combined (GFP ChIP)_ DPL1_GFP_L1 w peaks_bigbed_peaks",
- "displays" : [
- {
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "DPL-1 Combined (GFP ChIP)_ DPL1_GFP_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
- }
- ],
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/15145_details.gff.bb"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/15145_details.gff.bb",
+ "locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
- "name" : "__DPL-1 Combined (GFP ChIP), DPL1_GFP_L1 peaks",
- "description" : "Peak calls for DPL-1 Combined (GFP ChIP), DPL1_GFP_L1 w peaks"
- },
- {
"displays" : [
{
- "displayId" : "DPL-1 Combined (GFP ChIP)_ DPL-1_GFP_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 206.229603246312
+ "renderer" : {
+ "height" : 6,
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "DPL-1 Combined (GFP ChIP)_ DPL1_GFP_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
+ ]
+ },
+ {
+ "name" : "DPL-1 Combined (GFP ChIP), DPL-1_GFP_L4 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DPL-1 Combined (GFP ChIP)_ DPL-1_GFP_L4 w peaks",
+ "description" : "Identification of Transcription Factor NHR-6::GFP Binding Regions in L2 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DPL-1 Combined (GFP ChIP)_ DPL-1_GFP_L4 w peaks",
- "description" : "Identification of Transcription Factor NHR-6::GFP Binding Regions in L2 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/14815.bw"
- }
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/14815.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
},
- "name" : "DPL-1 Combined (GFP ChIP), DPL-1_GFP_L4 w peaks"
+ "displays" : [
+ {
+ "minScore" : 0,
+ "displayId" : "DPL-1 Combined (GFP ChIP)_ DPL-1_GFP_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 206.229603246312,
+ "type" : "LinearWiggleDisplay"
+ }
+ ]
},
{
- "description" : "Peak calls for DPL-1 Combined (GFP ChIP), DPL-1_GFP_L4 w peaks",
- "name" : "__DPL-1 Combined (GFP ChIP), DPL-1_GFP_L4 peaks",
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/14825_details.gff.bb",
- "locationType" : "UriLocation"
- }
- },
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "name" : "__DPL-1 Combined (GFP ChIP), DPL-1_GFP_L4 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DPL-1 Combined (GFP ChIP)_ DPL-1_GFP_L4 w peaks_bigbed_peaks",
+ "description" : "Peak calls for DPL-1 Combined (GFP ChIP), DPL-1_GFP_L4 w peaks",
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "height" : 6,
+ "showDescriptions" : false,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "DPL-1 Combined (GFP ChIP)_ DPL-1_GFP_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "displayId" : "DPL-1 Combined (GFP ChIP)_ DPL-1_GFP_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DPL-1 Combined (GFP ChIP)_ DPL-1_GFP_L4 w peaks_bigbed_peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ]
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/14825_details.gff.bb"
+ }
+ }
},
{
- "description" : "Identification of Transcription Factor NHR-6::GFP Binding Regions in L2 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "DPL-1 Combined (GFP ChIP), PIE1_DPL1_GFP_YA w peaks",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -22936,40 +22325,52 @@
"locationType" : "UriLocation"
}
},
- "type" : "QuantitativeTrack",
"displays" : [
{
- "displayId" : "DPL-1 Combined (GFP ChIP)_ PIE1_DPL1_GFP_YA w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "maxScore" : 56.1772226882565,
"type" : "LinearWiggleDisplay",
- "minScore" : 0
+ "displayId" : "DPL-1 Combined (GFP ChIP)_ PIE1_DPL1_GFP_YA w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 56.1772226882565
}
],
+ "description" : "Identification of Transcription Factor NHR-6::GFP Binding Regions in L2 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "DPL-1 Combined (GFP ChIP), PIE1_DPL1_GFP_YA w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DPL-1 Combined (GFP ChIP)_ PIE1_DPL1_GFP_YA w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
]
},
{
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9195_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
- "displayId" : "DPL-1 Combined (GFP ChIP)_ PIE1_DPL1_GFP_YA w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"showDescriptions" : false,
"height" : 6,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "deeppink"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "DPL-1 Combined (GFP ChIP)_ PIE1_DPL1_GFP_YA w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
],
+ "name" : "__DPL-1 Combined (GFP ChIP), PIE1_DPL1_GFP_YA peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DPL-1 Combined (GFP ChIP)_ PIE1_DPL1_GFP_YA w peaks_bigbed_peaks",
+ "description" : "Peak calls for DPL-1 Combined (GFP ChIP), PIE1_DPL1_GFP_YA w peaks",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -22977,112 +22378,109 @@
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "description" : "Peak calls for DPL-1 Combined (GFP ChIP), PIE1_DPL1_GFP_YA w peaks",
- "name" : "__DPL-1 Combined (GFP ChIP), PIE1_DPL1_GFP_YA peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9195_details.gff.bb"
- }
- }
+ ]
},
{
- "displays" : [
- {
- "displayId" : "EFL-1 Combined (GFP ChIP)_ EFL1 L2_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 479.867714224215,
- "minScore" : 167.160145693991
- }
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EFL-1 Combined (GFP ChIP)_ EFL1 L2",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : " Snyder_NHR-23_GFP_L2. Synchronized L2 larvae from C. elegans strain OP43 (a transgenic strain engineered to express a gene fusion between nhr-23 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"name" : "EFL-1 Combined (GFP ChIP), EFL1 L2",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EFL-1 Combined (GFP ChIP)_ EFL1 L2",
+ "description" : " Snyder_NHR-23_GFP_L2. Synchronized L2 larvae from C. elegans strain OP43 (a transgenic strain engineered to express a gene fusion between nhr-23 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "displayId" : "EFL-1 Combined (GFP ChIP)_ EFL1 L2_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 167.160145693991,
+ "maxScore" : 479.867714224215,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/9188.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/9188.bw"
}
- },
- "type" : "QuantitativeTrack"
+ }
},
{
- "name" : "EFL-1 Combined (GFP ChIP), EFL1 L1 recalled peaks w peaks",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18980.bw"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "description" : "Identification of Transcription Factor EGL-27::GFP Binding Regions in L1. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.
Additional note from Scott Cain: this track doesn't appear in the original modENCODE GBrowse tracks, but I'm nearly certain this 'recall' track should be here.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_EFL-1 Combined (GFP ChIP)_ EFL1 L1 recalled peaks w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "description" : "Identification of Transcription Factor EGL-27::GFP Binding Regions in L1. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.
Additional note from Scott Cain: this track doesn't appear in the original modENCODE GBrowse tracks, but I'm nearly certain this 'recall' track should be here.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_EFL-1 Combined (GFP ChIP)_ EFL1 L1 recalled peaks w peaks",
+ "name" : "EFL-1 Combined (GFP ChIP), EFL1 L1 recalled peaks w peaks",
"displays" : [
{
- "minScore" : 0,
- "maxScore" : 119.359462041189,
"type" : "LinearWiggleDisplay",
- "displayId" : "EFL-1 Combined (GFP ChIP)_ EFL1 L1 recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay"
+ "minScore" : 0,
+ "displayId" : "EFL-1 Combined (GFP ChIP)_ EFL1 L1 recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
+ "maxScore" : 119.359462041189
}
- ]
+ ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18980.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18985_details.gff.bb",
- "locationType" : "UriLocation"
- }
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18985_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
},
- "name" : "__EFL-1 Combined (GFP ChIP), EFL1 L1 recalled peaks peaks",
- "description" : "Peak calls for EFL-1 Combined (GFP ChIP), EFL1 L1 recalled peaks w peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP (Peak Recall)"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_EFL-1 Combined (GFP ChIP)_ EFL1 L1 recalled peaks w peaks_bigbed_peaks",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "EFL-1 Combined (GFP ChIP)_ EFL1 L1 recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks",
"renderer" : {
- "color1" : "deeppink",
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
+ "color1" : "deeppink",
"height" : 6,
- "showDescriptions" : false
- },
- "displayId" : "EFL-1 Combined (GFP ChIP)_ EFL1 L1 recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks"
+ "showDescriptions" : false,
+ "showLabels" : false
+ }
}
+ ],
+ "name" : "__EFL-1 Combined (GFP ChIP), EFL1 L1 recalled peaks peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_EFL-1 Combined (GFP ChIP)_ EFL1 L1 recalled peaks w peaks_bigbed_peaks",
+ "description" : "Peak calls for EFL-1 Combined (GFP ChIP), EFL1 L1 recalled peaks w peaks",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP (Peak Recall)"
]
},
{
- "description" : " Snyder_NHR-23_GFP_L2. Synchronized L2 larvae from C. elegans strain OP43 (a transgenic strain engineered to express a gene fusion between nhr-23 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "maxScore" : 104.010869785173,
+ "displayId" : "EFL-1 Combined (GFP ChIP)_ EFL1 L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -23090,41 +22488,23 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18980.bw"
}
},
- "type" : "QuantitativeTrack",
- "name" : "EFL-1 Combined (GFP ChIP), EFL1 L1 w peaks",
- "displays" : [
- {
- "displayId" : "EFL-1 Combined (GFP ChIP)_ EFL1 L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
- "maxScore" : 104.010869785173,
- "type" : "LinearWiggleDisplay"
- }
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EFL-1 Combined (GFP ChIP)_ EFL1 L1 w peaks"
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EFL-1 Combined (GFP ChIP)_ EFL1 L1 w peaks",
+ "name" : "EFL-1 Combined (GFP ChIP), EFL1 L1 w peaks",
+ "description" : " Snyder_NHR-23_GFP_L2. Synchronized L2 larvae from C. elegans strain OP43 (a transgenic strain engineered to express a gene fusion between nhr-23 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
- },
- "displayId" : "EFL-1 Combined (GFP ChIP)_ EFL1 L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
- }
- ],
+ "description" : "Peak calls for EFL-1 Combined (GFP ChIP), EFL1 L1 w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EFL-1 Combined (GFP ChIP)_ EFL1 L1 w peaks_bigbed_peaks",
+ "name" : "__EFL-1 Combined (GFP ChIP), EFL1 L1 peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -23133,123 +22513,124 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : "Peak calls for EFL-1 Combined (GFP ChIP), EFL1 L1 w peaks",
- "name" : "__EFL-1 Combined (GFP ChIP), EFL1 L1 peaks",
"type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9201_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- }
- },
- {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9201_details.gff.bb"
+ }
+ },
"displays" : [
{
- "displayId" : "EFL-1 Combined (GFP ChIP)_ N2 EFL1 anti-EFL1 L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 573.56567961182
+ "displayId" : "EFL-1 Combined (GFP ChIP)_ EFL1 L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "renderer" : {
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
}
- ],
+ ]
+ },
+ {
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EFL-1 Combined (GFP ChIP)_ N2 EFL1 anti-EFL1 L1 w peaks",
"description" : " Snyder_NHR-23_GFP_L2. Synchronized L2 larvae from C. elegans strain OP43 (a transgenic strain engineered to express a gene fusion between nhr-23 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
+ "name" : "EFL-1 Combined (GFP ChIP), N2 EFL1 anti-EFL1 L1 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EFL-1 Combined (GFP ChIP)_ N2 EFL1 anti-EFL1 L1 w peaks",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "displayId" : "EFL-1 Combined (GFP ChIP)_ N2 EFL1 anti-EFL1 L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 573.56567961182
+ }
+ ],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18847.bw",
- "locationType" : "UriLocation"
- }
- },
- "name" : "EFL-1 Combined (GFP ChIP), N2 EFL1 anti-EFL1 L1 w peaks"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18847.bw"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
- "description" : "Peak calls for EFL-1 Combined (GFP ChIP), N2 EFL1 anti-EFL1 L1 w peaks",
- "name" : "__EFL-1 Combined (GFP ChIP), N2 EFL1 anti-EFL1 L1 peaks",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18868_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "EFL-1 Combined (GFP ChIP)_ N2 EFL1 anti-EFL1 L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay",
+ "displayId" : "EFL-1 Combined (GFP ChIP)_ N2 EFL1 anti-EFL1 L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "deeppink",
+ "showLabels" : false,
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
+ "color1" : "deeppink"
}
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EFL-1 Combined (GFP ChIP)_ N2 EFL1 anti-EFL1 L1 w peaks_bigbed_peaks",
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18868_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
+ },
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ]
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EFL-1 Combined (GFP ChIP)_ N2 EFL1 anti-EFL1 L1 w peaks_bigbed_peaks",
+ "name" : "__EFL-1 Combined (GFP ChIP), N2 EFL1 anti-EFL1 L1 peaks",
+ "description" : "Peak calls for EFL-1 Combined (GFP ChIP), N2 EFL1 anti-EFL1 L1 w peaks"
},
{
- "displays" : [
- {
- "displayId" : "EFL-1 Combined (GFP ChIP)_ EFL1 YA w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 99.0096145025885
- }
- ],
+ "description" : " Snyder_NHR-23_GFP_L2. Synchronized L2 larvae from C. elegans strain OP43 (a transgenic strain engineered to express a gene fusion between nhr-23 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "EFL-1 Combined (GFP ChIP), EFL1 YA w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EFL-1 Combined (GFP ChIP)_ EFL1 YA w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EFL-1 Combined (GFP ChIP)_ EFL1 YA w peaks",
- "description" : " Snyder_NHR-23_GFP_L2. Synchronized L2 larvae from C. elegans strain OP43 (a transgenic strain engineered to express a gene fusion between nhr-23 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/9107.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/9107.bw",
+ "locationType" : "UriLocation"
}
},
- "type" : "QuantitativeTrack",
- "name" : "EFL-1 Combined (GFP ChIP), EFL1 YA w peaks"
- },
- {
"displays" : [
{
- "displayId" : "EFL-1 Combined (GFP ChIP)_ EFL1 YA w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
- },
- "type" : "LinearBasicDisplay"
+ "minScore" : 0,
+ "displayId" : "EFL-1 Combined (GFP ChIP)_ EFL1 YA w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 99.0096145025885,
+ "type" : "LinearWiggleDisplay"
}
- ],
+ ]
+ },
+ {
+ "description" : "Peak calls for EFL-1 Combined (GFP ChIP), EFL1 YA w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EFL-1 Combined (GFP ChIP)_ EFL1 YA w peaks_bigbed_peaks",
+ "name" : "__EFL-1 Combined (GFP ChIP), EFL1 YA peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -23258,92 +22639,93 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EFL-1 Combined (GFP ChIP)_ EFL1 YA w peaks_bigbed_peaks",
- "description" : "Peak calls for EFL-1 Combined (GFP ChIP), EFL1 YA w peaks",
"type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9114_details.gff.bb"
- },
- "type" : "BigBedAdapter"
+ }
},
- "name" : "__EFL-1 Combined (GFP ChIP), EFL1 YA peaks"
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false
+ },
+ "displayId" : "EFL-1 Combined (GFP ChIP)_ EFL1 YA w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EOR-1 Combined (GFP ChIP)_ EOR-1 GFP L3 w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
"displays" : [
{
- "minScore" : 0,
- "maxScore" : 53.3047448888567,
"type" : "LinearWiggleDisplay",
- "displayId" : "EOR-1 Combined (GFP ChIP)_ EOR-1 GFP L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "maxScore" : 53.3047448888567,
+ "displayId" : "EOR-1 Combined (GFP ChIP)_ EOR-1 GFP L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0
}
],
- "name" : "EOR-1 Combined (GFP ChIP), EOR-1 GFP L3 w peaks",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/7987.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/7987.bw"
+ }
},
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
"type" : "QuantitativeTrack",
- "description" : " Identification of Transcription Factor EGL-27::GFP Binding Regions in L1 ( project, subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : " Identification of Transcription Factor EGL-27::GFP Binding Regions in L1 ( project, subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "EOR-1 Combined (GFP ChIP), EOR-1 GFP L3 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EOR-1 Combined (GFP ChIP)_ EOR-1 GFP L3 w peaks"
},
{
- "description" : "Peak calls for EOR-1 Combined (GFP ChIP), EOR-1 GFP L3 w peaks",
- "name" : "__EOR-1 Combined (GFP ChIP), EOR-1 GFP L3 peaks",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7992_details.gff.bb",
- "locationType" : "UriLocation"
- }
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7992_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
"displays" : [
{
"displayId" : "EOR-1 Combined (GFP ChIP)_ EOR-1 GFP L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
"color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false
},
"type" : "LinearBasicDisplay"
}
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EOR-1 Combined (GFP ChIP)_ EOR-1 GFP L3 w peaks_bigbed_peaks",
+ "name" : "__EOR-1 Combined (GFP ChIP), EOR-1 GFP L3 peaks",
+ "description" : "Peak calls for EOR-1 Combined (GFP ChIP), EOR-1 GFP L3 w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
]
},
{
"type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8324.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "name" : "EOR-1 Combined (GFP ChIP), EOR-1 GFP L3.v2 w peaks",
- "description" : " Identification of Transcription Factor EGL-27::GFP Binding Regions in L1 ( project, subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -23352,30 +22734,27 @@
"Transcription Factors",
"GFP ChIP"
],
+ "name" : "EOR-1 Combined (GFP ChIP), EOR-1 GFP L3.v2 w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EOR-1 Combined (GFP ChIP)_ EOR-1 GFP L3.v2 w peaks",
+ "description" : " Identification of Transcription Factor EGL-27::GFP Binding Regions in L1 ( project, subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "displayId" : "EOR-1 Combined (GFP ChIP)_ EOR-1 GFP L3.v2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"maxScore" : 119.359452574373,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
+ "minScore" : 0,
+ "displayId" : "EOR-1 Combined (GFP ChIP)_ EOR-1 GFP L3.v2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8324.bw"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
- "displays" : [
- {
- "renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "EOR-1 Combined (GFP ChIP)_ EOR-1 GFP L3.v2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
- }
- ],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -23384,29 +22763,38 @@
"Transcription Factors",
"GFP ChIP"
],
+ "name" : "__EOR-1 Combined (GFP ChIP), EOR-1 GFP L3.v2 peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EOR-1 Combined (GFP ChIP)_ EOR-1 GFP L3.v2 w peaks_bigbed_peaks",
"description" : "Peak calls for EOR-1 Combined (GFP ChIP), EOR-1 GFP L3.v2 w peaks",
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6,
+ "color1" : "deeppink"
+ },
+ "displayId" : "EOR-1 Combined (GFP ChIP)_ EOR-1 GFP L3.v2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ }
+ ],
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8330_details.gff.bb"
- }
- },
- "name" : "__EOR-1 Combined (GFP ChIP), EOR-1 GFP L3.v2 peaks"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8330_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ }
},
{
- "description" : " Identification of Transcription Factor EGL-27::GFP Binding Regions in L1 ( project, subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/9283.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/9283.bw"
}
},
- "name" : "F16B12.6 Combined (GFP ChIP) w peaks",
"displays" : [
{
"type" : "LinearWiggleDisplay",
@@ -23415,28 +22803,24 @@
"displayId" : "F16B12.6 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
}
],
+ "name" : "F16B12.6 Combined (GFP ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_F16B12.6 Combined (GFP ChIP) w peaks",
+ "description" : " Identification of Transcription Factor EGL-27::GFP Binding Regions in L1 ( project, subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_F16B12.6 Combined (GFP ChIP) w peaks"
+ ]
},
{
"name" : "__F16B12.6 Combined (GFP ChIP) peaks",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9290_details.gff.bb"
- }
- },
- "type" : "FeatureTrack",
- "description" : "Peak calls for F16B12.6 Combined (GFP ChIP) w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_F16B12.6 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "description" : "Peak calls for F16B12.6 Combined (GFP ChIP) w peaks",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -23445,31 +22829,47 @@
"Transcription Factors",
"GFP ChIP"
],
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9290_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink",
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
+ "showLabels" : false,
+ "color1" : "deeppink"
},
"displayId" : "F16B12.6 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
]
},
{
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/15178.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/15178.bw",
+ "locationType" : "UriLocation"
}
},
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "displayId" : "F45C12.2 Combined (GFP ChIP)_ F45C12.2_GFP_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 37.2312440565428
+ }
+ ],
"name" : "F45C12.2 Combined (GFP ChIP), F45C12.2_GFP_L2 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_F45C12.2 Combined (GFP ChIP)_ F45C12.2_GFP_L2 w peaks",
"description" : " Identification of Transcription Factor EGL-27::GFP Binding Regions in L1 ( project, subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -23477,207 +22877,201 @@
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_F45C12.2 Combined (GFP ChIP)_ F45C12.2_GFP_L2 w peaks",
- "displays" : [
- {
- "maxScore" : 37.2312440565428,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0,
- "displayId" : "F45C12.2 Combined (GFP ChIP)_ F45C12.2_GFP_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
]
},
{
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_F45C12.2 Combined (GFP ChIP)_ F45C12.2_GFP_L2 w peaks_bigbed_peaks",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "F45C12.2 Combined (GFP ChIP)_ F45C12.2_GFP_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay"
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6
+ }
}
],
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/15185_details.gff.bb",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigBedAdapter"
},
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Peak calls for F45C12.2 Combined (GFP ChIP), F45C12.2_GFP_L2 w peaks",
"name" : "__F45C12.2 Combined (GFP ChIP), F45C12.2_GFP_L2 peaks",
- "description" : "Peak calls for F45C12.2 Combined (GFP ChIP), F45C12.2_GFP_L2 w peaks"
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_F45C12.2 Combined (GFP ChIP)_ F45C12.2_GFP_L2 w peaks_bigbed_peaks"
},
{
- "name" : "F45C12.2 Combined (GFP ChIP), F45C12.2_GFP_L1 w peaks",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/13531.bw"
- },
- "type" : "BigWigAdapter"
- },
"description" : " Identification of Transcription Factor EGL-27::GFP Binding Regions in L1 ( project, subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "F45C12.2 Combined (GFP ChIP), F45C12.2_GFP_L1 w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_F45C12.2 Combined (GFP ChIP)_ F45C12.2_GFP_L1 w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/13531.bw"
+ }
+ },
"displays" : [
{
+ "maxScore" : 86.2318899159955,
"displayId" : "F45C12.2 Combined (GFP ChIP)_ F45C12.2_GFP_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 86.2318899159955
+ "type" : "LinearWiggleDisplay"
}
]
},
{
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "F45C12.2 Combined (GFP ChIP)_ F45C12.2_GFP_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
"showDescriptions" : false,
"height" : 6,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay"
+ "showLabels" : false
+ }
}
],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/13543_details.gff.bb"
+ }
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_F45C12.2 Combined (GFP ChIP)_ F45C12.2_GFP_L1 w peaks_bigbed_peaks",
"description" : "Peak calls for F45C12.2 Combined (GFP ChIP), F45C12.2_GFP_L1 w peaks",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/13543_details.gff.bb",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "__F45C12.2 Combined (GFP ChIP), F45C12.2_GFP_L1 peaks"
+ "name" : "__F45C12.2 Combined (GFP ChIP), F45C12.2_GFP_L1 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_F45C12.2 Combined (GFP ChIP)_ F45C12.2_GFP_L1 w peaks_bigbed_peaks"
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : " Identification of Transcription Factor EGL-27::GFP Binding Regions in L1 ( project, subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "F45C12.2 Combined (GFP ChIP), F45C12.2_GFP_L3 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_F45C12.2 Combined (GFP ChIP)_ F45C12.2_GFP_L3 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_F45C12.2 Combined (GFP ChIP)_ F45C12.2_GFP_L3 w peaks",
- "displays" : [
- {
- "minScore" : 0,
- "maxScore" : 55.5754790662357,
- "type" : "LinearWiggleDisplay",
- "displayId" : "F45C12.2 Combined (GFP ChIP)_ F45C12.2_GFP_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8277.bw",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "name" : "F45C12.2 Combined (GFP ChIP), F45C12.2_GFP_L3 w peaks",
- "description" : " Identification of Transcription Factor EGL-27::GFP Binding Regions in L1 ( project, subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 55.5754790662357,
+ "minScore" : 0,
+ "displayId" : "F45C12.2 Combined (GFP ChIP)_ F45C12.2_GFP_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ }
+ ]
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "Peak calls for F45C12.2 Combined (GFP ChIP), F45C12.2_GFP_L3 w peaks",
+ "name" : "__F45C12.2 Combined (GFP ChIP), F45C12.2_GFP_L3 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_F45C12.2 Combined (GFP ChIP)_ F45C12.2_GFP_L3 w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_F45C12.2 Combined (GFP ChIP)_ F45C12.2_GFP_L3 w peaks_bigbed_peaks",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8282_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
"displayId" : "F45C12.2 Combined (GFP ChIP)_ F45C12.2_GFP_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "height" : 6,
+ "type" : "SvgFeatureRenderer",
"showDescriptions" : false,
- "color1" : "deeppink",
+ "height" : 6,
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "color1" : "deeppink"
},
"type" : "LinearBasicDisplay"
}
- ],
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8282_details.gff.bb"
- }
- },
- "type" : "FeatureTrack",
- "name" : "__F45C12.2 Combined (GFP ChIP), F45C12.2_GFP_L3 peaks",
- "description" : "Peak calls for F45C12.2 Combined (GFP ChIP), F45C12.2_GFP_L3 w peaks"
+ ]
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L1 w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
"displays" : [
{
- "minScore" : 0,
- "maxScore" : 92.1776777137065,
"type" : "LinearWiggleDisplay",
+ "maxScore" : 92.1776777137065,
+ "minScore" : 0,
"displayId" : "FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
}
],
- "name" : "FOS-1 Combined (GFP ChIP), FOS-1 GFP L1 w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8288.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8288.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
- "description" : " Identification of Transcription Factor EGL-27::GFP Binding Regions in L1 ( project, subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "description" : " Identification of Transcription Factor EGL-27::GFP Binding Regions in L1 ( project, subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L1 w peaks",
+ "name" : "FOS-1 Combined (GFP ChIP), FOS-1 GFP L1 w peaks"
},
{
+ "description" : "Peak calls for FOS-1 Combined (GFP ChIP), FOS-1 GFP L1 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L1 w peaks_bigbed_peaks",
+ "name" : "__FOS-1 Combined (GFP ChIP), FOS-1 GFP L1 peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -23686,40 +23080,48 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L1 w peaks_bigbed_peaks",
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8295_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "displayId" : "FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "showDescriptions" : false,
+ "height" : 6,
+ "color1" : "deeppink"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
- ],
+ ]
+ },
+ {
"adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8295_details.gff.bb",
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/13459.bw",
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "name" : "__FOS-1 Combined (GFP ChIP), FOS-1 GFP L1 peaks",
- "description" : "Peak calls for FOS-1 Combined (GFP ChIP), FOS-1 GFP L1 w peaks"
- },
- {
"displays" : [
{
- "type" : "LinearWiggleDisplay",
"maxScore" : 66.670160367636,
"minScore" : 0,
- "displayId" : "FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "displayId" : "FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
],
+ "name" : "FOS-1 Combined (GFP ChIP), FOS-1 GFP L3 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L3 w peaks",
+ "description" : " Identification of Transcription Factor EGL-27::GFP Binding Regions in L1 ( project, subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -23727,55 +23129,44 @@
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L3 w peaks",
- "description" : " Identification of Transcription Factor EGL-27::GFP Binding Regions in L1 ( project, subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/13459.bw"
- }
- },
- "type" : "QuantitativeTrack",
- "name" : "FOS-1 Combined (GFP ChIP), FOS-1 GFP L3 w peaks"
+ ]
},
{
- "name" : "__FOS-1 Combined (GFP ChIP), FOS-1 GFP L3 peaks",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/13466_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
"description" : "Peak calls for FOS-1 Combined (GFP ChIP), FOS-1 GFP L3 w peaks",
+ "name" : "__FOS-1 Combined (GFP ChIP), FOS-1 GFP L3 peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L3 w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/13466_details.gff.bb"
+ }
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
"showDescriptions" : false,
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink"
+ "showLabels" : false
},
- "displayId" : "FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
]
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L4 w peaks",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -23784,37 +23175,50 @@
"Transcription Factors",
"GFP ChIP"
],
+ "name" : "FOS-1 Combined (GFP ChIP), FOS-1 GFP L4 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L4 w peaks",
+ "description" : " Identification of Transcription Factor EGL-27::GFP Binding Regions in L1 ( project, subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "displayId" : "FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
"type" : "LinearWiggleDisplay",
- "maxScore" : 50.7500433582306
+ "maxScore" : 50.7500433582306,
+ "minScore" : 0,
+ "displayId" : "FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
}
],
- "name" : "FOS-1 Combined (GFP ChIP), FOS-1 GFP L4 w peaks",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/13477.bw",
"locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "description" : " Identification of Transcription Factor EGL-27::GFP Binding Regions in L1 ( project, subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
+ }
},
{
- "name" : "__FOS-1 Combined (GFP ChIP), FOS-1 GFP L4 peaks",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/13494_details.gff.bb",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/13494_details.gff.bb"
}
},
- "type" : "FeatureTrack",
- "description" : "Peak calls for FOS-1 Combined (GFP ChIP), FOS-1 GFP L4 w peaks",
+ "displays" : [
+ {
+ "renderer" : {
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
+ "name" : "__FOS-1 Combined (GFP ChIP), FOS-1 GFP L4 peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L4 w peaks_bigbed_peaks",
+ "description" : "Peak calls for FOS-1 Combined (GFP ChIP), FOS-1 GFP L4 w peaks",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -23822,149 +23226,143 @@
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
- },
- "displayId" : "FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
- }
]
},
{
- "description" : " Identification of Transcription Factor EGL-27::GFP Binding Regions in L1 ( project, subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "FOS-1 Combined (GFP ChIP), FOS-1 GFP L2 w peaks",
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8168.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8168.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
"displays" : [
{
+ "maxScore" : 113.996908157024,
"displayId" : "FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 113.996908157024
+ "type" : "LinearWiggleDisplay"
}
],
+ "description" : " Identification of Transcription Factor EGL-27::GFP Binding Regions in L1 ( project, subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "FOS-1 Combined (GFP ChIP), FOS-1 GFP L2 w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L2 w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
+ ],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
]
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L2 w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Peak calls for FOS-1 Combined (GFP ChIP), FOS-1 GFP L2 w peaks",
+ "name" : "__FOS-1 Combined (GFP ChIP), FOS-1 GFP L2 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L2 w peaks_bigbed_peaks",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
"showLabels" : false,
- "color1" : "deeppink"
+ "height" : 6,
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "FOS-1 Combined (GFP ChIP)_ FOS-1 GFP L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
],
- "name" : "__FOS-1 Combined (GFP ChIP), FOS-1 GFP L2 peaks",
"adapter" : {
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8183_details.gff.bb"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8183_details.gff.bb",
+ "locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Peak calls for FOS-1 Combined (GFP ChIP), FOS-1 GFP L2 w peaks"
+ }
},
{
"displays" : [
{
- "type" : "LinearWiggleDisplay",
- "maxScore" : 106.830290724075,
+ "displayId" : "GEI-11 Combined (GFP ChIP)_ GEI-11_Emb w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "displayId" : "GEI-11 Combined (GFP ChIP)_ GEI-11_Emb w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "maxScore" : 106.830290724075,
+ "type" : "LinearWiggleDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI-11_Emb w peaks",
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/20512.bw",
+ "locationType" : "UriLocation"
+ }
+ },
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : " Snyder_NHR-23_GFP_L2. Synchronized L2 larvae from C. elegans strain OP43 (a transgenic strain engineered to express a gene fusion between nhr-23 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI-11_Emb w peaks",
"name" : "SNPC-4 Combined (GFP ChIP), GEI-11_Emb w peaks",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/20512.bw"
- }
- }
+ "description" : " Snyder_NHR-23_GFP_L2. Synchronized L2 larvae from C. elegans strain OP43 (a transgenic strain engineered to express a gene fusion between nhr-23 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
"displays" : [
{
"displayId" : "GEI-11 Combined (GFP ChIP)_ GEI-11_Emb w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
+ "showLabels" : false,
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
}
],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/20519_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
+ },
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI-11_Emb w peaks_bigbed_peaks",
- "description" : "Peak calls for SNPC-4 (was GEI-11) Combined (GFP ChIP), GEI-11_Emb w peaks",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/20519_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "__SNPC-4 Combined (GFP ChIP), GEI-11_Emb peaks"
+ "name" : "__SNPC-4 Combined (GFP ChIP), GEI-11_Emb peaks",
+ "description" : "Peak calls for SNPC-4 (was GEI-11) Combined (GFP ChIP), GEI-11_Emb w peaks"
},
{
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "displayId" : "GEI-11 Combined (GFP ChIP)_ GEI11_L2_GFP w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 109.060743117613,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
@@ -23972,8 +23370,7 @@
},
"type" : "BigWigAdapter"
},
- "name" : "SNPC-4 Combined (GFP ChIP), GEI11_L2_GFP w peaks",
- "description" : " Snyder_NHR-23_GFP_L2. Synchronized L2 larvae from C. elegans strain OP43 (a transgenic strain engineered to express a gene fusion between nhr-23 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -23982,125 +23379,111 @@
"Transcription Factors",
"GFP ChIP"
],
+ "name" : "SNPC-4 Combined (GFP ChIP), GEI11_L2_GFP w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI11_L2_GFP w peaks",
- "displays" : [
- {
- "type" : "LinearWiggleDisplay",
- "maxScore" : 109.060743117613,
- "minScore" : 0,
- "displayId" : "GEI-11 Combined (GFP ChIP)_ GEI11_L2_GFP w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
- ]
+ "description" : " Snyder_NHR-23_GFP_L2. Synchronized L2 larvae from C. elegans strain OP43 (a transgenic strain engineered to express a gene fusion between nhr-23 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "description" : "Peak calls for SNPC-4 (was GEI-11) Combined (GFP ChIP), GEI11_L2_GFP w peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9269_details.gff.bb",
- "locationType" : "UriLocation"
- }
- },
- "name" : "__SNPC-4 Combined (GFP ChIP), GEI11_L2_GFP peaks",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "GEI-11 Combined (GFP ChIP)_ GEI11_L2_GFP w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "showDescriptions" : false,
"height" : 6,
+ "showDescriptions" : false,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay"
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9269_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI11_L2_GFP w peaks_bigbed_peaks"
- },
- {
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_GEI11_GFP_L3_combined_WS220.bw"
- }
- },
- "name" : "SNPC-4 Combined (GFP ChIP), GEI11_L3_GFP w peaks",
- "description" : " Snyder_NHR-23_GFP_L2. Synchronized L2 larvae from C. elegans strain OP43 (a transgenic strain engineered to express a gene fusion between nhr-23 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "description" : "Peak calls for SNPC-4 (was GEI-11) Combined (GFP ChIP), GEI11_L2_GFP w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI11_L2_GFP w peaks_bigbed_peaks",
+ "name" : "__SNPC-4 Combined (GFP ChIP), GEI11_L2_GFP peaks"
+ },
+ {
+ "displays" : [
+ {
+ "maxScore" : 101.794952873019,
+ "minScore" : 0,
+ "displayId" : "GEI-11 Combined (GFP ChIP)_ GEI11_L3_GFP w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_GEI11_GFP_L3_combined_WS220.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI11_L3_GFP w peaks",
- "displays" : [
- {
- "displayId" : "GEI-11 Combined (GFP ChIP)_ GEI11_L3_GFP w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 101.794952873019,
- "minScore" : 0
- }
- ]
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : " Snyder_NHR-23_GFP_L2. Synchronized L2 larvae from C. elegans strain OP43 (a transgenic strain engineered to express a gene fusion between nhr-23 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "SNPC-4 Combined (GFP ChIP), GEI11_L3_GFP w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI11_L3_GFP w peaks"
},
{
"displays" : [
{
- "displayId" : "GEI-11 Combined (GFP ChIP)_ GEI11_L3_GFP w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay",
+ "displayId" : "GEI-11 Combined (GFP ChIP)_ GEI11_L3_GFP w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink",
"showDescriptions" : false,
- "height" : 6
+ "height" : 6,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
}
}
],
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/11322_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI11_L3_GFP w peaks_bigbed_peaks",
- "description" : "Peak calls for SNPC-4 (was GEI-11) Combined (GFP ChIP), GEI11_L3_GFP w peaks",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/11322_details.gff.bb"
- }
- },
- "type" : "FeatureTrack",
- "name" : "__SNPC-4 Combined (GFP ChIP), GEI11_L3_GFP peaks"
+ "name" : "__SNPC-4 Combined (GFP ChIP), GEI11_L3_GFP peaks",
+ "description" : "Peak calls for SNPC-4 (was GEI-11) Combined (GFP ChIP), GEI11_L3_GFP w peaks"
},
{
- "name" : "SNPC-4 Combined (GFP ChIP), GEI11_L4_GFP w peaks",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_GEI11_GFP_L4_combined_WS220.bw",
- "locationType" : "UriLocation"
- }
- },
"description" : " Snyder_NHR-23_GFP_L2. Synchronized L2 larvae from C. elegans strain OP43 (a transgenic strain engineered to express a gene fusion between nhr-23 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI11_L4_GFP w peaks",
+ "name" : "SNPC-4 Combined (GFP ChIP), GEI11_L4_GFP w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -24109,68 +23492,66 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_GEI11_GFP_L4_combined_WS220.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "displayId" : "GEI-11 Combined (GFP ChIP)_ GEI11_L4_GFP w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"maxScore" : 48.0700305359699,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
+ "displayId" : "GEI-11 Combined (GFP ChIP)_ GEI11_L4_GFP w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
}
]
},
{
- "name" : "__SNPC-4 Combined (GFP ChIP), GEI11_L4_GFP peaks",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4360_details.gff.bb"
- },
- "type" : "BigBedAdapter"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4360_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
},
- "description" : "Peak calls for SNPC-4 (GEI-11) Combined (GFP ChIP), GEI11_L4_GFP w peaks",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI11_L4_GFP w peaks_bigbed_peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
- "displayId" : "GEI-11 Combined (GFP ChIP)_ GEI11_L4_GFP w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showLabels" : false,
"height" : 6,
"showDescriptions" : false,
- "color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
- }
+ "color1" : "deeppink"
+ },
+ "displayId" : "GEI-11 Combined (GFP ChIP)_ GEI11_L4_GFP w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
- ]
- },
- {
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI11_L4_GFP w peaks_bigbed_peaks",
+ "name" : "__SNPC-4 Combined (GFP ChIP), GEI11_L4_GFP peaks",
+ "description" : "Peak calls for SNPC-4 (GEI-11) Combined (GFP ChIP), GEI11_L4_GFP w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI-11_L1 w peaks",
+ "type" : "FeatureTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ]
+ },
+ {
"displays" : [
{
"displayId" : "GEI-11 Combined (GFP ChIP)_ GEI-11_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
"maxScore" : 173.075288047532,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
+ "type" : "LinearWiggleDisplay"
}
],
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -24178,62 +23559,83 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18808.bw"
}
},
- "name" : "SNPC-4 Combined (GFP ChIP), GEI-11_L1 w peaks",
- "description" : " Snyder_NHR-23_GFP_L2. Synchronized L2 larvae from C. elegans strain OP43 (a transgenic strain engineered to express a gene fusion between nhr-23 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : " Snyder_NHR-23_GFP_L2. Synchronized L2 larvae from C. elegans strain OP43 (a transgenic strain engineered to express a gene fusion between nhr-23 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "SNPC-4 Combined (GFP ChIP), GEI-11_L1 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI-11_L1 w peaks"
+ },
+ {
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "name" : "__SNPC-4 Combined (GFP ChIP), GEI-11_L1 peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI-11_L1 w peaks_bigbed_peaks",
+ "description" : "Peak calls for SNPC-4 (was GEI-11) Combined (GFP ChIP), GEI-11_L1 w peaks",
"displays" : [
{
- "displayId" : "GEI-11 Combined (GFP ChIP)_ GEI-11_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
"type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "deeppink",
"showDescriptions" : false,
- "height" : 6
+ "height" : 6,
+ "color1" : "deeppink"
},
+ "displayId" : "GEI-11 Combined (GFP ChIP)_ GEI-11_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay"
}
],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18819_details.gff.bb"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18819_details.gff.bb",
+ "locationType" : "UriLocation"
}
- },
- "type" : "FeatureTrack",
- "name" : "__SNPC-4 Combined (GFP ChIP), GEI-11_L1 peaks",
- "description" : "Peak calls for SNPC-4 (was GEI-11) Combined (GFP ChIP), GEI-11_L1 w peaks"
+ }
},
{
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI-11_YA w peaks",
+ "name" : "SNPC-4 Combined (GFP ChIP), GEI-11_YA w peaks",
"description" : " Snyder_NHR-23_GFP_L2. Synchronized L2 larvae from C. elegans strain OP43 (a transgenic strain engineered to express a gene fusion between nhr-23 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18895.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18895.bw",
+ "locationType" : "UriLocation"
}
},
- "name" : "SNPC-4 Combined (GFP ChIP), GEI-11_YA w peaks",
"displays" : [
{
- "type" : "LinearWiggleDisplay",
"maxScore" : 40.0880627032053,
+ "displayId" : "GEI-11 Combined (GFP ChIP)_ GEI-11_YA w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "displayId" : "GEI-11 Combined (GFP ChIP)_ GEI-11_YA w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
- ],
+ ]
+ },
+ {
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -24242,137 +23644,132 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI-11_YA w peaks"
- },
- {
+ "type" : "FeatureTrack",
"description" : "Peak calls for SNPC-4 (GEI-11) Combined (GFP ChIP), GEI-11_YA w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI-11_YA w peaks_bigbed_peaks",
"name" : "__SNPC-4 Combined (GFP ChIP), GEI-11_YA peaks",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18904_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "GEI-11 Combined (GFP ChIP)_ GEI-11_YA w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "showDescriptions" : false,
+ "height" : 6,
+ "color1" : "deeppink"
},
+ "displayId" : "GEI-11 Combined (GFP ChIP)_ GEI-11_YA w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_GEI-11 Combined (GFP ChIP)_ GEI-11_YA w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ]
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18904_details.gff.bb"
+ }
+ }
},
{
- "displays" : [
- {
- "minScore" : 27.2878870228302,
- "maxScore" : 64.9660212813035,
- "type" : "LinearWiggleDisplay",
- "displayId" : "LIN-15B Combined (GFP ChIP)_ LIN15B_GFP_L1_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
- ],
+ "description" : "Identification of Transcription Factor LIN-11::GFP Binding Regions in L2 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. br/>
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-15B Combined (GFP ChIP)_ LIN15B_GFP_L1",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "LIN-15B Combined (GFP ChIP), LIN15B_GFP_L1",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "description" : "Identification of Transcription Factor LIN-11::GFP Binding Regions in L2 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. br/>
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "LIN-15B Combined (GFP ChIP), LIN15B_GFP_L1",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/15180.bw"
- }
+ },
+ "type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack"
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 64.9660212813035,
+ "displayId" : "LIN-15B Combined (GFP ChIP)_ LIN15B_GFP_L1_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 27.2878870228302
+ }
+ ]
},
{
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_LIN-15B_GFP_L3_combined_WS220.bw",
- "locationType" : "UriLocation"
- }
- },
- "name" : "LIN-15B Combined (GFP ChIP), LIN15B_GFP_L3 w peaks",
- "description" : "Identification of Transcription Factor LIN-11::GFP Binding Regions in L2 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. br/>
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-15B Combined (GFP ChIP)_ LIN15B_GFP_L3 w peaks",
+ "name" : "LIN-15B Combined (GFP ChIP), LIN15B_GFP_L3 w peaks",
+ "description" : "Identification of Transcription Factor LIN-11::GFP Binding Regions in L2 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. br/>
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "minScore" : 0,
"type" : "LinearWiggleDisplay",
"maxScore" : 67.99403851799,
+ "minScore" : 0,
"displayId" : "LIN-15B Combined (GFP ChIP)_ LIN15B_GFP_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_LIN-15B_GFP_L3_combined_WS220.bw"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
- "description" : "Peak calls for LIN-15B Combined (GFP ChIP), LIN15B_GFP_L3 w peaks",
- "name" : "__LIN-15B Combined (GFP ChIP), LIN15B_GFP_L3 peaks",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/5466_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/5466_details.gff.bb"
+ }
},
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "LIN-15B Combined (GFP ChIP)_ LIN15B_GFP_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "color1" : "deeppink",
+ "showLabels" : false,
"height" : 6,
"showDescriptions" : false,
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "LIN-15B Combined (GFP ChIP)_ LIN15B_GFP_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
+ "description" : "Peak calls for LIN-15B Combined (GFP ChIP), LIN15B_GFP_L3 w peaks",
+ "name" : "__LIN-15B Combined (GFP ChIP), LIN15B_GFP_L3 peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-15B Combined (GFP ChIP)_ LIN15B_GFP_L3 w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
]
},
{
- "name" : "LIN-15B Combined (GFP ChIP), LIN15B_GFP_L4 w peaks",
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 43.68453526816,
+ "displayId" : "LIN-15B Combined (GFP ChIP)_ LIN15B_GFP_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0
+ }
+ ],
"adapter" : {
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/9120.bw",
@@ -24380,102 +23777,166 @@
},
"type" : "BigWigAdapter"
},
- "description" : "Identification of Transcription Factor LIN-11::GFP Binding Regions in L2 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. br/>
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-15B Combined (GFP ChIP)_ LIN15B_GFP_L4 w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-15B Combined (GFP ChIP)_ LIN15B_GFP_L4 w peaks",
+ "name" : "LIN-15B Combined (GFP ChIP), LIN15B_GFP_L4 w peaks",
+ "description" : "Identification of Transcription Factor LIN-11::GFP Binding Regions in L2 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. br/>
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ },
+ {
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "name" : "__LIN-15B Combined (GFP ChIP), LIN15B_GFP_L4 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-15B Combined (GFP ChIP)_ LIN15B_GFP_L4 w peaks_bigbed_peaks",
+ "description" : "Peak calls for LIN-15B Combined (GFP ChIP), LIN15B_GFP_L4 w peaks",
"displays" : [
{
- "displayId" : "LIN-15B Combined (GFP ChIP)_ LIN15B_GFP_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
- "maxScore" : 43.68453526816,
- "type" : "LinearWiggleDisplay"
+ "displayId" : "LIN-15B Combined (GFP ChIP)_ LIN15B_GFP_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
+ "height" : 6,
+ "showDescriptions" : false,
+ "showLabels" : false
+ },
+ "type" : "LinearBasicDisplay"
}
- ]
- },
- {
- "description" : "Peak calls for LIN-15B Combined (GFP ChIP), LIN15B_GFP_L4 w peaks",
+ ],
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9134_details.gff.bb"
- }
+ },
+ "type" : "BigBedAdapter"
+ }
+ },
+ {
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/9074.bw"
+ },
+ "type" : "BigWigAdapter"
},
- "type" : "FeatureTrack",
- "name" : "__LIN-15B Combined (GFP ChIP), LIN15B_GFP_L4 peaks",
"displays" : [
{
- "displayId" : "LIN-15B Combined (GFP ChIP)_ LIN15B_GFP_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 6,
- "showDescriptions" : false
- }
+ "type" : "LinearWiggleDisplay",
+ "displayId" : "MEF-2 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 40.2204916305852
}
],
+ "description" : "Identification of Transcription Factor LIN-11::GFP Binding Regions in L2 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. br/>
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "MEF-2 Combined (GFP ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_MEF-2 Combined (GFP ChIP) w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-15B Combined (GFP ChIP)_ LIN15B_GFP_L4 w peaks_bigbed_peaks"
+ ]
},
{
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "MEF-2 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ }
+ ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9081_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_MEF-2 Combined (GFP ChIP) w peaks",
+ "description" : "Peak calls for MEF-2 Combined (GFP ChIP) w peaks",
+ "name" : "__MEF-2 Combined (GFP ChIP) peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_MEF-2 Combined (GFP ChIP) w peaks_bigbed_peaks"
+ },
+ {
"displays" : [
{
+ "maxScore" : 115.945308436856,
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 40.2204916305852,
- "displayId" : "MEF-2 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "displayId" : "NHR-11 Combined (GFP ChIP)_ NHR-11_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/9074.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18234.bw"
}
},
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
- "name" : "MEF-2 Combined (GFP ChIP) w peaks",
- "description" : "Identification of Transcription Factor LIN-11::GFP Binding Regions in L2 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. br/>
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-11 Combined (GFP ChIP)_ NHR-11_L3 w peaks",
+ "name" : "NHR-11 Combined (GFP ChIP), NHR-11_L3 w peaks",
+ "description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
"displays" : [
{
- "displayId" : "MEF-2 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay",
+ "displayId" : "NHR-11 Combined (GFP ChIP)_ NHR-11_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "color1" : "deeppink",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"height" : 6,
- "showDescriptions" : false
- },
- "type" : "LinearBasicDisplay"
+ "showDescriptions" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ }
}
],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18248_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -24484,91 +23945,76 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_MEF-2 Combined (GFP ChIP) w peaks_bigbed_peaks",
- "description" : "Peak calls for MEF-2 Combined (GFP ChIP) w peaks",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9081_details.gff.bb",
- "locationType" : "UriLocation"
- }
- },
"type" : "FeatureTrack",
- "name" : "__MEF-2 Combined (GFP ChIP) peaks"
+ "description" : "Peak calls for NHR-11 Combined (GFP ChIP), NHR-11_L3 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-11 Combined (GFP ChIP)_ NHR-11_L3 w peaks_bigbed_peaks",
+ "name" : "__NHR-11 Combined (GFP ChIP), NHR-11_L3 peaks"
},
{
- "displays" : [
- {
- "displayId" : "NHR-11 Combined (GFP ChIP)_ NHR-11_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
- "maxScore" : 115.945308436856,
- "type" : "LinearWiggleDisplay"
- }
+ "name" : "NHR-11 Combined (GFP ChIP), NHR-11_L1 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-11 Combined (GFP ChIP)_ NHR-11_L1 w peaks",
+ "description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-11 Combined (GFP ChIP)_ NHR-11_L3 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "NHR-11 Combined (GFP ChIP), NHR-11_L3 w peaks",
"adapter" : {
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18234.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18199.bw",
"locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack"
- },
- {
"displays" : [
{
- "renderer" : {
- "color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 6,
- "showDescriptions" : false
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "NHR-11 Combined (GFP ChIP)_ NHR-11_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "minScore" : 0,
+ "displayId" : "NHR-11 Combined (GFP ChIP)_ NHR-11_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 122.015327034809,
+ "type" : "LinearWiggleDisplay"
}
- ],
+ ]
+ },
+ {
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-11 Combined (GFP ChIP)_ NHR-11_L1 w peaks_bigbed_peaks",
+ "name" : "__NHR-11 Combined (GFP ChIP), NHR-11_L1 peaks",
+ "description" : "Peak calls for NHR-11 Combined (GFP ChIP), NHR-11_L1 w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-11 Combined (GFP ChIP)_ NHR-11_L3 w peaks_bigbed_peaks",
- "description" : "Peak calls for NHR-11 Combined (GFP ChIP), NHR-11_L3 w peaks",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18248_details.gff.bb",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18228_details.gff.bb",
"locationType" : "UriLocation"
}
},
- "name" : "__NHR-11 Combined (GFP ChIP), NHR-11_L3 peaks"
- },
- {
"displays" : [
{
- "displayId" : "NHR-11 Combined (GFP ChIP)_ NHR-11_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
- "maxScore" : 122.015327034809,
- "type" : "LinearWiggleDisplay"
+ "type" : "LinearBasicDisplay",
+ "displayId" : "NHR-11 Combined (GFP ChIP)_ NHR-11_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6,
+ "color1" : "deeppink"
+ }
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-11 Combined (GFP ChIP)_ NHR-11_L1 w peaks",
+ ]
+ },
+ {
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -24577,70 +24023,49 @@
"Transcription Factors",
"GFP ChIP"
],
+ "name" : "NHR-11 Combined (GFP ChIP), NHR-11_LEMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-11 Combined (GFP ChIP)_ NHR-11_LEMB w peaks",
"description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "NHR-11 Combined (GFP ChIP), NHR-11_L1 w peaks",
+ "displays" : [
+ {
+ "minScore" : 0,
+ "displayId" : "NHR-11 Combined (GFP ChIP)_ NHR-11_LEMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 133.570407754896,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18199.bw"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18232.bw"
+ }
+ }
},
{
- "description" : "Peak calls for NHR-11 Combined (GFP ChIP), NHR-11_L1 w peaks",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18228_details.gff.bb",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18267_details.gff.bb",
"locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ }
},
- "type" : "FeatureTrack",
- "name" : "__NHR-11 Combined (GFP ChIP), NHR-11_L1 peaks",
"displays" : [
{
- "displayId" : "NHR-11 Combined (GFP ChIP)_ NHR-11_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
"height" : 6,
"showDescriptions" : false,
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
"showLabels" : false
- }
- }
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-11 Combined (GFP ChIP)_ NHR-11_L1 w peaks_bigbed_peaks"
- },
- {
- "description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18232.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "NHR-11 Combined (GFP ChIP), NHR-11_LEMB w peaks",
- "displays" : [
- {
- "minScore" : 0,
- "maxScore" : 133.570407754896,
- "type" : "LinearWiggleDisplay",
- "displayId" : "NHR-11 Combined (GFP ChIP)_ NHR-11_LEMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ },
+ "displayId" : "NHR-11 Combined (GFP ChIP)_ NHR-11_LEMB w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
],
+ "description" : "Peak calls for NHR-11 Combined (GFP ChIP), NHR-11_LEMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-11 Combined (GFP ChIP)_ NHR-11_LEMB w peaks_bigbed_peaks",
+ "name" : "__NHR-11 Combined (GFP ChIP), NHR-11_LEMB peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -24649,212 +24074,188 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-11 Combined (GFP ChIP)_ NHR-11_LEMB w peaks"
+ "type" : "FeatureTrack"
},
{
"displays" : [
{
- "renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "NHR-11 Combined (GFP ChIP)_ NHR-11_LEMB w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "type" : "LinearWiggleDisplay",
+ "displayId" : "NHR-11 Combined (GFP ChIP)_ NHR-11_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 114.458545263514
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-11 Combined (GFP ChIP)_ NHR-11_LEMB w peaks_bigbed_peaks",
- "description" : "Peak calls for NHR-11 Combined (GFP ChIP), NHR-11_LEMB w peaks",
"adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18267_details.gff.bb"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18201.bw"
}
},
- "type" : "FeatureTrack",
- "name" : "__NHR-11 Combined (GFP ChIP), NHR-11_LEMB peaks"
- },
- {
- "displays" : [
- {
- "displayId" : "NHR-11 Combined (GFP ChIP)_ NHR-11_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "maxScore" : 114.458545263514,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
- }
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-11 Combined (GFP ChIP)_ NHR-11_L4 w peaks",
"description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18201.bw",
- "locationType" : "UriLocation"
- }
- },
- "name" : "NHR-11 Combined (GFP ChIP), NHR-11_L4 w peaks"
+ "name" : "NHR-11 Combined (GFP ChIP), NHR-11_L4 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-11 Combined (GFP ChIP)_ NHR-11_L4 w peaks"
},
{
+ "name" : "__NHR-11 Combined (GFP ChIP), NHR-11_L4 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-11 Combined (GFP ChIP)_ NHR-11_L4 w peaks_bigbed_peaks",
"description" : "Peak calls for NHR-11 Combined (GFP ChIP), NHR-11_L4 w peaks",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18221_details.gff.bb",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18221_details.gff.bb"
},
"type" : "BigBedAdapter"
},
- "name" : "__NHR-11 Combined (GFP ChIP), NHR-11_L4 peaks",
"displays" : [
{
- "displayId" : "NHR-11 Combined (GFP ChIP)_ NHR-11_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "showDescriptions" : false,
+ "height" : 6,
+ "showLabels" : false
},
+ "displayId" : "NHR-11 Combined (GFP ChIP)_ NHR-11_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay"
}
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-11 Combined (GFP ChIP)_ NHR-11_L4 w peaks_bigbed_peaks"
+ ]
},
{
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/9123.bw"
+ }
+ },
"displays" : [
{
- "displayId" : "NHR-11 Combined (GFP ChIP)_ NHR11_GFP_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay",
- "maxScore" : 47.8384804318602,
- "minScore" : 0
+ "minScore" : 0,
+ "displayId" : "NHR-11 Combined (GFP ChIP)_ NHR11_GFP_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 47.8384804318602
}
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-11 Combined (GFP ChIP)_ NHR11_GFP_L2 w peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"name" : "NHR-11 Combined (GFP ChIP), NHR11_GFP_L2 w peaks",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/9123.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- }
- },
- {
- "name" : "__NHR-11 Combined (GFP ChIP), NHR11_GFP_L2 peaks",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9139_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Peak calls for NHR-11 Combined (GFP ChIP), NHR11_GFP_L2 w peaks",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-11 Combined (GFP ChIP)_ NHR11_GFP_L2 w peaks_bigbed_peaks",
+ "description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
+ ]
+ },
+ {
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "showDescriptions" : false,
+ "height" : 6,
+ "color1" : "deeppink"
},
- "type" : "LinearBasicDisplay",
"displayId" : "NHR-11 Combined (GFP ChIP)_ NHR11_GFP_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
- ]
- },
- {
+ ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9139_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-28 Combined (GFP ChIP)_ NHR-28_EMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-11 Combined (GFP ChIP)_ NHR11_GFP_L2 w peaks_bigbed_peaks",
+ "name" : "__NHR-11 Combined (GFP ChIP), NHR11_GFP_L2 peaks",
+ "description" : "Peak calls for NHR-11 Combined (GFP ChIP), NHR11_GFP_L2 w peaks"
+ },
+ {
"displays" : [
{
- "displayId" : "NHR-28 Combined (GFP ChIP)_ NHR-28_EMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
"maxScore" : 138.116870205568,
- "minScore" : 0
+ "minScore" : 0,
+ "displayId" : "NHR-28 Combined (GFP ChIP)_ NHR-28_EMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18292.bw",
- "locationType" : "UriLocation"
- }
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18292.bw"
+ },
+ "type" : "BigWigAdapter"
},
"type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
"name" : "NHR-28 Combined (GFP ChIP), NHR-28_EMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-28 Combined (GFP ChIP)_ NHR-28_EMB w peaks",
"description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18325_details.gff.bb"
+ }
+ },
"displays" : [
{
"displayId" : "NHR-28 Combined (GFP ChIP)_ NHR-28_EMB w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "color1" : "deeppink",
+ "showLabels" : false,
"height" : 6,
"showDescriptions" : false,
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
}
],
+ "name" : "__NHR-28 Combined (GFP ChIP), NHR-28_EMB peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-28 Combined (GFP ChIP)_ NHR-28_EMB w peaks_bigbed_peaks",
+ "description" : "Peak calls for NHR-28 Combined (GFP ChIP), NHR-28_EMB w peaks",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -24862,92 +24263,76 @@
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "description" : "Peak calls for NHR-28 Combined (GFP ChIP), NHR-28_EMB w peaks",
- "name" : "__NHR-28 Combined (GFP ChIP), NHR-28_EMB peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18325_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- }
+ ]
},
{
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "NHR-28 Combined (GFP ChIP), NHR-28_GFP_L3 w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-28 Combined (GFP ChIP)_ NHR-28_GFP_L3 w peaks",
+ "description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "minScore" : 0,
- "type" : "LinearWiggleDisplay",
"maxScore" : 68.768757566013,
- "displayId" : "NHR-28 Combined (GFP ChIP)_ NHR-28_GFP_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "displayId" : "NHR-28 Combined (GFP ChIP)_ NHR-28_GFP_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
}
],
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8266.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8266.bw",
+ "locationType" : "UriLocation"
}
- },
- "name" : "NHR-28 Combined (GFP ChIP), NHR-28_GFP_L3 w peaks",
- "description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
},
{
- "name" : "__NHR-28 Combined (GFP ChIP), NHR-28_GFP_L3 peaks",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8271_details.gff.bb"
- }
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "description" : "Peak calls for NHR-28 Combined (GFP ChIP), NHR-28_GFP_L3 w peaks",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-28 Combined (GFP ChIP)_ NHR-28_GFP_L3 w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "NHR-28 Combined (GFP ChIP)_ NHR-28_GFP_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "color1" : "deeppink",
"type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
"showLabels" : false,
"height" : 6,
"showDescriptions" : false
- },
- "displayId" : "NHR-28 Combined (GFP ChIP)_ NHR-28_GFP_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ }
}
+ ],
+ "name" : "__NHR-28 Combined (GFP ChIP), NHR-28_GFP_L3 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-28 Combined (GFP ChIP)_ NHR-28_GFP_L3 w peaks_bigbed_peaks",
+ "description" : "Peak calls for NHR-28 Combined (GFP ChIP), NHR-28_GFP_L3 w peaks",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
]
},
{
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8157.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
"name" : "NHR-28 Combined (GFP ChIP), NHR-28_GFP_L4 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-28 Combined (GFP ChIP)_ NHR-28_GFP_L4 w peaks",
"description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -24956,18 +24341,23 @@
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-28 Combined (GFP ChIP)_ NHR-28_GFP_L4 w peaks",
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8157.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "displayId" : "NHR-28 Combined (GFP ChIP)_ NHR-28_GFP_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"maxScore" : 129.200814481292,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
+ "displayId" : "NHR-28 Combined (GFP ChIP)_ NHR-28_GFP_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
}
]
},
{
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
@@ -24975,167 +24365,177 @@
},
"type" : "BigBedAdapter"
},
- "name" : "__NHR-28 Combined (GFP ChIP), NHR-28_GFP_L4 peaks",
- "description" : "Peak calls for NHR-28 Combined (GFP ChIP), NHR-28_GFP_L4 w peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-28 Combined (GFP ChIP)_ NHR-28_GFP_L4 w peaks_bigbed_peaks",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "height" : 6,
+ "showDescriptions" : false
},
- "type" : "LinearBasicDisplay",
"displayId" : "NHR-28 Combined (GFP ChIP)_ NHR-28_GFP_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
- ]
- },
- {
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-28 Combined (GFP ChIP)_ NHR-28_L1 w peaks",
+ ],
+ "description" : "Peak calls for NHR-28 Combined (GFP ChIP), NHR-28_GFP_L4 w peaks",
+ "name" : "__NHR-28 Combined (GFP ChIP), NHR-28_GFP_L4 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-28 Combined (GFP ChIP)_ NHR-28_GFP_L4 w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
+ ]
+ },
+ {
"displays" : [
{
- "minScore" : 0,
- "maxScore" : 90.2084019543955,
"type" : "LinearWiggleDisplay",
+ "maxScore" : 90.2084019543955,
+ "minScore" : 0,
"displayId" : "NHR-28 Combined (GFP ChIP)_ NHR-28_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
}
],
- "name" : "NHR-28 Combined (GFP ChIP), NHR-28_L1 w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18323.bw"
- },
- "type" : "BigWigAdapter"
+ }
},
- "description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-28 Combined (GFP ChIP)_ NHR-28_L1 w peaks",
+ "name" : "NHR-28 Combined (GFP ChIP), NHR-28_L1 w peaks"
},
{
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-28 Combined (GFP ChIP)_ NHR-28_L1 w peaks_bigbed_peaks",
+ "name" : "__NHR-28 Combined (GFP ChIP), NHR-28_L1 peaks",
+ "description" : "Peak calls for NHR-28 Combined (GFP ChIP), NHR-28_L1 w peaks",
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "deeppink",
+ "showLabels" : false,
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
+ "color1" : "deeppink"
},
- "displayId" : "NHR-28 Combined (GFP ChIP)_ NHR-28_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "displayId" : "NHR-28 Combined (GFP ChIP)_ NHR-28_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18348_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "__NHR-28 Combined (GFP ChIP), NHR-28_L1 peaks",
- "description" : "Peak calls for NHR-28 Combined (GFP ChIP), NHR-28_L1 w peaks"
+ }
+ }
},
{
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_R02D3.7 Combined (GFP ChIP)_ R02D3.7_L4 w peaks",
+ "name" : "R02D3.7 Combined (GFP ChIP), R02D3.7_L4 w peaks",
+ "description" : " Identification of Transcription Factor CEH-16::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP82 (a transgenic strain engineered to express a gene fusion between ceh-16 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_R02D3.7 Combined (GFP ChIP)_ R02D3.7_L4 w peaks",
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18715.bw"
+ }
+ },
"displays" : [
{
- "type" : "LinearWiggleDisplay",
- "maxScore" : 43.4952502003725,
+ "displayId" : "R02D3.7 Combined (GFP ChIP)_ R02D3.7_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "displayId" : "R02D3.7 Combined (GFP ChIP)_ R02D3.7_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "maxScore" : 43.4952502003725,
+ "type" : "LinearWiggleDisplay"
}
- ],
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18715.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "R02D3.7 Combined (GFP ChIP), R02D3.7_L4 w peaks",
- "description" : " Identification of Transcription Factor CEH-16::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP82 (a transgenic strain engineered to express a gene fusion between ceh-16 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ ]
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_R02D3.7 Combined (GFP ChIP)_ R02D3.7_L4 w peaks_bigbed_peaks",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "R02D3.7 Combined (GFP ChIP)_ R02D3.7_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
"showDescriptions" : false,
"height" : 6,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "R02D3.7 Combined (GFP ChIP)_ R02D3.7_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18721_details.gff.bb",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18721_details.gff.bb"
}
},
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Peak calls for R02D3.7 Combined (GFP ChIP), R02D3.7_L4 w peaks",
"name" : "__R02D3.7 Combined (GFP ChIP), R02D3.7_L4 peaks",
- "description" : "Peak calls for R02D3.7 Combined (GFP ChIP), R02D3.7_L4 w peaks"
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_R02D3.7 Combined (GFP ChIP)_ R02D3.7_L4 w peaks_bigbed_peaks"
},
{
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/14869.bw"
+ }
+ },
"displays" : [
{
- "minScore" : 0,
"maxScore" : 128.476609097668,
- "type" : "LinearWiggleDisplay",
- "displayId" : "R02D3.7 Combined (GFP ChIP)_ R02D3.7_GFP_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "displayId" : "R02D3.7 Combined (GFP ChIP)_ R02D3.7_GFP_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
}
],
+ "description" : " Identification of Transcription Factor CEH-16::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP82 (a transgenic strain engineered to express a gene fusion between ceh-16 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_R02D3.7 Combined (GFP ChIP)_ R02D3.7_GFP_L3 w peaks",
+ "name" : "R02D3.7 Combined (GFP ChIP), R02D3.7_GFP_L3 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -25144,125 +24544,106 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : " Identification of Transcription Factor CEH-16::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP82 (a transgenic strain engineered to express a gene fusion between ceh-16 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "R02D3.7 Combined (GFP ChIP), R02D3.7_GFP_L3 w peaks",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/14869.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
"type" : "QuantitativeTrack"
},
{
- "name" : "__R02D3.7 Combined (GFP ChIP), R02D3.7_GFP_L3 peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/14876_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "description" : "Peak calls for R02D3.7 Combined (GFP ChIP), R02D3.7_GFP_L3 w peaks",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_R02D3.7 Combined (GFP ChIP)_ R02D3.7_GFP_L3 w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "Peak calls for R02D3.7 Combined (GFP ChIP), R02D3.7_GFP_L3 w peaks",
+ "name" : "__R02D3.7 Combined (GFP ChIP), R02D3.7_GFP_L3 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_R02D3.7 Combined (GFP ChIP)_ R02D3.7_GFP_L3 w peaks_bigbed_peaks",
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "deeppink",
"type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
"showLabels" : false,
- "height" : 6,
- "showDescriptions" : false
+ "showDescriptions" : false,
+ "height" : 6
},
- "displayId" : "R02D3.7 Combined (GFP ChIP)_ R02D3.7_GFP_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "displayId" : "R02D3.7 Combined (GFP ChIP)_ R02D3.7_GFP_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
- ]
- },
- {
- "type" : "QuantitativeTrack",
+ ],
"adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8255.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/14876_details.gff.bb"
}
- },
- "name" : "R02D3.7 Combined (GFP ChIP), R02D3.7_GFP_L2 w peaks",
- "description" : " Identification of Transcription Factor CEH-16::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP82 (a transgenic strain engineered to express a gene fusion between ceh-16 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_R02D3.7 Combined (GFP ChIP)_ R02D3.7_GFP_L2 w peaks",
+ }
+ },
+ {
"displays" : [
{
"minScore" : 0,
+ "displayId" : "R02D3.7 Combined (GFP ChIP)_ R02D3.7_GFP_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"maxScore" : 90.7175243319905,
- "type" : "LinearWiggleDisplay",
- "displayId" : "R02D3.7 Combined (GFP ChIP)_ R02D3.7_GFP_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
- ]
- },
- {
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_R02D3.7 Combined (GFP ChIP)_ R02D3.7_GFP_L2 w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
],
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8255.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : " Identification of Transcription Factor CEH-16::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP82 (a transgenic strain engineered to express a gene fusion between ceh-16 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "R02D3.7 Combined (GFP ChIP), R02D3.7_GFP_L2 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_R02D3.7 Combined (GFP ChIP)_ R02D3.7_GFP_L2 w peaks"
+ },
+ {
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
+ "type" : "SvgFeatureRenderer",
"showDescriptions" : false,
- "color1" : "deeppink",
+ "height" : 6,
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "color1" : "deeppink"
},
- "type" : "LinearBasicDisplay",
"displayId" : "R02D3.7 Combined (GFP ChIP)_ R02D3.7_GFP_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
],
- "name" : "__R02D3.7 Combined (GFP ChIP), R02D3.7_GFP_L2 peaks",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8263_details.gff.bb",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigBedAdapter"
},
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "name" : "__R02D3.7 Combined (GFP ChIP), R02D3.7_GFP_L2 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_R02D3.7 Combined (GFP ChIP)_ R02D3.7_GFP_L2 w peaks_bigbed_peaks",
"description" : "Peak calls for R02D3.7 Combined (GFP ChIP), R02D3.7_GFP_L2 w peaks"
},
{
- "description" : "Identification of Transcription Factor PQM-1::GFP Binding Regions in L3 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/9299.bw"
- }
- },
- "name" : "SEA-2 Combined (GFP ChIP) w peaks",
"displays" : [
{
"displayId" : "SEA-2 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
@@ -25271,61 +24652,77 @@
"type" : "LinearWiggleDisplay"
}
],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/9299.bw"
+ }
+ },
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SEA-2 Combined (GFP ChIP) w peaks",
+ "name" : "SEA-2 Combined (GFP ChIP) w peaks",
+ "description" : "Identification of Transcription Factor PQM-1::GFP Binding Regions in L3 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ },
+ {
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SEA-2 Combined (GFP ChIP) w peaks"
- },
- {
- "description" : "Peak calls for SEA-2 Combined (GFP ChIP) w peaks",
- "name" : "__SEA-2 Combined (GFP ChIP) peaks",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9305_details.gff.bb",
- "locationType" : "UriLocation"
- }
- },
"type" : "FeatureTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SEA-2 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "name" : "__SEA-2 Combined (GFP ChIP) peaks",
+ "description" : "Peak calls for SEA-2 Combined (GFP ChIP) w peaks",
"displays" : [
{
"renderer" : {
+ "color1" : "deeppink",
+ "showLabels" : false,
"height" : 6,
"showDescriptions" : false,
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "SEA-2 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "displayId" : "SEA-2 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SEA-2 Combined (GFP ChIP) w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ]
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9305_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ }
},
{
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "displayId" : "UNC-62 Combined (GFP ChIP)_ UNC_62_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 70.6670074749285
+ }
+ ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18182.bw",
"locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ }
},
- "name" : "UNC-62 Combined (GFP ChIP), UNC_62_L4 w peaks",
- "description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -25334,41 +24731,48 @@
"Transcription Factors",
"GFP ChIP"
],
+ "name" : "UNC-62 Combined (GFP ChIP), UNC_62_L4 w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-62 Combined (GFP ChIP)_ UNC_62_L4 w peaks",
- "displays" : [
- {
- "displayId" : "UNC-62 Combined (GFP ChIP)_ UNC_62_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
- "maxScore" : 70.6670074749285,
- "type" : "LinearWiggleDisplay"
- }
- ]
+ "description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
"description" : "Peak calls for UNC-62 Combined (GFP ChIP), UNC_62_L4 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-62 Combined (GFP ChIP)_ UNC_62_L4 w peaks_bigbed_peaks",
"name" : "__UNC-62 Combined (GFP ChIP), UNC_62_L4 peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18193_details.gff.bb"
- },
- "type" : "BigBedAdapter"
+ }
},
"displays" : [
{
"displayId" : "UNC-62 Combined (GFP ChIP)_ UNC_62_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"height" : 6,
"showDescriptions" : false
- }
+ },
+ "type" : "LinearBasicDisplay"
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-62 Combined (GFP ChIP)_ UNC_62_L4 w peaks_bigbed_peaks",
+ ]
+ },
+ {
+ "description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_L1 w peaks",
+ "name" : "UNC-62 Combined (GFP ChIP), UNC-62_GFP_L1 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -25376,52 +24780,49 @@
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
- },
- {
+ ],
+ "type" : "QuantitativeTrack",
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8187.bw"
+ }
+ },
"displays" : [
{
- "minScore" : 0,
"type" : "LinearWiggleDisplay",
- "maxScore" : 71.547518627323,
- "displayId" : "UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "displayId" : "UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 71.547518627323
}
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_L1 w peaks",
- "description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ ]
+ },
+ {
"adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8187.bw",
- "locationType" : "UriLocation"
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8196_details.gff.bb"
},
- "type" : "BigWigAdapter"
+ "type" : "BigBedAdapter"
},
- "type" : "QuantitativeTrack",
- "name" : "UNC-62 Combined (GFP ChIP), UNC-62_GFP_L1 w peaks"
- },
- {
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
"height" : 6,
- "showDescriptions" : false
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
},
"displayId" : "UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
],
+ "name" : "__UNC-62 Combined (GFP ChIP), UNC-62_GFP_L1 peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_L1 w peaks_bigbed_peaks",
+ "description" : "Peak calls for UNC-62 Combined (GFP ChIP), UNC-62_GFP_L1 w peaks",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -25429,50 +24830,38 @@
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "description" : "Peak calls for UNC-62 Combined (GFP ChIP), UNC-62_GFP_L1 w peaks",
- "name" : "__UNC-62 Combined (GFP ChIP), UNC-62_GFP_L1 peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8196_details.gff.bb",
- "locationType" : "UriLocation"
- }
- }
+ ]
},
{
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-62 Combined (GFP ChIP)_ UNC_62_EMB w peaks",
+ "name" : "UNC-62 Combined (GFP ChIP), UNC_62_EMB w peaks",
+ "description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "displayId" : "UNC-62 Combined (GFP ChIP)_ UNC_62_EMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "maxScore" : 172.265391968405,
"type" : "LinearWiggleDisplay",
- "minScore" : 0
+ "minScore" : 0,
+ "displayId" : "UNC-62 Combined (GFP ChIP)_ UNC_62_EMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 172.265391968405
}
],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18274.bw"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "UNC-62 Combined (GFP ChIP), UNC_62_EMB w peaks",
- "description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
+ }
},
{
- "description" : "Peak calls for UNC-62 Combined (GFP ChIP), UNC_62_EMB w peaks",
- "name" : "__UNC-62 Combined (GFP ChIP), UNC_62_EMB peaks",
"adapter" : {
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18299_details.gff.bb",
@@ -25480,28 +24869,30 @@
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "UNC-62 Combined (GFP ChIP)_ UNC_62_EMB w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "deeppink",
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
+ "color1" : "deeppink",
+ "showDescriptions" : false,
"height" : 6,
- "showDescriptions" : false
- }
+ "showLabels" : false
+ },
+ "displayId" : "UNC-62 Combined (GFP ChIP)_ UNC_62_EMB w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
+ "description" : "Peak calls for UNC-62 Combined (GFP ChIP), UNC_62_EMB w peaks",
+ "name" : "__UNC-62 Combined (GFP ChIP), UNC_62_EMB peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-62 Combined (GFP ChIP)_ UNC_62_EMB w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
]
},
{
@@ -25513,100 +24904,114 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
+ "description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_L2 w peaks",
+ "name" : "UNC-62 Combined (GFP ChIP), UNC-62_GFP_L2 w peaks",
"displays" : [
{
- "maxScore" : 61.465683914924,
- "type" : "LinearWiggleDisplay",
"minScore" : 0,
- "displayId" : "UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "displayId" : "UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 61.465683914924,
+ "type" : "LinearWiggleDisplay"
}
],
- "type" : "QuantitativeTrack",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8304.bw",
"locationType" : "UriLocation"
- }
- },
- "name" : "UNC-62 Combined (GFP ChIP), UNC-62_GFP_L2 w peaks",
- "description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
"description" : "Peak calls for UNC-62 Combined (GFP ChIP), UNC-62_GFP_L2 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_L2 w peaks_bigbed_peaks",
+ "name" : "__UNC-62 Combined (GFP ChIP), UNC-62_GFP_L2 peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8309_details.gff.bb"
- }
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8309_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "name" : "__UNC-62 Combined (GFP ChIP), UNC-62_GFP_L2 peaks",
"displays" : [
{
- "displayId" : "UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
+ "color1" : "deeppink",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
+ "height" : 6,
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
},
+ "displayId" : "UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay"
}
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_L2 w peaks_bigbed_peaks"
+ ]
},
{
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8135.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8135.bw"
}
},
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "minScore" : 0,
+ "displayId" : "UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 60.227605901689
+ }
+ ],
"name" : "UNC-62 Combined (GFP ChIP), UNC-62_GFP_L3 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_L3 w peaks",
"description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_L3 w peaks",
- "displays" : [
- {
- "displayId" : "UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "maxScore" : 60.227605901689,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
- }
]
},
{
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8142_details.gff.bb",
- "locationType" : "UriLocation"
- }
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8142_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
},
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
+ "height" : 6,
+ "showLabels" : false,
+ "color1" : "deeppink"
+ }
+ }
+ ],
"name" : "__UNC-62 Combined (GFP ChIP), UNC-62_GFP_L3 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_L3 w peaks_bigbed_peaks",
"description" : "Peak calls for UNC-62 Combined (GFP ChIP), UNC-62_GFP_L3 w peaks",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -25614,47 +25019,33 @@
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_L3 w peaks_bigbed_peaks",
- "displays" : [
- {
- "renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
- }
]
},
{
- "name" : "UNC-62 Combined (GFP ChIP), UNC-62_GFP_YA w peaks",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/13503.bw"
- }
- },
"description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_YA w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "UNC-62 Combined (GFP ChIP), UNC-62_GFP_YA w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/13503.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
+ "type" : "LinearWiggleDisplay",
"displayId" : "UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_YA w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
"maxScore" : 51.4758339388165
}
]
@@ -25662,56 +25053,57 @@
{
"description" : "Peak calls for UNC-62 Combined (GFP ChIP), UNC-62_GFP_YA w peaks",
"name" : "__UNC-62 Combined (GFP ChIP), UNC-62_GFP_YA peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_YA w peaks_bigbed_peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/13510_details.gff.bb"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/13510_details.gff.bb",
+ "locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_YA w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "color1" : "deeppink",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
+ "showLabels" : false,
"height" : 6,
- "showDescriptions" : false
- },
- "displayId" : "UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_YA w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "showDescriptions" : false,
+ "color1" : "deeppink"
+ }
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-62 Combined (GFP ChIP)_ UNC-62_GFP_YA w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
]
},
{
- "description" : " Identification of Transcription Factor UNC-130::GFP Binding Regions in L1 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/9273.bw"
- },
- "type" : "BigWigAdapter"
+ }
},
- "name" : "W03F9.2 Combined (GFP ChIP) w peaks",
"displays" : [
{
- "minScore" : 0,
"type" : "LinearWiggleDisplay",
- "maxScore" : 125.129242178291,
- "displayId" : "W03F9.2 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "displayId" : "W03F9.2 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 125.129242178291
}
],
+ "name" : "W03F9.2 Combined (GFP ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_W03F9.2 Combined (GFP ChIP) w peaks",
+ "description" : " Identification of Transcription Factor UNC-130::GFP Binding Regions in L1 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -25719,63 +25111,61 @@
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_W03F9.2 Combined (GFP ChIP) w peaks"
+ ]
},
{
- "name" : "__W03F9.2 Combined (GFP ChIP) peaks",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9280_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Peak calls for W03F9.2 Combined (GFP ChIP) w peaks",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_W03F9.2 Combined (GFP ChIP) w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Peak calls for W03F9.2 Combined (GFP ChIP) w peaks",
+ "name" : "__W03F9.2 Combined (GFP ChIP) peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_W03F9.2 Combined (GFP ChIP) w peaks_bigbed_peaks",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "W03F9.2 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
+ "height" : 6,
+ "showDescriptions" : false,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
- },
- "displayId" : "W03F9.2 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "type" : "SvgFeatureRenderer"
+ }
}
- ]
+ ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9280_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ }
},
{
- "description" : " Identification of Transcription Factor UNC-130::GFP Binding Regions in L1 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "ZAG-1 Combined (GFP ChIP), ZAG-1_GFP_L3 w peaks",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8200.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8200.bw"
+ }
},
- "type" : "QuantitativeTrack",
"displays" : [
{
- "minScore" : 0,
"maxScore" : 48.4812896925974,
- "type" : "LinearWiggleDisplay",
- "displayId" : "ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "displayId" : "ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
}
],
+ "description" : " Identification of Transcription Factor UNC-130::GFP Binding Regions in L1 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L3 w peaks",
+ "name" : "ZAG-1 Combined (GFP ChIP), ZAG-1_GFP_L3 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -25783,72 +25173,85 @@
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
+ ],
+ "type" : "QuantitativeTrack"
},
{
- "description" : "Peak calls for ZAG-1 Combined (GFP ChIP), ZAG-1_GFP_L3 w peaks",
- "name" : "__ZAG-1 Combined (GFP ChIP), ZAG-1_GFP_L3 peaks",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8206_details.gff.bb",
- "locationType" : "UriLocation"
- }
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8206_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
},
"displays" : [
{
+ "displayId" : "ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "deeppink",
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
+ "showLabels" : false,
+ "color1" : "deeppink"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
],
+ "name" : "__ZAG-1 Combined (GFP ChIP), ZAG-1_GFP_L3 peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L3 w peaks_bigbed_peaks",
+ "description" : "Peak calls for ZAG-1 Combined (GFP ChIP), ZAG-1_GFP_L3 w peaks",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
]
},
{
- "description" : " Identification of Transcription Factor UNC-130::GFP Binding Regions in L1 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "maxScore" : 44.9598559724877,
+ "minScore" : 0,
+ "displayId" : "ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8226.bw"
- },
- "type" : "BigWigAdapter"
- },
- "name" : "ZAG-1 Combined (GFP ChIP), ZAG-1_GFP_L1 w peaks",
- "displays" : [
- {
- "displayId" : "ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 44.9598559724877,
- "minScore" : 0
}
+ },
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : " Identification of Transcription Factor UNC-130::GFP Binding Regions in L1 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "ZAG-1 Combined (GFP ChIP), ZAG-1_GFP_L1 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L1 w peaks"
+ },
+ {
+ "description" : "Peak calls for ZAG-1 Combined (GFP ChIP), ZAG-1_GFP_L1 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L1 w peaks_bigbed_peaks",
+ "name" : "__ZAG-1 Combined (GFP ChIP), ZAG-1_GFP_L1 peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L1 w peaks"
- },
- {
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
@@ -25856,29 +25259,17 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8251_details.gff.bb"
}
},
- "type" : "FeatureTrack",
- "name" : "__ZAG-1 Combined (GFP ChIP), ZAG-1_GFP_L1 peaks",
- "description" : "Peak calls for ZAG-1 Combined (GFP ChIP), ZAG-1_GFP_L1 w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L1 w peaks_bigbed_peaks",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
+ "color1" : "deeppink",
"height" : 6,
"showDescriptions" : false,
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
]
},
@@ -25886,43 +25277,33 @@
"displays" : [
{
"type" : "LinearWiggleDisplay",
- "maxScore" : 48.5440435563361,
"minScore" : 0,
- "displayId" : "ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "displayId" : "ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 48.5440435563361
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L2 w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8118.bw"
+ }
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"description" : " Identification of Transcription Factor UNC-130::GFP Binding Regions in L1 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"name" : "ZAG-1 Combined (GFP ChIP), ZAG-1_GFP_L2 w peaks",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8118.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- }
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L2 w peaks"
},
{
- "name" : "__ZAG-1 Combined (GFP ChIP), ZAG-1_GFP_L2 peaks",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8127_details.gff.bb",
- "locationType" : "UriLocation"
- }
- },
"type" : "FeatureTrack",
- "description" : "Peak calls for ZAG-1 Combined (GFP ChIP), ZAG-1_GFP_L2 w peaks",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L2 w peaks_bigbed_peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -25931,85 +25312,106 @@
"Transcription Factors",
"GFP ChIP"
],
+ "name" : "__ZAG-1 Combined (GFP ChIP), ZAG-1_GFP_L2 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L2 w peaks_bigbed_peaks",
+ "description" : "Peak calls for ZAG-1 Combined (GFP ChIP), ZAG-1_GFP_L2 w peaks",
"displays" : [
{
- "displayId" : "ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
"color1" : "deeppink",
"showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false,
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
- ]
+ ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8127_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ }
},
{
- "description" : " Identification of Transcription Factor UNC-130::GFP Binding Regions in L1 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "ZAG-1 Combined (GFP ChIP), ZAG-1_GFP_L4 w peaks",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 87.155955736759,
+ "displayId" : "ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0
+ }
+ ],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/13375.bw"
- }
+ },
+ "type" : "BigWigAdapter"
},
"type" : "QuantitativeTrack",
- "displays" : [
- {
- "displayId" : "ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 87.155955736759
- }
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L4 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ]
+ "name" : "ZAG-1 Combined (GFP ChIP), ZAG-1_GFP_L4 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L4 w peaks",
+ "description" : " Identification of Transcription Factor UNC-130::GFP Binding Regions in L1 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "description" : "Peak calls for ZAG-1 Combined (GFP ChIP), ZAG-1_GFP_L4 w peaks",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/13381_details.gff.bb"
- },
- "type" : "BigBedAdapter"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/13381_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
},
- "type" : "FeatureTrack",
- "name" : "__ZAG-1 Combined (GFP ChIP), ZAG-1_GFP_L4 peaks",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
- },
- "displayId" : "ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
+ }
}
],
+ "description" : "Peak calls for ZAG-1 Combined (GFP ChIP), ZAG-1_GFP_L4 w peaks",
+ "name" : "__ZAG-1 Combined (GFP ChIP), ZAG-1_GFP_L4 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L4 w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZAG-1 Combined (GFP ChIP)_ ZAG-1_GFP_L4 w peaks_bigbed_peaks"
+ ]
},
{
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_DPY-27 Combined (GFP ChIP) recalled peaks w peaks",
"name" : "DPY-27 Combined (GFP ChIP) recalled peaks w peaks",
+ "description" : " Identification of Dosage Compensation Complex Protein DPY-27::GFP Binding Regions in Embryos. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP (Peak Recall)"
+ ],
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
@@ -26017,534 +25419,532 @@
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "description" : " Identification of Dosage Compensation Complex Protein DPY-27::GFP Binding Regions in Embryos. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_DPY-27 Combined (GFP ChIP) recalled peaks w peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP (Peak Recall)"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
+ "maxScore" : 35.6926441979147,
"displayId" : "DPY-27 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
"minScore" : 0,
- "maxScore" : 35.6926441979147,
"type" : "LinearWiggleDisplay"
}
]
},
{
- "description" : "Peak calls for DPY-27 Combined (GFP ChIP) recalled peaks w peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10181_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "__DPY-27 Combined (GFP ChIP) recalled peaks peaks",
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "showDescriptions" : false,
+ "height" : 6
},
- "displayId" : "DPY-27 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks"
+ "displayId" : "DPY-27 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10181_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_DPY-27 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks"
- },
- {
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_EGL-5 Combined (GFP ChIP) recalled peaks w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP (Peak Recall)"
- ],
+ "type" : "FeatureTrack",
+ "description" : "Peak calls for DPY-27 Combined (GFP ChIP) recalled peaks w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_DPY-27 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
+ "name" : "__DPY-27 Combined (GFP ChIP) recalled peaks peaks"
+ },
+ {
"displays" : [
{
+ "displayId" : "EGL-5 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
"maxScore" : 47.1086058678193,
- "displayId" : "EGL-5 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
],
- "name" : "EGL-5 Combined (GFP ChIP) recalled peaks w peaks",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/7975.bw",
"locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ }
},
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP (Peak Recall)"
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_EGL-5 Combined (GFP ChIP) recalled peaks w peaks",
+ "name" : "EGL-5 Combined (GFP ChIP) recalled peaks w peaks",
"description" : " Identification of Dosage Compensation Complex Protein DPY-27::GFP Binding Regions in Embryos. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_EGL-5 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
+ "name" : "__EGL-5 Combined (GFP ChIP) recalled peaks peaks",
+ "description" : "Peak calls for EGL-5 Combined (GFP ChIP) recalled peaks w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_EGL-5 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8076_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "displayId" : "EGL-5 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
"color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "showDescriptions" : false,
+ "height" : 6,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
},
+ "displayId" : "EGL-5 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks",
"type" : "LinearBasicDisplay"
}
- ],
+ ]
+ },
+ {
"adapter" : {
- "bigBedLocation" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8076_details.gff.bb"
- },
- "type" : "BigBedAdapter"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8322.bw"
+ }
},
- "type" : "FeatureTrack",
- "name" : "__EGL-5 Combined (GFP ChIP) recalled peaks peaks",
- "description" : "Peak calls for EGL-5 Combined (GFP ChIP) recalled peaks w peaks"
- },
- {
"displays" : [
{
- "minScore" : 0,
- "maxScore" : 119.359462041189,
"type" : "LinearWiggleDisplay",
- "displayId" : "EOR-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay"
+ "minScore" : 0,
+ "displayId" : "EOR-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
+ "maxScore" : 119.359462041189
}
],
+ "description" : "Identification of Transcription Factor EGL-27::GFP Binding Regions in L1. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "EOR-1 Combined (GFP ChIP) recalled peaks w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_EOR-1 Combined (GFP ChIP) recalled peaks w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
- "description" : "Identification of Transcription Factor EGL-27::GFP Binding Regions in L1. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "EOR-1 Combined (GFP ChIP) recalled peaks w peaks",
"type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/8322.bw"
- },
- "type" : "BigWigAdapter"
- }
- },
- {
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_EOR-1 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
+ ]
+ },
+ {
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Peak calls for EOR-1 Combined (GFP ChIP) recalled peaks w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_EOR-1 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
+ "name" : "__EOR-1 Combined (GFP ChIP) recalled peaks peaks",
"displays" : [
{
- "displayId" : "EOR-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks",
"type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "deeppink",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
"height" : 6,
- "showDescriptions" : false
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "EOR-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks"
}
],
- "name" : "__EOR-1 Combined (GFP ChIP) recalled peaks peaks",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9871_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Peak calls for EOR-1 Combined (GFP ChIP) recalled peaks w peaks"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9871_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
- "description" : "Identification of Transcription Factor EGL-27::GFP Binding Regions in L1. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_GEI11_GFP_L4_combined_WS220.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP (Peak Recall)"
+ ],
"type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Identification of Transcription Factor EGL-27::GFP Binding Regions in L1. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"name" : "SNPC-4 Combined (GFP ChIP) recalled peaks w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_GEI-11 Combined (GFP ChIP) recalled peaks w peaks",
"displays" : [
{
+ "displayId" : "GEI-11 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
"minScore" : 0,
"maxScore" : 48.0700305359699,
- "type" : "LinearWiggleDisplay",
- "displayId" : "GEI-11 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP (Peak Recall)"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_GEI-11 Combined (GFP ChIP) recalled peaks w peaks"
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_GEI11_GFP_L4_combined_WS220.bw"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8063_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8063_details.gff.bb"
+ }
},
- "name" : "__SNPC-4 Combined (GFP ChIP) recalled peaks peaks",
- "description" : "Peak calls for SNPC-4 (was GEI-11) Combined (GFP ChIP) recalled peaks w peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP (Peak Recall)"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_GEI-11 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"showDescriptions" : false,
"height" : 6,
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
"color1" : "deeppink"
},
- "type" : "LinearBasicDisplay",
"displayId" : "GEI-11 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks"
}
+ ],
+ "name" : "__SNPC-4 Combined (GFP ChIP) recalled peaks peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_GEI-11 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
+ "description" : "Peak calls for SNPC-4 (was GEI-11) Combined (GFP ChIP) recalled peaks w peaks",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP (Peak Recall)"
]
},
{
- "displays" : [
- {
- "displayId" : "HLH-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 79.5190577603035,
- "minScore" : 0
- }
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "HLH-1 Combined (GFP ChIP) recalled peaks w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_HLH-1 Combined (GFP ChIP) recalled peaks w peaks",
"description" : "Identification of Transcription Factor EGL-27::GFP Binding Regions in L1. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 79.5190577603035,
+ "minScore" : 0,
+ "displayId" : "HLH-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_HLH-1_GFP_emb_combined_WS220.bw",
"locationType" : "UriLocation"
- }
- },
- "type" : "QuantitativeTrack",
- "name" : "HLH-1 Combined (GFP ChIP) recalled peaks w peaks"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
- "name" : "__HLH-1 Combined (GFP ChIP) recalled peaks peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8069_details.gff.bb"
- }
- },
- "description" : "Peak calls for HLH-1 Combined (GFP ChIP) recalled peaks w peaks",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_HLH-1 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "Peak calls for HLH-1 Combined (GFP ChIP) recalled peaks w peaks",
+ "name" : "__HLH-1 Combined (GFP ChIP) recalled peaks peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_HLH-1 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "HLH-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks",
"renderer" : {
- "color1" : "deeppink",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
"height" : 6,
- "showDescriptions" : false
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "color1" : "deeppink"
},
- "displayId" : "HLH-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8069_details.gff.bb"
+ }
+ }
},
{
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_LIN-11_GFP_L2_combined_WS220.bw"
+ }
+ },
"displays" : [
{
"displayId" : "LIN-11 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
+ "minScore" : 0,
"maxScore" : 75.4369828428075,
- "minScore" : 0
+ "type" : "LinearWiggleDisplay"
}
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_LIN-11 Combined (GFP ChIP) recalled peaks w peaks",
+ "name" : "LIN-11 Combined (GFP ChIP) recalled peaks w peaks",
+ "description" : " Identification of transcription factor binding regions (Snyder project,Snyder group) General Description We used the program Peakseq to define binding peaks of each factor, and used PeakRanger to identify the multiple summits inside each broad region found by PeakSeq. PeakRanger takes the broad regions and uses second-derivative information to find local summits. We extended each of these summits with a 100 bp flanking each side (if the initial region was smaller than 200 bp we just kept the small region size). The narrow binding regions (maximum 200 bp) around the summit found by PeakRanger were defined as narrow summit peaks.We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
- ],
- "description" : " Identification of transcription factor binding regions (Snyder project,Snyder group) General Description We used the program Peakseq to define binding peaks of each factor, and used PeakRanger to identify the multiple summits inside each broad region found by PeakSeq. PeakRanger takes the broad regions and uses second-derivative information to find local summits. We extended each of these summits with a 100 bp flanking each side (if the initial region was smaller than 200 bp we just kept the small region size). The narrow binding regions (maximum 200 bp) around the summit found by PeakRanger were defined as narrow summit peaks.We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "LIN-11 Combined (GFP ChIP) recalled peaks w peaks",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_LIN-11_GFP_L2_combined_WS220.bw"
- }
- },
- "type" : "QuantitativeTrack"
+ ]
},
{
"description" : "Peak calls for LIN-11 Combined (GFP ChIP) recalled peaks w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_LIN-11 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
"name" : "__LIN-11 Combined (GFP ChIP) recalled peaks peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP (Peak Recall)"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8056_details.gff.bb"
- }
+ },
+ "type" : "BigBedAdapter"
},
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "LIN-11 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks",
"renderer" : {
+ "color1" : "deeppink",
"showDescriptions" : false,
"height" : 6,
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "deeppink"
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "LIN-11 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_LIN-11 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ ]
+ },
+ {
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
- ]
- },
- {
- "displays" : [
- {
- "minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 67.99403851799,
- "displayId" : "LIN-15B Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay"
- }
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP (Peak Recall)"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_LIN-15B Combined (GFP ChIP) recalled peaks w peaks",
- "description" : " Identification of Transcription Factor LIN-13::GFP Binding Regions in Embryos. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"type" : "QuantitativeTrack",
+ "description" : " Identification of Transcription Factor LIN-13::GFP Binding Regions in Embryos. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_LIN-15B Combined (GFP ChIP) recalled peaks w peaks",
+ "name" : "LIN-15B Combined (GFP ChIP) recalled peaks w peaks",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "displayId" : "LIN-15B Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 67.99403851799
+ }
+ ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_LIN-15B_GFP_L3_combined_WS220.bw"
- },
- "type" : "BigWigAdapter"
- },
- "name" : "LIN-15B Combined (GFP ChIP) recalled peaks w peaks"
+ }
+ }
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_LIN-15B Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP (Peak Recall)"
- ],
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "LIN-15B Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks",
"renderer" : {
+ "color1" : "deeppink",
"showDescriptions" : false,
"height" : 6,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
- },
- "displayId" : "LIN-15B Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks"
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "name" : "__LIN-15B Combined (GFP ChIP) recalled peaks peaks",
"adapter" : {
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8071_details.gff.bb"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8071_details.gff.bb",
+ "locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP (Peak Recall)"
+ ],
"type" : "FeatureTrack",
- "description" : "Peak calls for LIN-15B Combined (GFP ChIP) recalled peaks w peaks"
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Peak calls for LIN-15B Combined (GFP ChIP) recalled peaks w peaks",
+ "name" : "__LIN-15B Combined (GFP ChIP) recalled peaks peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_LIN-15B Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks"
},
{
- "name" : "LIN-39 Combined (GFP ChIP) recalled peaks w peaks",
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 79.9724096516235,
+ "displayId" : "LIN-39 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
+ "minScore" : 0
+ }
+ ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_LIN-39-GFP_L3_combined_WS220.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_LIN-39-GFP_L3_combined_WS220.bw"
+ }
},
- "description" : " Identification of Transcription Factor LIN-13::GFP Binding Regions in Embryos. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_LIN-39 Combined (GFP ChIP) recalled peaks w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
- "displays" : [
- {
- "displayId" : "LIN-39 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
- "minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 79.9724096516235
- }
- ]
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_LIN-39 Combined (GFP ChIP) recalled peaks w peaks",
+ "name" : "LIN-39 Combined (GFP ChIP) recalled peaks w peaks",
+ "description" : " Identification of Transcription Factor LIN-13::GFP Binding Regions in Embryos. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8053_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "LIN-39 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "LIN-39 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks"
+ "color1" : "deeppink",
+ "height" : 6,
+ "showDescriptions" : false,
+ "showLabels" : false
+ }
}
],
+ "description" : "Peak calls for LIN-39 Combined (GFP ChIP) recalled peaks w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_LIN-39 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "__LIN-39 Combined (GFP ChIP) recalled peaks peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
- "description" : "Peak calls for LIN-39 Combined (GFP ChIP) recalled peaks w peaks",
- "name" : "__LIN-39 Combined (GFP ChIP) recalled peaks peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8053_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- }
- },
- {
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP (Peak Recall)"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_CEH-14 Combined (GFP ChIP) recalled peaks w peaks",
+ "type" : "FeatureTrack"
+ },
+ {
"displays" : [
{
- "displayId" : "CEH-14 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay",
"minScore" : 0,
- "maxScore" : 46.27065750062,
- "type" : "LinearWiggleDisplay"
+ "displayId" : "CEH-14 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
+ "maxScore" : 46.27065750062
}
],
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_CEH-14_GFP_L2_combined_WS220.bw"
- },
- "type" : "BigWigAdapter"
+ }
},
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP (Peak Recall)"
+ ],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : " Identification of Transcription Factor CEH-14::GFP Binding Regions in L2. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"name" : "CEH-14 Combined (GFP ChIP) recalled peaks w peaks",
- "description" : " Identification of Transcription Factor CEH-14::GFP Binding Regions in L2. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_CEH-14 Combined (GFP ChIP) recalled peaks w peaks"
},
{
- "description" : "Peak calls for CEH-14 Combined (GFP ChIP) recalled peaks w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_CEH-14 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
"name" : "__CEH-14 Combined (GFP ChIP) recalled peaks peaks",
+ "description" : "Peak calls for CEH-14 Combined (GFP ChIP) recalled peaks w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP (Peak Recall)"
+ ],
"adapter" : {
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10175_details.gff.bb",
@@ -26554,47 +25954,69 @@
},
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"height" : 6,
"showDescriptions" : false
},
- "type" : "LinearBasicDisplay",
"displayId" : "CEH-14 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks"
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_CEH-14 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
+ ]
+ },
+ {
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
- "GFP ChIP (Peak Recall)"
- ]
- },
- {
- "description" : "Identification of Pol II Binding Regions in AMA-1::GFP L4 Young Adult. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "PolII ChIP"
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_AMA-1 Combined (Pol II ChIP) w peaks",
"name" : "AMA-1 Combined (Pol II ChIP) w peaks",
+ "description" : "Identification of Pol II Binding Regions in AMA-1::GFP L4 Young Adult. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "maxScore" : 157.655735791747,
+ "minScore" : 0,
+ "displayId" : "AMA-1 Combined (Pol II ChIP) w peaks_Transcription Factors_PolII ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_AMA1_POLII_L4YA_combined_WS220.bw"
},
"type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
+ }
+ },
+ {
"displays" : [
{
- "displayId" : "AMA-1 Combined (Pol II ChIP) w peaks_Transcription Factors_PolII ChIP-LinearWiggleDisplay",
- "minScore" : 0,
- "maxScore" : 157.655735791747,
- "type" : "LinearWiggleDisplay"
+ "type" : "LinearBasicDisplay",
+ "displayId" : "AMA-1 Combined (Pol II ChIP) w peaks_Transcription Factors_PolII ChIP_bigbed_peaks",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6,
+ "color1" : "deeppink"
+ }
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_AMA-1 Combined (Pol II ChIP) w peaks",
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4298_details.gff.bb"
+ }
+ },
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -26602,121 +26024,81 @@
"modENCODE data (2014)",
"Transcription Factors",
"PolII ChIP"
- ]
- },
- {
+ ],
"name" : "__AMA-1 Combined (Pol II ChIP) peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4298_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "description" : "Peak calls for AMA-1 Combined (Pol II ChIP) w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_AMA-1 Combined (Pol II ChIP) w peaks_bigbed_peaks",
+ "description" : "Peak calls for AMA-1 Combined (Pol II ChIP) w peaks"
+ },
+ {
+ "description" : " Identification of Pol II Binding Regions in DAF-16::GFP L4 Young Adults. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "DAF-16 Combined (Pol II ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_DAF-16 Combined (Pol II ChIP) w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"PolII ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "displays" : [
- {
- "renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "AMA-1 Combined (Pol II ChIP) w peaks_Transcription Factors_PolII ChIP_bigbed_peaks"
- }
- ]
- },
- {
- "description" : " Identification of Pol II Binding Regions in DAF-16::GFP L4 Young Adults. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "DAF-16 Combined (Pol II ChIP) w peaks",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_DAF16_POLII_L4YA_combined_WS220.bw"
- },
- "type" : "BigWigAdapter"
+ }
},
- "type" : "QuantitativeTrack",
"displays" : [
{
+ "type" : "LinearWiggleDisplay",
"displayId" : "DAF-16 Combined (Pol II ChIP) w peaks_Transcription Factors_PolII ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
"maxScore" : 61.1366354884765
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_DAF-16 Combined (Pol II ChIP) w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "PolII ChIP"
]
},
{
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"PolII ChIP"
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_DAF-16 Combined (Pol II ChIP) w peaks_bigbed_peaks",
+ "name" : "__DAF-16 Combined (Pol II ChIP) peaks",
+ "description" : "Peak calls for DAF-16 Combined (Pol II ChIP) w peaks",
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
"type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false
},
- "displayId" : "DAF-16 Combined (Pol II ChIP) w peaks_Transcription Factors_PolII ChIP_bigbed_peaks"
+ "displayId" : "DAF-16 Combined (Pol II ChIP) w peaks_Transcription Factors_PolII ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4281_details.gff.bb"
- }
- },
- "type" : "FeatureTrack",
- "name" : "__DAF-16 Combined (Pol II ChIP) peaks",
- "description" : "Peak calls for DAF-16 Combined (Pol II ChIP) w peaks"
+ },
+ "type" : "BigBedAdapter"
+ }
},
{
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "PolII ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_EGL-5 Combined (Pol II ChIP) w peaks",
"displays" : [
{
"displayId" : "EGL-5 Combined (Pol II ChIP) w peaks_Transcription Factors_PolII ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 125.800223544584
+ "maxScore" : 125.800223544584,
+ "type" : "LinearWiggleDisplay"
}
],
"adapter" : {
@@ -26726,35 +26108,41 @@
},
"type" : "BigWigAdapter"
},
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "PolII ChIP"
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_EGL-5 Combined (Pol II ChIP) w peaks",
"name" : "EGL-5 Combined (Pol II ChIP) w peaks",
"description" : " Identification of Pol II Binding Regions in L3 EGL-5::GFP. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "description" : "Peak calls for EGL-5 Combined (Pol II ChIP) w peaks",
- "name" : "__EGL-5 Combined (Pol II ChIP) peaks",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/5736_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
"displays" : [
{
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 6,
"showDescriptions" : false,
- "color1" : "deeppink",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "color1" : "deeppink"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "EGL-5 Combined (Pol II ChIP) w peaks_Transcription Factors_PolII ChIP_bigbed_peaks"
+ "displayId" : "EGL-5 Combined (Pol II ChIP) w peaks_Transcription Factors_PolII ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_EGL-5 Combined (Pol II ChIP) w peaks_bigbed_peaks",
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/5736_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -26762,28 +26150,31 @@
"modENCODE data (2014)",
"Transcription Factors",
"PolII ChIP"
- ]
+ ],
+ "name" : "__EGL-5 Combined (Pol II ChIP) peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_EGL-5 Combined (Pol II ChIP) w peaks_bigbed_peaks",
+ "description" : "Peak calls for EGL-5 Combined (Pol II ChIP) w peaks"
},
{
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_EOR-1_POLII_L3_combined_WS220.bw",
- "locationType" : "UriLocation"
- }
- },
- "name" : "EOR-1 Combined (Pol II ChIP) w peaks",
"description" : " Identification of Pol II Binding Regions in L3 EOR-1::GFP. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "EOR-1 Combined (Pol II ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_EOR-1 Combined (Pol II ChIP) w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"PolII ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_EOR-1 Combined (Pol II ChIP) w peaks",
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_EOR-1_POLII_L3_combined_WS220.bw"
+ }
+ },
"displays" : [
{
"type" : "LinearWiggleDisplay",
@@ -26794,17 +26185,6 @@
]
},
{
- "name" : "__EOR-1 Combined (Pol II ChIP) peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/6101_details.gff.bb"
- }
- },
- "description" : "Peak calls for EOR-1 Combined (Pol II ChIP) w peaks",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_EOR-1 Combined (Pol II ChIP) w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -26813,64 +26193,84 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "description" : "Peak calls for EOR-1 Combined (Pol II ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_EOR-1 Combined (Pol II ChIP) w peaks_bigbed_peaks",
+ "name" : "__EOR-1 Combined (Pol II ChIP) peaks",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
"height" : 6,
- "showDescriptions" : false
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "EOR-1 Combined (Pol II ChIP) w peaks_Transcription Factors_PolII ChIP_bigbed_peaks"
}
- ]
+ ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/6101_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ }
},
{
- "description" : " Identification of Pol II Binding Regions in L3 HLH-8::GFP. Synchronized L3 larvae from C. elegans strain OP74 (a transgenic strain engineered to express a gene fusion between hlh-8 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_HLH-8_POLII_L3_combined_WS220.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_HLH-8_POLII_L3_combined_WS220.bw",
+ "locationType" : "UriLocation"
}
},
- "name" : "HLH-8 Combined (Pol II ChIP) w peaks",
"displays" : [
{
- "maxScore" : 125.525107354199,
"type" : "LinearWiggleDisplay",
"minScore" : 0,
- "displayId" : "HLH-8 Combined (Pol II ChIP) w peaks_Transcription Factors_PolII ChIP-LinearWiggleDisplay"
+ "displayId" : "HLH-8 Combined (Pol II ChIP) w peaks_Transcription Factors_PolII ChIP-LinearWiggleDisplay",
+ "maxScore" : 125.525107354199
}
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_HLH-8 Combined (Pol II ChIP) w peaks",
+ "name" : "HLH-8 Combined (Pol II ChIP) w peaks",
+ "description" : " Identification of Pol II Binding Regions in L3 HLH-8::GFP. Synchronized L3 larvae from C. elegans strain OP74 (a transgenic strain engineered to express a gene fusion between hlh-8 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"PolII ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_HLH-8 Combined (Pol II ChIP) w peaks"
+ ]
},
{
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/5872_details.gff.bb"
+ }
+ },
"displays" : [
{
"renderer" : {
+ "height" : 6,
+ "showDescriptions" : false,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "HLH-8 Combined (Pol II ChIP) w peaks_Transcription Factors_PolII ChIP_bigbed_peaks"
+ "displayId" : "HLH-8 Combined (Pol II ChIP) w peaks_Transcription Factors_PolII ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
+ "description" : "Peak calls for HLH-8 Combined (Pol II ChIP) w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_HLH-8 Combined (Pol II ChIP) w peaks_bigbed_peaks",
+ "name" : "__HLH-8 Combined (Pol II ChIP) peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -26879,28 +26279,13 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : "Peak calls for HLH-8 Combined (Pol II ChIP) w peaks",
- "name" : "__HLH-8 Combined (Pol II ChIP) peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/5872_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- }
+ "type" : "FeatureTrack"
},
{
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_MAB5_POLII_L3_combined_WS220.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
"name" : "MAB-5 Combined (Pol II ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_MAB-5 Combined (Pol II ChIP) w peaks",
"description" : " Identification of Pol II Binding Regions in MAB-5::GFP L3. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -26909,31 +26294,26 @@
"Transcription Factors",
"PolII ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_MAB-5 Combined (Pol II ChIP) w peaks",
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_MAB5_POLII_L3_combined_WS220.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "displayId" : "MAB-5 Combined (Pol II ChIP) w peaks_Transcription Factors_PolII ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay",
"minScore" : 0,
- "maxScore" : 229.245518185801,
- "type" : "LinearWiggleDisplay"
+ "displayId" : "MAB-5 Combined (Pol II ChIP) w peaks_Transcription Factors_PolII ChIP-LinearWiggleDisplay",
+ "maxScore" : 229.245518185801
}
]
},
{
- "displays" : [
- {
- "renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "MAB-5 Combined (Pol II ChIP) w peaks_Transcription Factors_PolII ChIP_bigbed_peaks"
- }
- ],
+ "description" : "Peak calls for MAB-5 Combined (Pol II ChIP) w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_MAB-5 Combined (Pol II ChIP) w peaks_bigbed_peaks",
+ "name" : "__MAB-5 Combined (Pol II ChIP) peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -26942,20 +26322,37 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : "Peak calls for MAB-5 Combined (Pol II ChIP) w peaks",
- "name" : "__MAB-5 Combined (Pol II ChIP) peaks",
"type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4269_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- }
+ }
+ },
+ "displays" : [
+ {
+ "renderer" : {
+ "showDescriptions" : false,
+ "height" : 6,
+ "showLabels" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "MAB-5 Combined (Pol II ChIP) w peaks_Transcription Factors_PolII ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
- "description" : " Identification of Transcription Factor ALR-1::GFP Binding Regions in L2. Synchronized L2 larvae from C. elegans strain OP200 (a transgenic strain engineered to express a gene fusion between alr-1 and GFP) were treated with the cross-linking reagent formaldehyde. After lysis and sonication, the chromatin was immunoprecipitated with an affinity-purified antibody that recognizes GFP. The bound DNA was purified and sequenced in an Illumina GA-2. A sample of the input DNA was sequenced in parallel. The ChIP-seq data generated by this experiment was analyzed using the PeakSeq peak-calling algorithm to predict protein binding sites in the C. elegans genome.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "ALR-1 Combined (GFP ChIP) recalled peaks w peaks",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "displayId" : "ALR-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 80.5518783819215
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -26963,40 +26360,20 @@
"locationType" : "UriLocation"
}
},
- "type" : "QuantitativeTrack",
- "displays" : [
- {
- "maxScore" : 80.5518783819215,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0,
- "displayId" : "ALR-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay"
- }
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_ALR-1 Combined (GFP ChIP) recalled peaks w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
+ ],
+ "description" : " Identification of Transcription Factor ALR-1::GFP Binding Regions in L2. Synchronized L2 larvae from C. elegans strain OP200 (a transgenic strain engineered to express a gene fusion between alr-1 and GFP) were treated with the cross-linking reagent formaldehyde. After lysis and sonication, the chromatin was immunoprecipitated with an affinity-purified antibody that recognizes GFP. The bound DNA was purified and sequenced in an Illumina GA-2. A sample of the input DNA was sequenced in parallel. The ChIP-seq data generated by this experiment was analyzed using the PeakSeq peak-calling algorithm to predict protein binding sites in the C. elegans genome.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "ALR-1 Combined (GFP ChIP) recalled peaks w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_ALR-1 Combined (GFP ChIP) recalled peaks w peaks"
},
{
- "displays" : [
- {
- "displayId" : "ALR-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink"
- }
- }
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_ALR-1 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -27005,37 +26382,51 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"description" : "Peak calls for ALR-1 Combined (GFP ChIP) recalled peaks w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_ALR-1 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
"name" : "__ALR-1 Combined (GFP ChIP) recalled peaks peaks",
+ "displays" : [
+ {
+ "displayId" : "ALR-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
+ "height" : 6,
+ "showLabels" : false,
+ "color1" : "deeppink"
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7738_details.gff.bb"
- }
- },
- "type" : "FeatureTrack"
+ },
+ "type" : "BigBedAdapter"
+ }
},
{
- "description" : "Identification of Transcription Factor BLMP-1::GFP Binding Regions in L1 (Snyder project,Snyder subgroup)
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "BLMP-1 Combined (GFP ChIP) recalled peaks w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/5426_Snyder_BLMP-1_GFP_L1_combined.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/5426_Snyder_BLMP-1_GFP_L1_combined.bw"
+ }
},
"displays" : [
{
"displayId" : "BLMP-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 397.978209851521
+ "maxScore" : 397.978209851521,
+ "type" : "LinearWiggleDisplay"
}
],
+ "name" : "BLMP-1 Combined (GFP ChIP) recalled peaks w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_BLMP-1 Combined (GFP ChIP) recalled peaks w peaks",
+ "description" : "Identification of Transcription Factor BLMP-1::GFP Binding Regions in L1 (Snyder project,Snyder subgroup)
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -27047,42 +26438,39 @@
},
{
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/9873_details.gff.bb",
"locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ }
},
- "type" : "FeatureTrack",
- "name" : "__BLMP-1 Combined (GFP ChIP) recalled peaks peaks",
- "description" : "Peak calls for BLMP-1 Combined (GFP ChIP) recalled peaks w peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP (Peak Recall)"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_BLMP-1 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
"displays" : [
{
"displayId" : "BLMP-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showLabels" : false,
"height" : 6,
"showDescriptions" : false,
- "color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "color1" : "deeppink"
},
"type" : "LinearBasicDisplay"
}
+ ],
+ "description" : "Peak calls for BLMP-1 Combined (GFP ChIP) recalled peaks w peaks",
+ "name" : "__BLMP-1 Combined (GFP ChIP) recalled peaks peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_BLMP-1 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP (Peak Recall)"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
]
},
{
- "description" : " Identification of Transcription Factor MAB-5::GFP Binding Regions in L3. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "MAB-5 Combined (GFP ChIP) recalled peaks w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
@@ -27093,12 +26481,15 @@
"displays" : [
{
"maxScore" : 60.3547276894595,
- "type" : "LinearWiggleDisplay",
+ "displayId" : "MAB-5 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
"minScore" : 0,
- "displayId" : "MAB-5 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
],
+ "name" : "MAB-5 Combined (GFP ChIP) recalled peaks w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_MAB-5 Combined (GFP ChIP) recalled peaks w peaks",
+ "description" : " Identification of Transcription Factor MAB-5::GFP Binding Regions in L3. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -27109,19 +26500,7 @@
]
},
{
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 6,
- "showDescriptions" : false
- },
- "displayId" : "MAB-5 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks"
- }
- ],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -27130,20 +26509,43 @@
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
+ "name" : "__MAB-5 Combined (GFP ChIP) recalled peaks peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_MAB-5 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
"description" : "Peak calls for MAB-5 Combined (GFP ChIP) recalled peaks w peaks",
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
+ "height" : 6,
+ "showLabels" : false,
+ "color1" : "deeppink"
+ },
+ "displayId" : "MAB-5 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8051_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "__MAB-5 Combined (GFP ChIP) recalled peaks peaks"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8051_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
"description" : " Identification of Transcription Factor SKN-1::GFP Binding Regions in L1. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_SKN-1 Combined (GFP ChIP) recalled peaks w peaks",
+ "name" : "SKN-1 Combined (GFP ChIP) recalled peaks w peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP (Peak Recall)"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
@@ -27151,28 +26553,20 @@
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "name" : "SKN-1 Combined (GFP ChIP) recalled peaks w peaks",
"displays" : [
{
- "type" : "LinearWiggleDisplay",
- "maxScore" : 192.130600688404,
"minScore" : 0,
- "displayId" : "SKN-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay"
+ "displayId" : "SKN-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
+ "maxScore" : 192.130600688404,
+ "type" : "LinearWiggleDisplay"
}
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP (Peak Recall)"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_SKN-1 Combined (GFP ChIP) recalled peaks w peaks"
+ ]
},
{
+ "name" : "__SKN-1 Combined (GFP ChIP) recalled peaks peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_SKN-1 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
+ "description" : "Peak calls for SKN-1 Combined (GFP ChIP) recalled peaks w peaks",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -27181,33 +26575,36 @@
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8000_details.gff.bb"
+ }
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
"type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "showDescriptions" : false,
+ "height" : 6,
+ "showLabels" : false,
+ "color1" : "deeppink"
},
- "displayId" : "SKN-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks"
+ "displayId" : "SKN-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
- ],
- "name" : "__SKN-1 Combined (GFP ChIP) recalled peaks peaks",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8000_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Peak calls for SKN-1 Combined (GFP ChIP) recalled peaks w peaks"
+ ]
},
{
- "description" : "Identification of Transcription Factor EGL-27::GFP Binding Regions in L1. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "EGL-27 Combined (GFP ChIP) recalled peaks w peaks",
+ "displays" : [
+ {
+ "minScore" : 0,
+ "displayId" : "EGL-27 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
+ "maxScore" : 51.8171481175507,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -27216,78 +26613,72 @@
}
},
"type" : "QuantitativeTrack",
- "displays" : [
- {
- "type" : "LinearWiggleDisplay",
- "maxScore" : 51.8171481175507,
- "minScore" : 0,
- "displayId" : "EGL-27 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay"
- }
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_EGL-27 Combined (GFP ChIP) recalled peaks w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ]
+ "name" : "EGL-27 Combined (GFP ChIP) recalled peaks w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_EGL-27 Combined (GFP ChIP) recalled peaks w peaks",
+ "description" : "Identification of Transcription Factor EGL-27::GFP Binding Regions in L1. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "displays" : [
- {
- "renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "EGL-27 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks"
- }
- ],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_EGL-27 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
+ "name" : "__EGL-27 Combined (GFP ChIP) recalled peaks peaks",
"description" : "Peak calls for EGL-27 Combined (GFP ChIP) recalled peaks w peaks",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "EGL-27 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false
+ }
+ }
+ ],
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7820_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "__EGL-27 Combined (GFP ChIP) recalled peaks peaks"
- },
- {
- "name" : "LIN-13 Combined (GFP ChIP) recalled peaks w peaks",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_LIN-13_GFP_emb_combined_WS220.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7820_details.gff.bb",
"locationType" : "UriLocation"
}
- },
+ }
+ },
+ {
"description" : " Identification of Transcription Factor LIN-13::GFP Binding Regions in Embryos. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_LIN-13 Combined (GFP ChIP) recalled peaks w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "LIN-13 Combined (GFP ChIP) recalled peaks w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_LIN-13_GFP_emb_combined_WS220.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
"type" : "LinearWiggleDisplay",
@@ -27298,32 +26689,32 @@
]
},
{
- "name" : "__LIN-13 Combined (GFP ChIP) recalled peaks peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10179_details.gff.bb"
- }
- },
"description" : "Peak calls for LIN-13 Combined (GFP ChIP) recalled peaks w peaks",
+ "name" : "__LIN-13 Combined (GFP ChIP) recalled peaks peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_LIN-13 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10179_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
"displayId" : "LIN-13 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"height" : 6,
"showDescriptions" : false
},
@@ -27332,16 +26723,22 @@
]
},
{
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 129.528529573466,
+ "displayId" : "MDL-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
+ "minScore" : 0
+ }
+ ],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_MDL-1_GFP_L1_combined_WS220.bw"
- }
+ },
+ "type" : "BigWigAdapter"
},
- "name" : "MDL-1 Combined (GFP ChIP) recalled peaks w peaks",
- "description" : "Identification of Transcription Factor MDL-1::GFP Binding Regions in L1. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -27350,144 +26747,150 @@
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
+ "name" : "MDL-1 Combined (GFP ChIP) recalled peaks w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_MDL-1 Combined (GFP ChIP) recalled peaks w peaks",
- "displays" : [
- {
- "type" : "LinearWiggleDisplay",
- "maxScore" : 129.528529573466,
- "minScore" : 0,
- "displayId" : "MDL-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay"
- }
- ]
+ "description" : "Identification of Transcription Factor MDL-1::GFP Binding Regions in L1. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "name" : "__MDL-1 Combined (GFP ChIP) recalled peaks peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8048_details.gff.bb"
- }
- },
- "description" : "Peak calls for MDL-1 Combined (GFP ChIP) recalled peaks w peaks",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_MDL-1 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Peak calls for MDL-1 Combined (GFP ChIP) recalled peaks w peaks",
+ "name" : "__MDL-1 Combined (GFP ChIP) recalled peaks peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_MDL-1 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
"color1" : "deeppink",
"showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false,
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "MDL-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8048_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
- "displays" : [
- {
- "type" : "LinearWiggleDisplay",
- "maxScore" : 63.885069054761,
- "minScore" : 0,
- "displayId" : "MEP-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay"
- }
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_MEP-1 Combined (GFP ChIP) recalled peaks w peaks",
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : "Identification of Transcription Factor MEP-1::GFP Binding Regions in Embryos. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_MEP-1 Combined (GFP ChIP) recalled peaks w peaks",
"name" : "MEP-1 Combined (GFP ChIP) recalled peaks w peaks",
+ "description" : "Identification of Transcription Factor MEP-1::GFP Binding Regions in Embryos. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "displayId" : "MEP-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 63.885069054761
+ }
+ ],
"adapter" : {
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_MEP-1_GFP_emb_combined_WS220.bw",
"locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack"
+ }
},
{
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP (Peak Recall)"
+ ],
+ "name" : "__MEP-1 Combined (GFP ChIP) recalled peaks peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_MEP-1 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
+ "description" : "Peak calls for MEP-1 Combined (GFP ChIP) recalled peaks w peaks",
"displays" : [
{
"renderer" : {
+ "showLabels" : false,
"height" : 6,
"showDescriptions" : false,
"color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "MEP-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks"
+ "displayId" : "MEP-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_MEP-1 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP (Peak Recall)"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : "Peak calls for MEP-1 Combined (GFP ChIP) recalled peaks w peaks",
- "name" : "__MEP-1 Combined (GFP ChIP) recalled peaks peaks",
"adapter" : {
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8043_details.gff.bb",
"locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack"
+ }
},
{
"name" : "PES-1 Combined (GFP ChIP) recalled peaks w peaks",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PES1_GFP_L4_combined_WS220.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "description" : " Identification of Transcription Factor PES-1::GFP Binding Regions in L4. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_PES-1 Combined (GFP ChIP) recalled peaks w peaks",
+ "description" : " Identification of Transcription Factor PES-1::GFP Binding Regions in L4. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PES1_GFP_L4_combined_WS220.bw",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
"type" : "LinearWiggleDisplay",
- "maxScore" : 77.4447456704205,
+ "displayId" : "PES-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
"minScore" : 0,
- "displayId" : "PES-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay"
+ "maxScore" : 77.4447456704205
}
]
},
{
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "PES-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
+ "showDescriptions" : false,
+ "height" : 6,
+ "showLabels" : false
+ }
+ }
+ ],
"adapter" : {
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8040_details.gff.bb",
@@ -27495,8 +26898,7 @@
},
"type" : "BigBedAdapter"
},
- "name" : "__PES-1 Combined (GFP ChIP) recalled peaks peaks",
- "description" : "Peak calls for PES-1 Combined (GFP ChIP) recalled peaks w peaks",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -27505,75 +26907,29 @@
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
+ "name" : "__PES-1 Combined (GFP ChIP) recalled peaks peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_PES-1 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
- "displays" : [
- {
- "displayId" : "PES-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks",
- "renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay"
- }
- ]
+ "description" : "Peak calls for PES-1 Combined (GFP ChIP) recalled peaks w peaks"
},
{
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP (Peak Recall)"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_PQM-1 Combined (GFP ChIP) recalled peaks w peaks",
- "displays" : [
- {
- "displayId" : "PQM-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
- "minScore" : 0,
- "maxScore" : 58.6622629749755,
- "type" : "LinearWiggleDisplay"
- }
- ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PQM-1_GFP_L3_combined_WS220.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "PQM-1 Combined (GFP ChIP) recalled peaks w peaks",
- "description" : "Identification of Transcription Factor PQM-1::GFP Binding Regions in L3. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
- "description" : "Peak calls for PQM-1 Combined (GFP ChIP) recalled peaks w peaks",
- "name" : "__PQM-1 Combined (GFP ChIP) recalled peaks peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8017_details.gff.bb"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PQM-1_GFP_L3_combined_WS220.bw"
}
},
"displays" : [
{
- "displayId" : "PQM-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks",
- "renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay"
+ "maxScore" : 58.6622629749755,
+ "minScore" : 0,
+ "displayId" : "PQM-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_PQM-1 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
+ "description" : "Identification of Transcription Factor PQM-1::GFP Binding Regions in L3. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_PQM-1 Combined (GFP ChIP) recalled peaks w peaks",
+ "name" : "PQM-1 Combined (GFP ChIP) recalled peaks w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -27581,61 +26937,86 @@
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
+ ],
+ "type" : "QuantitativeTrack"
},
{
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_UNC-130 Combined (GFP ChIP) recalled peaks w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_PQM-1 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
+ "name" : "__PQM-1 Combined (GFP ChIP) recalled peaks peaks",
+ "description" : "Peak calls for PQM-1 Combined (GFP ChIP) recalled peaks w peaks",
"displays" : [
{
- "type" : "LinearWiggleDisplay",
- "maxScore" : 61.2915800678,
- "minScore" : 0,
- "displayId" : "UNC-130 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay"
+ "displayId" : "PQM-1 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "height" : 6,
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "color1" : "deeppink"
+ },
+ "type" : "LinearBasicDisplay"
}
],
"adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_UNC-130_GFP_L1_combined_WS220.bw",
- "locationType" : "UriLocation"
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8017_details.gff.bb",
+ "locationType" : "UriLocation"
}
- },
- "type" : "QuantitativeTrack",
- "name" : "UNC-130 Combined (GFP ChIP) recalled peaks w peaks",
- "description" : " Identification of Transcription Factor UNC-130::GFP Binding Regions in L1. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
},
{
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_UNC-130_GFP_L1_combined_WS220.bw",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
- },
- "displayId" : "UNC-130 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks"
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 61.2915800678,
+ "displayId" : "UNC-130 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
+ "minScore" : 0
}
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_UNC-130 Combined (GFP ChIP) recalled peaks w peaks",
+ "name" : "UNC-130 Combined (GFP ChIP) recalled peaks w peaks",
+ "description" : " Identification of Transcription Factor UNC-130::GFP Binding Regions in L1. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
+ ]
+ },
+ {
+ "displays" : [
+ {
+ "displayId" : "UNC-130 Combined (GFP ChIP) recalled peaks w peaks_Transcription Factors_GFP ChIP (Peak Recall)_bigbed_peaks",
+ "renderer" : {
+ "color1" : "deeppink",
+ "showDescriptions" : false,
+ "height" : 6,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
+ }
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_UNC-130 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks",
- "description" : "Peak calls for UNC-130 Combined (GFP ChIP) recalled peaks w peaks",
"adapter" : {
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7997_details.gff.bb",
@@ -27643,32 +27024,42 @@
},
"type" : "BigBedAdapter"
},
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP (Peak Recall)"
+ ],
"type" : "FeatureTrack",
- "name" : "__UNC-130 Combined (GFP ChIP) recalled peaks peaks"
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Peak calls for UNC-130 Combined (GFP ChIP) recalled peaks w peaks",
+ "name" : "__UNC-130 Combined (GFP ChIP) recalled peaks peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_UNC-130 Combined (GFP ChIP) recalled peaks w peaks_bigbed_peaks"
},
{
- "description" : "Identification of Transcription Factor AHA-1::GFP Binding Regions in L4. Synchronized L4 larvae from C. elegans strain OP124 (a transgenic strain engineered to express a gene fusion between aha-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "AHA-1 Combined (GFP ChIP), AHA-1_L4 w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/15207.bw",
"locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ }
},
"displays" : [
{
+ "displayId" : "AHA-1 Combined (GFP ChIP)_ AHA-1_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0,
"maxScore" : 50.3078235248767,
- "type" : "LinearWiggleDisplay",
- "displayId" : "AHA-1 Combined (GFP ChIP)_ AHA-1_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_AHA-1 Combined (GFP ChIP)_ AHA-1_L4 w peaks",
+ "name" : "AHA-1 Combined (GFP ChIP), AHA-1_L4 w peaks",
+ "description" : "Identification of Transcription Factor AHA-1::GFP Binding Regions in L4. Synchronized L4 larvae from C. elegans strain OP124 (a transgenic strain engineered to express a gene fusion between aha-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -27676,118 +27067,109 @@
]
},
{
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/15214_details.gff.bb"
- }
- },
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_AHA-1 Combined (GFP ChIP)_ AHA-1_L4 w peaks_bigbed_peaks",
"name" : "__AHA-1 Combined (GFP ChIP), AHA-1_L4 peaks",
"description" : "Peak calls for AHA-1 Combined (GFP ChIP), AHA-1_L4 w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_AHA-1 Combined (GFP ChIP)_ AHA-1_L4 w peaks_bigbed_peaks",
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/15214_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "AHA-1 Combined (GFP ChIP)_ AHA-1_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showLabels" : false,
"height" : 6,
"showDescriptions" : false,
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "displayId" : "AHA-1 Combined (GFP ChIP)_ AHA-1_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "color1" : "deeppink"
+ }
}
]
},
{
- "displays" : [
- {
- "displayId" : "AHA-1 Combined (GFP ChIP)_ AHA-1_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 24.4372563611185
- }
- ],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_AHA-1 Combined (GFP ChIP)_ AHA-1_L1 w peaks",
+ "name" : "AHA-1 Combined (GFP ChIP), AHA-1_L1 w peaks",
"description" : "Identification of Transcription Factor AHA-1::GFP Binding Regions in L4. Synchronized L4 larvae from C. elegans strain OP124 (a transgenic strain engineered to express a gene fusion between aha-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "displayId" : "AHA-1 Combined (GFP ChIP)_ AHA-1_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 24.4372563611185
+ }
+ ],
"adapter" : {
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18770.bw",
"locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "AHA-1 Combined (GFP ChIP), AHA-1_L1 w peaks"
+ }
},
{
+ "description" : "Peak calls for AHA-1 Combined (GFP ChIP), AHA-1_L1 w peaks",
+ "name" : "__AHA-1 Combined (GFP ChIP), AHA-1_L1 peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_AHA-1 Combined (GFP ChIP)_ AHA-1_L1 w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18777_details.gff.bb"
+ }
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "AHA-1 Combined (GFP ChIP)_ AHA-1_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
"color1" : "deeppink",
+ "showLabels" : false,
"showDescriptions" : false,
"height" : 6
- },
- "type" : "LinearBasicDisplay"
- }
- ],
- "name" : "__AHA-1 Combined (GFP ChIP), AHA-1_L1 peaks",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18777_details.gff.bb",
- "locationType" : "UriLocation"
+ }
}
- },
- "type" : "FeatureTrack",
- "description" : "Peak calls for AHA-1 Combined (GFP ChIP), AHA-1_L1 w peaks"
+ ]
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ALR-1 Combined (GFP ChIP) w peaks",
"displays" : [
{
- "displayId" : "ALR-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"maxScore" : 80.5518783819215,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
+ "minScore" : 0,
+ "displayId" : "ALR-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
],
"adapter" : {
@@ -27797,181 +27179,199 @@
},
"type" : "BigWigAdapter"
},
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
"type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : " Identification of Transcription Factor ALR-1::GFP Binding Regions in L2. General Description Synchronized L2 larvae from C. elegans strain OP200 (a transgenic strain engineered to express a gene fusion between alr-1 and GFP) were treated with the cross-linking reagent formaldehyde.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"name" : "ALR-1 Combined (GFP ChIP) w peaks",
- "description" : " Identification of Transcription Factor ALR-1::GFP Binding Regions in L2. General Description Synchronized L2 larvae from C. elegans strain OP200 (a transgenic strain engineered to express a gene fusion between alr-1 and GFP) were treated with the cross-linking reagent formaldehyde.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ALR-1 Combined (GFP ChIP) w peaks"
},
{
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Peak calls for ALR-1 Combined (GFP ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ALR-1 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "name" : "__ALR-1 Combined (GFP ChIP) peaks",
"displays" : [
{
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showLabels" : false,
"showDescriptions" : false,
"height" : 6,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "deeppink"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "ALR-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "displayId" : "ALR-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ALR-1 Combined (GFP ChIP) w peaks_bigbed_peaks",
- "description" : "Peak calls for ALR-1 Combined (GFP ChIP) w peaks",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7896_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "__ALR-1 Combined (GFP ChIP) peaks"
+ }
+ }
},
{
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_AMA-1 Combined (GFP ChIP) w peaks",
+ "name" : "AMA-1 Combined (GFP ChIP) w peaks",
+ "description" : " Identification of AMA-1::GFP Binding Regions in L4 Young Adult (Snyder project,Snyder subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "displays" : [
- {
- "type" : "LinearWiggleDisplay",
- "maxScore" : 224.944881042423,
- "minScore" : 0,
- "displayId" : "AMA-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
- ],
- "name" : "AMA-1 Combined (GFP ChIP) w peaks",
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_AMA1_GFP_L4YA_combined_WS220.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_AMA1_GFP_L4YA_combined_WS220.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "description" : " Identification of AMA-1::GFP Binding Regions in L4 Young Adult (Snyder project,Snyder subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "displayId" : "AMA-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 224.944881042423
+ }
+ ]
},
{
"displays" : [
{
"displayId" : "AMA-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
"showLabels" : false,
- "color1" : "deeppink"
+ "height" : 6,
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
},
"type" : "LinearBasicDisplay"
}
],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4206_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
+ },
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_AMA-1 Combined (GFP ChIP) w peaks_bigbed_peaks",
- "description" : "Peak calls for AMA-1 Combined (GFP ChIP) w peaks",
+ "name" : "__AMA-1 Combined (GFP ChIP) peaks",
+ "description" : "Peak calls for AMA-1 Combined (GFP ChIP) w peaks"
+ },
+ {
"adapter" : {
- "bigBedLocation" : {
+ "bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4206_details.gff.bb"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/14844.bw"
},
- "type" : "BigBedAdapter"
+ "type" : "BigWigAdapter"
},
- "type" : "FeatureTrack",
- "name" : "__AMA-1 Combined (GFP ChIP) peaks"
- },
- {
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_C16A3.4 Combined (GFP ChIP) w peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
- "displayId" : "C16A3.4 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay",
- "maxScore" : 136.115750504335,
- "minScore" : 0
+ "minScore" : 0,
+ "displayId" : "C16A3.4 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 136.115750504335
}
],
"name" : "C16A3.4 Combined (GFP ChIP) w peaks",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/14844.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_C16A3.4 Combined (GFP ChIP) w peaks",
+ "description" : " Identification of Transcription Factor C16A3.4::GFP Binding Regions in L1. Synchronized L1 larvae from C. elegans strain OP345 (a transgenic strain engineered to express a gene fusion between C16A3.4 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"type" : "QuantitativeTrack",
- "description" : " Identification of Transcription Factor C16A3.4::GFP Binding Regions in L1. Synchronized L1 larvae from C. elegans strain OP345 (a transgenic strain engineered to express a gene fusion between C16A3.4 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ]
},
{
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/14851_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "displayId" : "C16A3.4 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
+ "showLabels" : false,
"showDescriptions" : false,
- "height" : 6
- }
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "C16A3.4 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "Peak calls for C16A3.4 Combined (GFP ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_C16A3.4 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "name" : "__C16A3.4 Combined (GFP ChIP) peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_C16A3.4 Combined (GFP ChIP) w peaks_bigbed_peaks",
- "description" : "Peak calls for C16A3.4 Combined (GFP ChIP) w peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/14851_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "__C16A3.4 Combined (GFP ChIP) peaks"
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack"
},
{
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18373.bw",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "maxScore" : 219.878666459523,
+ "minScore" : 0,
+ "displayId" : "C34F6.9 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"name" : "C34F6.9 Combined (GFP ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_C34F6.9 Combined (GFP ChIP) w peaks",
"description" : " Identification of Transcription Factor C34F6.9::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP324 (a transgenic strain engineered to express a gene fusion between C34F6.9 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -27979,31 +27379,33 @@
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_C34F6.9 Combined (GFP ChIP) w peaks",
- "displays" : [
- {
- "displayId" : "C34F6.9 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 219.878666459523
- }
]
},
{
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18378_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "C34F6.9 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
"color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
+ "showDescriptions" : false,
"height" : 6,
- "showDescriptions" : false
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "C34F6.9 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
],
+ "name" : "__C34F6.9 Combined (GFP ChIP) peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_C34F6.9 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "description" : "Peak calls for C34F6.9 Combined (GFP ChIP) w peaks",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -28011,92 +27413,154 @@
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_C34F6.9 Combined (GFP ChIP) w peaks_bigbed_peaks",
- "description" : "Peak calls for C34F6.9 Combined (GFP ChIP) w peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18378_details.gff.bb",
- "locationType" : "UriLocation"
- }
- },
- "name" : "__C34F6.9 Combined (GFP ChIP) peaks"
+ ]
},
{
- "displays" : [
- {
- "displayId" : "CEH-16 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
- "maxScore" : 52.4482323912284,
- "type" : "LinearWiggleDisplay"
- }
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-16 Combined (GFP ChIP) w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"description" : " Identification of Transcription Factor CEH-16::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP82 (a transgenic strain engineered to express a gene fusion between ceh-16 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"name" : "CEH-16 Combined (GFP ChIP) w peaks",
- "type" : "QuantitativeTrack",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-16 Combined (GFP ChIP) w peaks",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "minScore" : 0,
+ "displayId" : "CEH-16 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 52.4482323912284
+ }
+ ],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18783.bw"
- }
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18783.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
}
},
{
- "description" : "Peak calls for CEH-16 Combined (GFP ChIP) w peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
+ "description" : "Peak calls for CEH-16 Combined (GFP ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-16 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "name" : "__CEH-16 Combined (GFP ChIP) peaks",
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6
+ },
+ "displayId" : "CEH-16 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18793_details.gff.bb"
},
"type" : "BigBedAdapter"
- },
- "name" : "__CEH-16 Combined (GFP ChIP) peaks",
+ }
+ },
+ {
"displays" : [
{
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 6,
- "showDescriptions" : false
- },
- "displayId" : "CEH-16 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "maxScore" : 253.577233875179,
+ "displayId" : "CEH-28 Combined (GFP ChIP)_ CEH-28_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18047.bw",
+ "locationType" : "UriLocation"
}
+ },
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
+ "description" : " Snyder_CEH-28_GFP_L4. Synchronized L4 larvae from C. elegans strain OP241 (a transgenic strain engineered to express a gene fusion between ceh-38 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-28 Combined (GFP ChIP)_ CEH-28_L3 w peaks",
+ "name" : "CEH-28 Combined (GFP ChIP), CEH-28_L3 w peaks"
+ },
+ {
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-16 Combined (GFP ChIP) w peaks_bigbed_peaks"
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-28 Combined (GFP ChIP)_ CEH-28_L3 w peaks_bigbed_peaks",
+ "name" : "__CEH-28 Combined (GFP ChIP), CEH-28_L3 peaks",
+ "description" : "Peak calls for CEH-28 Combined (GFP ChIP), CEH-28_L3 w peaks",
+ "displays" : [
+ {
+ "renderer" : {
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "CEH-28 Combined (GFP ChIP)_ CEH-28_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18076_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ }
},
{
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18027.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "displayId" : "CEH-28 Combined (GFP ChIP)_ CEH-28_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "maxScore" : 253.577233875179,
"type" : "LinearWiggleDisplay",
+ "maxScore" : 152.505241769774,
+ "displayId" : "CEH-28 Combined (GFP ChIP)_ CEH-28_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-28 Combined (GFP ChIP)_ CEH-28_L3 w peaks",
+ "name" : "CEH-28 Combined (GFP ChIP), CEH-28_L4 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-28 Combined (GFP ChIP)_ CEH-28_L4 w peaks",
+ "description" : " Snyder_CEH-28_GFP_L4. Synchronized L4 larvae from C. elegans strain OP241 (a transgenic strain engineered to express a gene fusion between ceh-38 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -28104,197 +27568,188 @@
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "description" : " Snyder_CEH-28_GFP_L4. Synchronized L4 larvae from C. elegans strain OP241 (a transgenic strain engineered to express a gene fusion between ceh-38 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "CEH-28 Combined (GFP ChIP), CEH-28_L3 w peaks",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18047.bw",
- "locationType" : "UriLocation"
- }
- },
- "type" : "QuantitativeTrack"
+ ]
},
{
- "description" : "Peak calls for CEH-28 Combined (GFP ChIP), CEH-28_L3 w peaks",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18076_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "__CEH-28 Combined (GFP ChIP), CEH-28_L3 peaks",
"displays" : [
{
- "displayId" : "CEH-28 Combined (GFP ChIP)_ CEH-28_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay",
+ "displayId" : "CEH-28 Combined (GFP ChIP)_ CEH-28_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer",
"height" : 6,
+ "showDescriptions" : false,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "deeppink"
}
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-28 Combined (GFP ChIP)_ CEH-28_L3 w peaks_bigbed_peaks"
- },
- {
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-28 Combined (GFP ChIP)_ CEH-28_L4 w peaks",
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18049_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "Peak calls for CEH-28 Combined (GFP ChIP), CEH-28_L4 w peaks",
+ "name" : "__CEH-28 Combined (GFP ChIP), CEH-28_L4 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-28 Combined (GFP ChIP)_ CEH-28_L4 w peaks_bigbed_peaks"
+ },
+ {
"displays" : [
{
- "displayId" : "CEH-28 Combined (GFP ChIP)_ CEH-28_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "maxScore" : 152.505241769774,
+ "displayId" : "CEH-39 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 151.297264632628,
"type" : "LinearWiggleDisplay"
}
],
- "name" : "CEH-28 Combined (GFP ChIP), CEH-28_L4 w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18027.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18655.bw",
+ "locationType" : "UriLocation"
}
},
- "description" : " Snyder_CEH-28_GFP_L4. Synchronized L4 larvae from C. elegans strain OP241 (a transgenic strain engineered to express a gene fusion between ceh-38 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-39 Combined (GFP ChIP) w peaks",
+ "name" : "CEH-39 Combined (GFP ChIP) w peaks",
+ "description" : " Identification of Transcription Factor CEH-39::GFP Binding Regions in EMB. Synchronized embyros from C. elegans strain OP169 (a transgenic strain engineered to express a gene fusion between ceh-39 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
"displays" : [
{
- "displayId" : "CEH-28 Combined (GFP ChIP)_ CEH-28_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showLabels" : false,
"height" : 6,
"showDescriptions" : false,
- "color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
- }
+ "color1" : "deeppink"
+ },
+ "displayId" : "CEH-39 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-28 Combined (GFP ChIP)_ CEH-28_L4 w peaks_bigbed_peaks",
- "description" : "Peak calls for CEH-28 Combined (GFP ChIP), CEH-28_L4 w peaks",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18049_details.gff.bb",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18665_details.gff.bb"
},
"type" : "BigBedAdapter"
},
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
"type" : "FeatureTrack",
- "name" : "__CEH-28 Combined (GFP ChIP), CEH-28_L4 peaks"
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Peak calls for CEH-39 Combined (GFP ChIP) w peaks",
+ "name" : "__CEH-39 Combined (GFP ChIP) peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-39 Combined (GFP ChIP) w peaks_bigbed_peaks"
},
{
- "description" : " Identification of Transcription Factor CEH-39::GFP Binding Regions in EMB. Synchronized embyros from C. elegans strain OP169 (a transgenic strain engineered to express a gene fusion between ceh-39 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18655.bw",
- "locationType" : "UriLocation"
- }
- },
- "name" : "CEH-39 Combined (GFP ChIP) w peaks",
"displays" : [
{
- "displayId" : "CEH-39 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 46.27065750062,
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 151.297264632628
+ "displayId" : "CEH-14 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
],
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_CEH-14_GFP_L2_combined_WS220.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-39 Combined (GFP ChIP) w peaks"
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-14 Combined (GFP ChIP) w peaks",
+ "name" : "CEH-14 Combined (GFP ChIP) w peaks",
+ "description" : " Identification of Transcription Factor CEH-14::GFP Binding Regions in L2 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-39 Combined (GFP ChIP) w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "CEH-14 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
+ "showLabels" : false,
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
- },
- "displayId" : "CEH-39 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "name" : "__CEH-39 Combined (GFP ChIP) peaks",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18665_details.gff.bb"
- }
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4169_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
},
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
- "description" : "Peak calls for CEH-39 Combined (GFP ChIP) w peaks"
+ "description" : "Peak calls for CEH-14 Combined (GFP ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-14 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "name" : "__CEH-14 Combined (GFP ChIP) peaks"
},
{
- "description" : " Identification of Transcription Factor CEH-14::GFP Binding Regions in L2 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"adapter" : {
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_CEH-14_GFP_L2_combined_WS220.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_BLMP-1_GFP_L1_combined_WS220.bw",
"locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "name" : "CEH-14 Combined (GFP ChIP) w peaks",
"displays" : [
{
- "type" : "LinearWiggleDisplay",
- "maxScore" : 46.27065750062,
"minScore" : 0,
- "displayId" : "CEH-14 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "displayId" : "BLMP-1 Combined (GFP ChIP)_ BLMP1_GFP_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 397.978084466755,
+ "type" : "LinearWiggleDisplay"
}
],
+ "name" : "BLMP-1 Combined (GFP ChIP), BLMP1_GFP_L1 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_BLMP-1 Combined (GFP ChIP)_ BLMP1_GFP_L1 w peaks",
+ "description" : "Identification of Transcription Factor BLMP-1::GFP Binding Regions in L1. Synchronized fed L1 larvae from C. elegans strain OP109 (a transgenic strain engineered to express a gene fusion between blmp-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -28302,20 +27757,30 @@
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-14 Combined (GFP ChIP) w peaks"
+ ]
},
{
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "BLMP-1 Combined (GFP ChIP)_ BLMP1_GFP_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "renderer" : {
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ }
+ }
+ ],
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4169_details.gff.bb"
- }
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/5418_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
},
"type" : "FeatureTrack",
- "name" : "__CEH-14 Combined (GFP ChIP) peaks",
- "description" : "Peak calls for CEH-14 Combined (GFP ChIP) w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -28324,217 +27789,132 @@
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-14 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "name" : "__BLMP-1 Combined (GFP ChIP), BLMP1_GFP_L1 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_BLMP-1 Combined (GFP ChIP)_ BLMP1_GFP_L1 w peaks_bigbed_peaks",
+ "description" : "Peak calls for BLMP-1 Combined (GFP ChIP), BLMP1_GFP_L1 w peaks"
+ },
+ {
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18246.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "displayId" : "CEH-14 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "type" : "LinearBasicDisplay"
+ "minScore" : 37.7283447218828,
+ "displayId" : "BLMP-1 Combined (GFP ChIP)_ BLMP-1_Emb_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 82.371347642069,
+ "type" : "LinearWiggleDisplay"
}
- ]
- },
- {
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_BLMP-1 Combined (GFP ChIP)_ BLMP1_GFP_L1 w peaks",
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_BLMP-1 Combined (GFP ChIP)_ BLMP-1_Emb",
+ "name" : "BLMP-1 Combined (GFP ChIP), BLMP-1_Emb",
+ "description" : "Identification of Transcription Factor BLMP-1::GFP Binding Regions in L1. Synchronized fed L1 larvae from C. elegans strain OP109 (a transgenic strain engineered to express a gene fusion between blmp-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "displays" : [
- {
- "minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 397.978084466755,
- "displayId" : "BLMP-1 Combined (GFP ChIP)_ BLMP1_GFP_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
- ],
- "name" : "BLMP-1 Combined (GFP ChIP), BLMP1_GFP_L1 w peaks",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_BLMP-1_GFP_L1_combined_WS220.bw"
- }
- },
- "type" : "QuantitativeTrack",
- "description" : "Identification of Transcription Factor BLMP-1::GFP Binding Regions in L1. Synchronized fed L1 larvae from C. elegans strain OP109 (a transgenic strain engineered to express a gene fusion between blmp-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ ]
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_BLMP-1 Combined (GFP ChIP)_ BLMP1_GFP_L1 w peaks_bigbed_peaks",
+ "description" : "Identification of Transcription Factor CEH-30::GFP Binding Regions in Late Embyros (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "CEH-30 Combined (GFP ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-30 Combined (GFP ChIP) w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "displays" : [
- {
- "renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "BLMP-1 Combined (GFP ChIP)_ BLMP1_GFP_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
- }
- ],
- "name" : "__BLMP-1 Combined (GFP ChIP), BLMP1_GFP_L1 peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/5418_details.gff.bb",
- "locationType" : "UriLocation"
- }
- },
- "description" : "Peak calls for BLMP-1 Combined (GFP ChIP), BLMP1_GFP_L1 w peaks"
- },
- {
- "name" : "BLMP-1 Combined (GFP ChIP), BLMP-1_Emb",
- "type" : "QuantitativeTrack",
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18246.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_CEH-30_GFP_lemb_combined_WS220.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
- "description" : "Identification of Transcription Factor BLMP-1::GFP Binding Regions in L1. Synchronized fed L1 larvae from C. elegans strain OP109 (a transgenic strain engineered to express a gene fusion between blmp-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_BLMP-1 Combined (GFP ChIP)_ BLMP-1_Emb",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
- "minScore" : 37.7283447218828,
"type" : "LinearWiggleDisplay",
- "maxScore" : 82.371347642069,
- "displayId" : "BLMP-1 Combined (GFP ChIP)_ BLMP-1_Emb_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "maxScore" : 74.304448578503,
+ "minScore" : 0,
+ "displayId" : "CEH-30 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
}
]
},
{
- "displays" : [
- {
- "displayId" : "CEH-30 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "maxScore" : 74.304448578503,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
- }
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-30 Combined (GFP ChIP) w peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : "Identification of Transcription Factor CEH-30::GFP Binding Regions in Late Embyros (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "CEH-30 Combined (GFP ChIP) w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_CEH-30_GFP_lemb_combined_WS220.bw"
- }
- }
- },
- {
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/5438_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
+ "displayId" : "CEH-30 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
+ "color1" : "deeppink",
+ "showLabels" : false,
"showDescriptions" : false,
"height" : 6,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "CEH-30 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
],
+ "description" : "Peak calls for CEH-30 Combined (GFP ChIP) w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_CEH-30 Combined (GFP ChIP) w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "__CEH-30 Combined (GFP ChIP) peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "description" : "Peak calls for CEH-30 Combined (GFP ChIP) w peaks",
- "name" : "__CEH-30 Combined (GFP ChIP) peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/5438_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- }
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack"
},
{
- "name" : "DAF-16 Combined (GFP ChIP) w peaks",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_DAF16_GFP_L4YA_combined_WS220.bw",
- "locationType" : "UriLocation"
- }
- },
- "type" : "QuantitativeTrack",
"description" : "Identification of Transcription Factor DAF-16::GFP Binding Regions in L4 Young Adult (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "DAF-16 Combined (GFP ChIP) w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DAF-16 Combined (GFP ChIP) w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_DAF16_GFP_L4YA_combined_WS220.bw",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "displayId" : "DAF-16 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay",
"minScore" : 0,
- "maxScore" : 127.117494465201,
- "type" : "LinearWiggleDisplay"
+ "displayId" : "DAF-16 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 127.117494465201
}
]
},
{
- "name" : "__DAF-16 Combined (GFP ChIP) peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4294_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "description" : "Peak calls for DAF-16 Combined (GFP ChIP) w peaks",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DAF-16 Combined (GFP ChIP) w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -28543,136 +27923,137 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "description" : "Peak calls for DAF-16 Combined (GFP ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DAF-16 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "name" : "__DAF-16 Combined (GFP ChIP) peaks",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
"color1" : "deeppink",
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
+ "showLabels" : false
},
- "type" : "LinearBasicDisplay",
"displayId" : "DAF-16 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4294_details.gff.bb"
+ }
+ }
},
{
- "description" : " Identification of Transcription Factor EGL-27::GFP Binding Regions in L1 ( project, subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "EGL-27 Combined (GFP ChIP), EGL27 L2 w peaks",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/20469.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
"displays" : [
{
"displayId" : "EGL-27 Combined (GFP ChIP)_ EGL27 L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
"maxScore" : 65.901674609707,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
+ "type" : "LinearWiggleDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EGL-27 Combined (GFP ChIP)_ EGL27 L2 w peaks",
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/20469.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ]
+ "name" : "EGL-27 Combined (GFP ChIP), EGL27 L2 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EGL-27 Combined (GFP ChIP)_ EGL27 L2 w peaks",
+ "description" : " Identification of Transcription Factor EGL-27::GFP Binding Regions in L1 ( project, subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "EGL-27 Combined (GFP ChIP)_ EGL27 L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
+ "color1" : "deeppink",
+ "showLabels" : false,
"height" : 6,
"showDescriptions" : false,
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "type" : "LinearBasicDisplay"
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EGL-27 Combined (GFP ChIP)_ EGL27 L2 w peaks_bigbed_peaks",
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/20474_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : "Peak calls for EGL-27 Combined (GFP ChIP), EGL27 L2 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EGL-27 Combined (GFP ChIP)_ EGL27 L2 w peaks_bigbed_peaks",
"name" : "__EGL-27 Combined (GFP ChIP), EGL27 L2 peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/20474_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- }
+ "description" : "Peak calls for EGL-27 Combined (GFP ChIP), EGL27 L2 w peaks"
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EGL-27 Combined (GFP ChIP)_ EGL27 L1 w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EGL-27 Combined (GFP ChIP)_ EGL27 L1 w peaks",
+ "name" : "EGL-27 Combined (GFP ChIP), EGL27 L1 w peaks",
+ "description" : " Identification of Transcription Factor EGL-27::GFP Binding Regions in L1 ( project, subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "minScore" : 0,
"maxScore" : 51.8171481175507,
- "type" : "LinearWiggleDisplay",
- "displayId" : "EGL-27 Combined (GFP ChIP)_ EGL27 L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "minScore" : 0,
+ "displayId" : "EGL-27 Combined (GFP ChIP)_ EGL27 L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
],
- "name" : "EGL-27 Combined (GFP ChIP), EGL27 L1 w peaks",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_EGL-27_GFP_L1_combined_WS220.bw"
}
- },
- "type" : "QuantitativeTrack",
- "description" : " Identification of Transcription Factor EGL-27::GFP Binding Regions in L1 ( project, subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
},
{
"displays" : [
{
- "displayId" : "EGL-27 Combined (GFP ChIP)_ EGL27 L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
"height" : 6,
"showDescriptions" : false,
+ "showLabels" : false,
"color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "EGL-27 Combined (GFP ChIP)_ EGL27 L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EGL-27 Combined (GFP ChIP)_ EGL27 L1 w peaks_bigbed_peaks",
- "description" : "Peak calls for EGL-27 Combined (GFP ChIP), EGL27 L1 w peaks",
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
@@ -28680,8 +28061,18 @@
},
"type" : "BigBedAdapter"
},
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
- "name" : "__EGL-27 Combined (GFP ChIP), EGL27 L1 peaks"
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EGL-27 Combined (GFP ChIP)_ EGL27 L1 w peaks_bigbed_peaks",
+ "name" : "__EGL-27 Combined (GFP ChIP), EGL27 L1 peaks",
+ "description" : "Peak calls for EGL-27 Combined (GFP ChIP), EGL27 L1 w peaks"
},
{
"category" : [
@@ -28692,80 +28083,69 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
+ "description" : " Identification of Transcription Factor EGL-5::GFP Binding Regions in L3 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EGL-5 Combined (GFP ChIP) w peaks",
+ "name" : "EGL-5 Combined (GFP ChIP) w peaks",
"displays" : [
{
- "minScore" : 0,
- "maxScore" : 47.1086058678193,
"type" : "LinearWiggleDisplay",
+ "maxScore" : 47.1086058678193,
+ "minScore" : 0,
"displayId" : "EGL-5 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
}
],
- "type" : "QuantitativeTrack",
"adapter" : {
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_EGL5_GFP_L3_combined_WS220.bw",
"locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
- },
- "name" : "EGL-5 Combined (GFP ChIP) w peaks",
- "description" : " Identification of Transcription Factor EGL-5::GFP Binding Regions in L3 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
},
{
- "description" : "Peak calls for EGL-5 Combined (GFP ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EGL-5 Combined (GFP ChIP) w peaks_bigbed_peaks",
"name" : "__EGL-5 Combined (GFP ChIP) peaks",
+ "description" : "Peak calls for EGL-5 Combined (GFP ChIP) w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7983_details.gff.bb",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigBedAdapter"
},
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "EGL-5 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
+ "height" : 6,
+ "showDescriptions" : false,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "EGL-5 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_EGL-5 Combined (GFP ChIP) w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
]
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ELT-3 Combined (GFP ChIP)_ ELT3 EMB",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
"displays" : [
{
- "type" : "LinearWiggleDisplay",
"maxScore" : 64.7892308271845,
"minScore" : 29.4271461729709,
- "displayId" : "ELT-3 Combined (GFP ChIP)_ ELT3 EMB_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "displayId" : "ELT-3 Combined (GFP ChIP)_ ELT3 EMB_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
],
- "name" : "ELT-3 Combined (GFP ChIP), ELT3 EMB",
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -28773,9 +28153,24 @@
"locationType" : "UriLocation"
}
},
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "name" : "ELT-3 Combined (GFP ChIP), ELT3 EMB",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ELT-3 Combined (GFP ChIP)_ ELT3 EMB",
"description" : " Identification of Transcription Factor ELT-3::GFP Binding Regions in L3. Details Snyder_ELT-3_GFP_L3 (Snyder project, Snyder subgroup) Synchronized L3 larvae from C. elegans strain OP75 (a transgenic strain engineered to express a gene fusion between elt-3 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
+ "name" : "ELT-3 Combined (GFP ChIP), ELT3 L3 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ELT-3 Combined (GFP ChIP)_ ELT3 L3 w peaks",
+ "description" : " Identification of Transcription Factor ELT-3::GFP Binding Regions in L3. Details Snyder_ELT-3_GFP_L3 (Snyder project, Snyder subgroup) Synchronized L3 larvae from C. elegans strain OP75 (a transgenic strain engineered to express a gene fusion between elt-3 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -28784,38 +28179,24 @@
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ELT-3 Combined (GFP ChIP)_ ELT3 L3 w peaks",
- "displays" : [
- {
- "displayId" : "ELT-3 Combined (GFP ChIP)_ ELT3 L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "maxScore" : 47.4994912650819,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
- }
- ],
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/20327.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/20327.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "name" : "ELT-3 Combined (GFP ChIP), ELT3 L3 w peaks",
- "description" : " Identification of Transcription Factor ELT-3::GFP Binding Regions in L3. Details Snyder_ELT-3_GFP_L3 (Snyder project, Snyder subgroup) Synchronized L3 larvae from C. elegans strain OP75 (a transgenic strain engineered to express a gene fusion between elt-3 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 47.4994912650819,
+ "displayId" : "ELT-3 Combined (GFP ChIP)_ ELT3 L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0
+ }
+ ]
},
{
- "name" : "__ELT-3 Combined (GFP ChIP), ELT3 L3 peaks",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/20330_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
"type" : "FeatureTrack",
- "description" : "Peak calls for ELT-3 Combined (GFP ChIP), ELT3 L3 w peaks",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ELT-3 Combined (GFP ChIP)_ ELT3 L3 w peaks_bigbed_peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -28824,30 +28205,50 @@
"Transcription Factors",
"GFP ChIP"
],
+ "name" : "__ELT-3 Combined (GFP ChIP), ELT3 L3 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ELT-3 Combined (GFP ChIP)_ ELT3 L3 w peaks_bigbed_peaks",
+ "description" : "Peak calls for ELT-3 Combined (GFP ChIP), ELT3 L3 w peaks",
"displays" : [
{
- "displayId" : "ELT-3 Combined (GFP ChIP)_ ELT3 L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink",
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
- }
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "ELT-3 Combined (GFP ChIP)_ ELT3 L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/20330_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_ELT-3_GFP_L1_combined_WS220.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
+ "maxScore" : 81.5937803987925,
"displayId" : "ELT-3 Combined (GFP ChIP)_ ELT3 L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "maxScore" : 81.5937803987925,
"type" : "LinearWiggleDisplay"
}
],
+ "name" : "ELT-3 Combined (GFP ChIP), ELT3 L1 w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ELT-3 Combined (GFP ChIP)_ ELT3 L1 w peaks",
+ "description" : " Identification of Transcription Factor ELT-3::GFP Binding Regions in L3. Details Snyder_ELT-3_GFP_L3 (Snyder project, Snyder subgroup) Synchronized L3 larvae from C. elegans strain OP75 (a transgenic strain engineered to express a gene fusion between elt-3 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -28855,53 +28256,47 @@
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "description" : " Identification of Transcription Factor ELT-3::GFP Binding Regions in L3. Details Snyder_ELT-3_GFP_L3 (Snyder project, Snyder subgroup) Synchronized L3 larvae from C. elegans strain OP75 (a transgenic strain engineered to express a gene fusion between elt-3 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "ELT-3 Combined (GFP ChIP), ELT3 L1 w peaks",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_ELT-3_GFP_L1_combined_WS220.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack"
+ ]
},
{
- "displays" : [
- {
- "renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "ELT-3 Combined (GFP ChIP)_ ELT3 L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
- }
- ],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ELT-3 Combined (GFP ChIP)_ ELT3 L1 w peaks_bigbed_peaks",
+ "name" : "__ELT-3 Combined (GFP ChIP), ELT3 L1 peaks",
"description" : "Peak calls for ELT-3 Combined (GFP ChIP), ELT3 L1 w peaks",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "ELT-3 Combined (GFP ChIP)_ ELT3 L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "height" : 6,
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "color1" : "deeppink"
+ }
+ }
+ ],
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/5408_details.gff.bb",
"locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "__ELT-3 Combined (GFP ChIP), ELT3 L1 peaks"
+ },
+ "type" : "BigBedAdapter"
+ }
},
{
+ "name" : "HLH-1 Combined (GFP ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HLH-1 Combined (GFP ChIP) w peaks",
+ "description" : "Identification of Transcription Factor HLH-1::GFP Binding Regions in Embryos (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -28910,15 +28305,6 @@
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HLH-1 Combined (GFP ChIP) w peaks",
- "displays" : [
- {
- "minScore" : 0,
- "maxScore" : 79.5190577603035,
- "type" : "LinearWiggleDisplay",
- "displayId" : "HLH-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
- ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -28926,53 +28312,55 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_HLH-1_GFP_emb_combined_WS220.bw"
}
},
- "type" : "QuantitativeTrack",
- "name" : "HLH-1 Combined (GFP ChIP) w peaks",
- "description" : "Identification of Transcription Factor HLH-1::GFP Binding Regions in Embryos (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "displays" : [
+ {
+ "minScore" : 0,
+ "displayId" : "HLH-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 79.5190577603035,
+ "type" : "LinearWiggleDisplay"
+ }
+ ]
},
{
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HLH-1 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "name" : "__HLH-1 Combined (GFP ChIP) peaks",
+ "description" : "Peak calls for HLH-1 Combined (GFP ChIP) w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HLH-1 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4315_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
- "displayId" : "HLH-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
+ "color1" : "deeppink",
"height" : 6,
"showDescriptions" : false,
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
},
+ "displayId" : "HLH-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay"
}
- ],
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4315_details.gff.bb",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "__HLH-1 Combined (GFP ChIP) peaks",
- "description" : "Peak calls for HLH-1 Combined (GFP ChIP) w peaks"
+ ]
},
{
- "description" : " Identification of Transcription Factor LIN-13::GFP Binding Regions in Embryos (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "LIN-13 Combined (GFP ChIP), LIN-13_L2 w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/17875.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/17875.bw",
+ "locationType" : "UriLocation"
}
},
"displays" : [
@@ -28983,19 +28371,20 @@
"displayId" : "LIN-13 Combined (GFP ChIP)_ LIN-13_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
}
],
+ "description" : " Identification of Transcription Factor LIN-13::GFP Binding Regions in Embryos (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "LIN-13 Combined (GFP ChIP), LIN-13_L2 w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-13 Combined (GFP ChIP)_ LIN-13_L2 w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
+ ],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
]
},
{
- "name" : "__LIN-13 Combined (GFP ChIP), LIN-13_L2 peaks",
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
@@ -29003,71 +28392,22 @@
},
"type" : "BigBedAdapter"
},
- "description" : "Peak calls for LIN-13 Combined (GFP ChIP), LIN-13_L2 w peaks",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-13 Combined (GFP ChIP)_ LIN-13_L2 w peaks_bigbed_peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
- "displayId" : "LIN-13 Combined (GFP ChIP)_ LIN-13_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay",
+ "displayId" : "LIN-13 Combined (GFP ChIP)_ LIN-13_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
"type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "deeppink",
"showDescriptions" : false,
- "height" : 6
+ "height" : 6,
+ "color1" : "deeppink"
}
}
- ]
- },
- {
- "displays" : [
- {
- "displayId" : "LIN-13 Combined (GFP ChIP)_ LIN-13_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 120.180363589631,
- "minScore" : 0
- }
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-13 Combined (GFP ChIP)_ LIN-13_L1 w peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
],
- "description" : " Identification of Transcription Factor LIN-13::GFP Binding Regions in Embryos (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "LIN-13 Combined (GFP ChIP), LIN-13_L1 w peaks",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/17843.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack"
- },
- {
- "name" : "__LIN-13 Combined (GFP ChIP), LIN-13_L1 peaks",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/17881_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Peak calls for LIN-13 Combined (GFP ChIP), LIN-13_L1 w peaks",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-13 Combined (GFP ChIP)_ LIN-13_L1 w peaks_bigbed_peaks",
+ "description" : "Peak calls for LIN-13 Combined (GFP ChIP), LIN-13_L2 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-13 Combined (GFP ChIP)_ LIN-13_L2 w peaks_bigbed_peaks",
+ "name" : "__LIN-13 Combined (GFP ChIP), LIN-13_L2 peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -29076,39 +28416,27 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 6,
- "showDescriptions" : false
- },
- "displayId" : "LIN-13 Combined (GFP ChIP)_ LIN-13_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
- }
- ]
+ "type" : "FeatureTrack"
},
{
- "description" : " Identification of Transcription Factor LIN-13::GFP Binding Regions in Embryos (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"adapter" : {
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/17915.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/17843.bw",
"locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "name" : "LIN-13 Combined (GFP ChIP), LIN-13_L4 w peaks",
"displays" : [
{
- "displayId" : "LIN-13 Combined (GFP ChIP)_ LIN-13_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "maxScore" : 115.346221144958,
+ "displayId" : "LIN-13 Combined (GFP ChIP)_ LIN-13_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 120.180363589631,
"type" : "LinearWiggleDisplay"
}
],
+ "description" : " Identification of Transcription Factor LIN-13::GFP Binding Regions in Embryos (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-13 Combined (GFP ChIP)_ LIN-13_L1 w peaks",
+ "name" : "LIN-13 Combined (GFP ChIP), LIN-13_L1 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -29117,116 +28445,158 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-13 Combined (GFP ChIP)_ LIN-13_L4 w peaks"
+ "type" : "QuantitativeTrack"
},
{
- "description" : "Peak calls for LIN-13 Combined (GFP ChIP), LIN-13_L4 w peaks",
- "name" : "__LIN-13 Combined (GFP ChIP), LIN-13_L4 peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/17937_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
"displays" : [
{
- "displayId" : "LIN-13 Combined (GFP ChIP)_ LIN-13_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "displayId" : "LIN-13 Combined (GFP ChIP)_ LIN-13_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
"showDescriptions" : false,
- "height" : 6
+ "height" : 6,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
},
"type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-13 Combined (GFP ChIP)_ LIN-13_L4 w peaks_bigbed_peaks",
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/17881_details.gff.bb"
+ }
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
+ ],
+ "description" : "Peak calls for LIN-13 Combined (GFP ChIP), LIN-13_L1 w peaks",
+ "name" : "__LIN-13 Combined (GFP ChIP), LIN-13_L1 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-13 Combined (GFP ChIP)_ LIN-13_L1 w peaks_bigbed_peaks"
},
{
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-13 Combined (GFP ChIP)_ LIN-13_L4 w peaks",
+ "name" : "LIN-13 Combined (GFP ChIP), LIN-13_L4 w peaks",
"description" : " Identification of Transcription Factor LIN-13::GFP Binding Regions in Embryos (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "LIN-13 Combined (GFP ChIP), LIN13_GFP_emb w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_LIN-13_GFP_emb_combined_WS220.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/17915.bw",
"locationType" : "UriLocation"
}
},
- "type" : "QuantitativeTrack",
"displays" : [
{
- "displayId" : "LIN-13 Combined (GFP ChIP)_ LIN13_GFP_emb w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay",
- "maxScore" : 84.5613963705775,
- "minScore" : 0
+ "maxScore" : 115.346221144958,
+ "minScore" : 0,
+ "displayId" : "LIN-13 Combined (GFP ChIP)_ LIN-13_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ }
+ ]
+ },
+ {
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "LIN-13 Combined (GFP ChIP)_ LIN-13_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "renderer" : {
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-13 Combined (GFP ChIP)_ LIN13_GFP_emb w peaks",
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/17937_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ]
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-13 Combined (GFP ChIP)_ LIN-13_L4 w peaks_bigbed_peaks",
+ "name" : "__LIN-13 Combined (GFP ChIP), LIN-13_L4 peaks",
+ "description" : "Peak calls for LIN-13 Combined (GFP ChIP), LIN-13_L4 w peaks"
},
{
+ "displays" : [
+ {
+ "maxScore" : 84.5613963705775,
+ "minScore" : 0,
+ "displayId" : "LIN-13 Combined (GFP ChIP)_ LIN13_GFP_emb w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_LIN-13_GFP_emb_combined_WS220.bw"
+ }
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-13 Combined (GFP ChIP)_ LIN13_GFP_emb w peaks_bigbed_peaks",
+ "description" : " Identification of Transcription Factor LIN-13::GFP Binding Regions in Embryos (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "LIN-13 Combined (GFP ChIP), LIN13_GFP_emb w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-13 Combined (GFP ChIP)_ LIN13_GFP_emb w peaks"
+ },
+ {
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/5417_details.gff.bb"
+ }
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "LIN-13 Combined (GFP ChIP)_ LIN13_GFP_emb w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "LIN-13 Combined (GFP ChIP)_ LIN13_GFP_emb w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/5417_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
+ "description" : "Peak calls for LIN-13 Combined (GFP ChIP), LIN13_GFP_emb w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-13 Combined (GFP ChIP)_ LIN13_GFP_emb w peaks_bigbed_peaks",
"name" : "__LIN-13 Combined (GFP ChIP), LIN13_GFP_emb peaks",
- "description" : "Peak calls for LIN-13 Combined (GFP ChIP), LIN13_GFP_emb w peaks"
- },
- {
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_LIN-39-GFP_L3_combined_WS220.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "LIN-39 Combined (GFP ChIP), LIN39_L3_GFP w peaks",
- "description" : " Identification of Transcription Factor LIN-39::GFP Binding Regions in L3 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -29235,20 +28605,50 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-39 Combined (GFP ChIP)_ LIN39_L3_GFP w peaks",
+ "type" : "FeatureTrack"
+ },
+ {
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_LIN-39-GFP_L3_combined_WS220.bw"
+ }
+ },
"displays" : [
{
- "minScore" : 0,
- "maxScore" : 79.9724096516235,
"type" : "LinearWiggleDisplay",
- "displayId" : "LIN-39 Combined (GFP ChIP)_ LIN39_L3_GFP w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "minScore" : 0,
+ "displayId" : "LIN-39 Combined (GFP ChIP)_ LIN39_L3_GFP w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 79.9724096516235
}
+ ],
+ "name" : "LIN-39 Combined (GFP ChIP), LIN39_L3_GFP w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-39 Combined (GFP ChIP)_ LIN39_L3_GFP w peaks",
+ "description" : " Identification of Transcription Factor LIN-39::GFP Binding Regions in L3 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
]
},
{
- "description" : "Peak calls for LIN-39 Combined (GFP ChIP), LIN39_L3_GFP w peaks",
"name" : "__LIN-39 Combined (GFP ChIP), LIN39_L3_GFP peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-39 Combined (GFP ChIP)_ LIN39_L3_GFP w peaks_bigbed_peaks",
+ "description" : "Peak calls for LIN-39 Combined (GFP ChIP), LIN39_L3_GFP w peaks",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
@@ -29260,34 +28660,20 @@
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
"color1" : "deeppink",
"showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false,
"type" : "SvgFeatureRenderer"
},
"displayId" : "LIN-39 Combined (GFP ChIP)_ LIN39_L3_GFP w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-39 Combined (GFP ChIP)_ LIN39_L3_GFP w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
]
},
{
- "displays" : [
- {
- "displayId" : "LIN-39 Combined (GFP ChIP)_ LIN-39_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
- "maxScore" : 114.511331583459,
- "type" : "LinearWiggleDisplay"
- }
- ],
+ "description" : " Identification of Transcription Factor LIN-39::GFP Binding Regions in L3 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-39 Combined (GFP ChIP)_ LIN-39_L1 w peaks",
+ "name" : "LIN-39 Combined (GFP ChIP), LIN-39_L1 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -29296,43 +28682,37 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-39 Combined (GFP ChIP)_ LIN-39_L1 w peaks",
- "description" : " Identification of Transcription Factor LIN-39::GFP Binding Regions in L3 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"type" : "QuantitativeTrack",
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18261.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18261.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
- "name" : "LIN-39 Combined (GFP ChIP), LIN-39_L1 w peaks"
+ "displays" : [
+ {
+ "maxScore" : 114.511331583459,
+ "minScore" : 0,
+ "displayId" : "LIN-39 Combined (GFP ChIP)_ LIN-39_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
+ }
+ ]
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-39 Combined (GFP ChIP)_ LIN-39_L1 w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
"displays" : [
{
- "displayId" : "LIN-39 Combined (GFP ChIP)_ LIN-39_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "showDescriptions" : false,
+ "color1" : "deeppink",
"height" : 6,
+ "showDescriptions" : false,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
+ "type" : "SvgFeatureRenderer"
},
+ "displayId" : "LIN-39 Combined (GFP ChIP)_ LIN-39_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay"
}
],
- "name" : "__LIN-39 Combined (GFP ChIP), LIN-39_L1 peaks",
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18283_details.gff.bb",
@@ -29340,154 +28720,147 @@
},
"type" : "BigBedAdapter"
},
- "description" : "Peak calls for LIN-39 Combined (GFP ChIP), LIN-39_L1 w peaks"
- },
- {
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-39 Combined (GFP ChIP)_ LIN-39_L4 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-39 Combined (GFP ChIP)_ LIN-39_L1 w peaks_bigbed_peaks",
+ "name" : "__LIN-39 Combined (GFP ChIP), LIN-39_L1 peaks",
+ "description" : "Peak calls for LIN-39 Combined (GFP ChIP), LIN-39_L1 w peaks"
+ },
+ {
"displays" : [
{
- "minScore" : 0,
"type" : "LinearWiggleDisplay",
"maxScore" : 72.992971500427,
- "displayId" : "LIN-39 Combined (GFP ChIP)_ LIN-39_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "displayId" : "LIN-39 Combined (GFP ChIP)_ LIN-39_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0
}
],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18338.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18338.bw"
+ }
},
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-39 Combined (GFP ChIP)_ LIN-39_L4 w peaks",
"name" : "LIN-39 Combined (GFP ChIP), LIN-39_L4 w peaks",
"description" : " Identification of Transcription Factor LIN-39::GFP Binding Regions in L3 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-39 Combined (GFP ChIP)_ LIN-39_L4 w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "Peak calls for LIN-39 Combined (GFP ChIP), LIN-39_L4 w peaks",
+ "name" : "__LIN-39 Combined (GFP ChIP), LIN-39_L4 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-39 Combined (GFP ChIP)_ LIN-39_L4 w peaks_bigbed_peaks",
"displays" : [
{
"displayId" : "LIN-39 Combined (GFP ChIP)_ LIN-39_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"showDescriptions" : false,
"height" : 6,
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
"color1" : "deeppink"
- }
+ },
+ "type" : "LinearBasicDisplay"
}
],
- "name" : "__LIN-39 Combined (GFP ChIP), LIN-39_L4 peaks",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18357_details.gff.bb",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "description" : "Peak calls for LIN-39 Combined (GFP ChIP), LIN-39_L4 w peaks"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18357_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ }
},
{
- "displays" : [
- {
- "displayId" : "LIN-39 Combined (GFP ChIP)_ LIN-39_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
- "maxScore" : 86.6547866971845,
- "type" : "LinearWiggleDisplay"
- }
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-39 Combined (GFP ChIP)_ LIN-39_L2 w peaks",
"description" : " Identification of Transcription Factor LIN-39::GFP Binding Regions in L3 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "LIN-39 Combined (GFP ChIP), LIN-39_L2 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-39 Combined (GFP ChIP)_ LIN-39_L2 w peaks",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "minScore" : 0,
+ "displayId" : "LIN-39 Combined (GFP ChIP)_ LIN-39_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 86.6547866971845
+ }
+ ],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18183.bw",
"locationType" : "UriLocation"
- }
- },
- "type" : "QuantitativeTrack",
- "name" : "LIN-39 Combined (GFP ChIP), LIN-39_L2 w peaks"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18210_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
- "name" : "__LIN-39 Combined (GFP ChIP), LIN-39_L2 peaks",
- "description" : "Peak calls for LIN-39 Combined (GFP ChIP), LIN-39_L2 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-39 Combined (GFP ChIP)_ LIN-39_L2 w peaks_bigbed_peaks",
+ "name" : "__LIN-39 Combined (GFP ChIP), LIN-39_L2 peaks",
+ "description" : "Peak calls for LIN-39 Combined (GFP ChIP), LIN-39_L2 w peaks",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "deeppink",
"showDescriptions" : false,
- "height" : 6
+ "height" : 6,
+ "showLabels" : false,
+ "color1" : "deeppink"
},
- "type" : "LinearBasicDisplay",
"displayId" : "LIN-39 Combined (GFP ChIP)_ LIN-39_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
- ]
- },
- {
- "description" : " Identification of Transcription Factor MAB-5::GFP Binding Regions in L3 (Snyder project,Snyder subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "MAB-5 Combined (GFP ChIP), MAB-5_EMB w peaks",
- "type" : "QuantitativeTrack",
+ ],
"adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18635.bw",
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18210_details.gff.bb",
"locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "displays" : [
- {
- "displayId" : "MAB-5 Combined (GFP ChIP)_ MAB-5_EMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 53.2735070597855,
- "minScore" : 0
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_MAB-5 Combined (GFP ChIP)_ MAB-5_EMB w peaks",
+ }
+ },
+ {
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -29495,9 +28868,28 @@
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ]
+ ],
+ "name" : "MAB-5 Combined (GFP ChIP), MAB-5_EMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_MAB-5 Combined (GFP ChIP)_ MAB-5_EMB w peaks",
+ "description" : " Identification of Transcription Factor MAB-5::GFP Binding Regions in L3 (Snyder project,Snyder subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 53.2735070597855,
+ "displayId" : "MAB-5 Combined (GFP ChIP)_ MAB-5_EMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0
+ }
+ ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18635.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -29506,151 +28898,150 @@
"Transcription Factors",
"GFP ChIP"
],
+ "name" : "__MAB-5 Combined (GFP ChIP), MAB-5_EMB peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_MAB-5 Combined (GFP ChIP)_ MAB-5_EMB w peaks_bigbed_peaks",
+ "description" : "Peak calls for MAB-5 Combined (GFP ChIP), MAB-5_EMB w peaks",
"displays" : [
{
+ "displayId" : "MAB-5 Combined (GFP ChIP)_ MAB-5_EMB w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "height" : 6,
+ "showDescriptions" : false
},
- "type" : "LinearBasicDisplay",
- "displayId" : "MAB-5 Combined (GFP ChIP)_ MAB-5_EMB w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18652_details.gff.bb",
"locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "__MAB-5 Combined (GFP ChIP), MAB-5_EMB peaks",
- "description" : "Peak calls for MAB-5 Combined (GFP ChIP), MAB-5_EMB w peaks"
+ }
+ }
},
{
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"description" : " Identification of Transcription Factor MAB-5::GFP Binding Regions in L3 (Snyder project,Snyder subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"name" : "MAB-5 Combined (GFP ChIP), MAB-5_L2 w peaks",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18826.bw",
- "locationType" : "UriLocation"
- }
- },
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_MAB-5 Combined (GFP ChIP)_ MAB-5_L2 w peaks",
"displays" : [
{
"type" : "LinearWiggleDisplay",
"maxScore" : 58.5765359206545,
- "minScore" : 0,
- "displayId" : "MAB-5 Combined (GFP ChIP)_ MAB-5_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "displayId" : "MAB-5 Combined (GFP ChIP)_ MAB-5_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_MAB-5 Combined (GFP ChIP)_ MAB-5_L2 w peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ]
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18826.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
+ "displays" : [
+ {
+ "displayId" : "MAB-5 Combined (GFP ChIP)_ MAB-5_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "renderer" : {
+ "height" : 6,
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18834_details.gff.bb"
- }
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "name" : "__MAB-5 Combined (GFP ChIP), MAB-5_L2 peaks",
- "description" : "Peak calls for MAB-5 Combined (GFP ChIP), MAB-5_L2 w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_MAB-5 Combined (GFP ChIP)_ MAB-5_L2 w peaks_bigbed_peaks",
- "displays" : [
- {
- "displayId" : "MAB-5 Combined (GFP ChIP)_ MAB-5_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
- },
- "type" : "LinearBasicDisplay"
- }
- ]
+ "name" : "__MAB-5 Combined (GFP ChIP), MAB-5_L2 peaks",
+ "description" : "Peak calls for MAB-5 Combined (GFP ChIP), MAB-5_L2 w peaks"
},
{
- "name" : "MAB-5 Combined (GFP ChIP), MAB5_L3_GFP w peaks",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_MAB5_GFP_L3_combined_WS220.bw",
- "locationType" : "UriLocation"
- }
- },
"description" : " Identification of Transcription Factor MAB-5::GFP Binding Regions in L3 (Snyder project,Snyder subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "MAB-5 Combined (GFP ChIP), MAB5_L3_GFP w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_MAB-5 Combined (GFP ChIP)_ MAB5_L3_GFP w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_MAB5_GFP_L3_combined_WS220.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "displayId" : "MAB-5 Combined (GFP ChIP)_ MAB5_L3_GFP w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
"type" : "LinearWiggleDisplay",
- "maxScore" : 60.3547276894595
+ "maxScore" : 60.3547276894595,
+ "displayId" : "MAB-5 Combined (GFP ChIP)_ MAB5_L3_GFP w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0
}
]
},
{
- "description" : "Peak calls for MAB-5 Combined (GFP ChIP), MAB5_L3_GFP w peaks",
- "name" : "__MAB-5 Combined (GFP ChIP), MAB5_L3_GFP peaks",
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4279_details.gff.bb"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4279_details.gff.bb",
+ "locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
"displays" : [
{
"renderer" : {
- "color1" : "deeppink",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"height" : 6,
- "showDescriptions" : false
+ "showDescriptions" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "MAB-5 Combined (GFP ChIP)_ MAB5_L3_GFP w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "displayId" : "MAB-5 Combined (GFP ChIP)_ MAB5_L3_GFP w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_MAB-5 Combined (GFP ChIP)_ MAB5_L3_GFP w peaks_bigbed_peaks",
+ "name" : "__MAB-5 Combined (GFP ChIP), MAB5_L3_GFP peaks",
+ "description" : "Peak calls for MAB-5 Combined (GFP ChIP), MAB5_L3_GFP w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -29658,99 +29049,98 @@
]
},
{
- "description" : "Identification of Transcription Factor MDL-1::GFP Binding Regions in L1 (Snyder project,Snyder subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "MDL-1 Combined (GFP ChIP)",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_MDL-1_GFP_L1_combined_WS220.bw",
- "locationType" : "UriLocation"
- }
- },
"displays" : [
{
- "displayId" : "MDL-1 Combined (GFP ChIP)_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 48.6069147592438,
"maxScore" : 129.528529573466,
+ "minScore" : 48.6069147592438,
+ "displayId" : "MDL-1 Combined (GFP ChIP)_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_MDL-1 Combined (GFP ChIP)",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_MDL-1_GFP_L1_combined_WS220.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ]
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "description" : "Identification of Transcription Factor MDL-1::GFP Binding Regions in L1 (Snyder project,Snyder subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_MDL-1 Combined (GFP ChIP)",
+ "name" : "MDL-1 Combined (GFP ChIP)"
},
{
- "displays" : [
- {
- "displayId" : "MEP-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 63.885069054761,
- "minScore" : 0
- }
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "MEP-1 Combined (GFP ChIP) w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_MEP-1 Combined (GFP ChIP) w peaks",
"description" : "Identification of Transcription Factor MEP-1::GFP Binding Regions in Embryos (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "minScore" : 0,
+ "displayId" : "MEP-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 63.885069054761,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_MEP-1_GFP_emb_combined_WS220.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_MEP-1_GFP_emb_combined_WS220.bw"
},
"type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "MEP-1 Combined (GFP ChIP) w peaks"
+ }
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_MEP-1 Combined (GFP ChIP) w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "MEP-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "deeppink",
"showDescriptions" : false,
- "height" : 6
+ "height" : 6,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "MEP-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
],
- "name" : "__MEP-1 Combined (GFP ChIP) peaks",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/5396_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/5396_details.gff.bb"
+ }
},
- "description" : "Peak calls for MEP-1 Combined (GFP ChIP) w peaks"
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Peak calls for MEP-1 Combined (GFP ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_MEP-1 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "name" : "__MEP-1 Combined (GFP ChIP) peaks"
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-6.v2 Combined (GFP ChIP) w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -29759,62 +29149,73 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
+ "description" : "Identification of Transcription Factor NHR-6::GFP Binding Regions in L2 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-6.v2 Combined (GFP ChIP) w peaks",
+ "name" : "NHR-6.v2 Combined (GFP ChIP) w peaks",
"displays" : [
{
- "minScore" : 0,
"type" : "LinearWiggleDisplay",
- "maxScore" : 155.459083742589,
- "displayId" : "NHR-6.v2 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "displayId" : "NHR-6.v2 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 155.459083742589
}
],
- "name" : "NHR-6.v2 Combined (GFP ChIP) w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_NHR-6v2_GFP_L2_combined_WS220.bw"
}
- },
- "description" : "Identification of Transcription Factor NHR-6::GFP Binding Regions in L2 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
},
{
- "displays" : [
- {
- "renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "NHR-6.v2 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
- }
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "Peak calls for NHR-6.v2 Combined (GFP ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-6.v2 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "name" : "__NHR-6.v2 Combined (GFP ChIP) peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-6.v2 Combined (GFP ChIP) w peaks_bigbed_peaks",
- "description" : "Peak calls for NHR-6.v2 Combined (GFP ChIP) w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8321_details.gff.bb",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8321_details.gff.bb"
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "name" : "__NHR-6.v2 Combined (GFP ChIP) peaks"
+ "displays" : [
+ {
+ "displayId" : "NHR-6.v2 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "renderer" : {
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
"description" : " Identification of Transcription Factor PES-1::GFP Binding Regions in L4 (Snyder project,Snyder subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"name" : "PES-1 Combined (GFP ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PES-1 Combined (GFP ChIP) w peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -29822,267 +29223,251 @@
"locationType" : "UriLocation"
}
},
- "type" : "QuantitativeTrack",
"displays" : [
{
- "displayId" : "PES-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 77.4447456704205,
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 77.4447456704205
+ "displayId" : "PES-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PES-1 Combined (GFP ChIP) w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
]
},
{
- "description" : "Peak calls for PES-1 Combined (GFP ChIP) w peaks",
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7971_details.gff.bb",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7971_details.gff.bb"
},
"type" : "BigBedAdapter"
},
- "name" : "__PES-1 Combined (GFP ChIP) peaks",
"displays" : [
{
- "displayId" : "PES-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
"height" : 6,
"showDescriptions" : false,
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
"showLabels" : false
- }
+ },
+ "displayId" : "PES-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
],
+ "description" : "Peak calls for PES-1 Combined (GFP ChIP) w peaks",
+ "name" : "__PES-1 Combined (GFP ChIP) peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PES-1 Combined (GFP ChIP) w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PES-1 Combined (GFP ChIP) w peaks_bigbed_peaks"
+ ]
},
{
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 58.6622629749755,
+ "minScore" : 0,
+ "displayId" : "PQM-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PQM-1_GFP_L3_combined_WS220.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PQM-1_GFP_L3_combined_WS220.bw",
+ "locationType" : "UriLocation"
}
},
- "name" : "PQM-1 Combined (GFP ChIP) w peaks",
- "description" : "Identification of Transcription Factor PQM-1::GFP Binding Regions in L3 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PQM-1 Combined (GFP ChIP) w peaks",
- "displays" : [
- {
- "displayId" : "PQM-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
- "maxScore" : 58.6622629749755,
- "type" : "LinearWiggleDisplay"
- }
- ]
+ "description" : "Identification of Transcription Factor PQM-1::GFP Binding Regions in L3 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "PQM-1 Combined (GFP ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PQM-1 Combined (GFP ChIP) w peaks"
},
{
+ "name" : "__PQM-1 Combined (GFP ChIP) peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PQM-1 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "description" : "Peak calls for PQM-1 Combined (GFP ChIP) w peaks",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/5447_details.gff.bb"
+ }
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "height" : 6,
+ "showDescriptions" : false
},
- "displayId" : "PQM-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "displayId" : "PQM-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
- ],
- "name" : "__PQM-1 Combined (GFP ChIP) peaks",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/5447_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Peak calls for PQM-1 Combined (GFP ChIP) w peaks"
+ ]
},
{
- "name" : "SKN-1 Combined (GFP ChIP), SKN1_L1 w peaks",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_SKN-1_GFP_L1_combined_WS220.bw"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "description" : " Snyder_SKN-1_GFP_L4. Synchronized L4 larvae from C. elegans strain OP342 (a transgenic strain engineered to express a gene fusion between skn-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SKN-1 Combined (GFP ChIP)_ SKN1_L1 w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "minScore" : 0,
+ "displayId" : "SKN-1 Combined (GFP ChIP)_ SKN1_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 192.130600688404
+ }
],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_SKN-1_GFP_L1_combined_WS220.bw",
+ "locationType" : "UriLocation"
+ }
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "displays" : [
- {
- "displayId" : "SKN-1 Combined (GFP ChIP)_ SKN1_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 192.130600688404,
- "minScore" : 0
- }
- ]
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : " Snyder_SKN-1_GFP_L4. Synchronized L4 larvae from C. elegans strain OP342 (a transgenic strain engineered to express a gene fusion between skn-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "SKN-1 Combined (GFP ChIP), SKN1_L1 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SKN-1 Combined (GFP ChIP)_ SKN1_L1 w peaks"
},
{
- "description" : "Peak calls for SKN-1 Combined (GFP ChIP), SKN1_L1 w peaks",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/5423_details.gff.bb"
- },
- "type" : "BigBedAdapter"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/5423_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
},
- "name" : "__SKN-1 Combined (GFP ChIP), SKN1_L1 peaks",
"displays" : [
{
- "displayId" : "SKN-1 Combined (GFP ChIP)_ SKN1_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
+ "showLabels" : false,
"showDescriptions" : false,
"height" : 6
- }
+ },
+ "displayId" : "SKN-1 Combined (GFP ChIP)_ SKN1_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
],
+ "name" : "__SKN-1 Combined (GFP ChIP), SKN1_L1 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SKN-1 Combined (GFP ChIP)_ SKN1_L1 w peaks_bigbed_peaks",
+ "description" : "Peak calls for SKN-1 Combined (GFP ChIP), SKN1_L1 w peaks",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SKN-1 Combined (GFP ChIP)_ SKN1_L1 w peaks_bigbed_peaks"
+ ]
},
{
- "name" : "SKN-1 Combined (GFP ChIP), SKN1_L4 w peaks",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/17890.bw"
- },
- "type" : "BigWigAdapter"
- },
"type" : "QuantitativeTrack",
- "description" : " Snyder_SKN-1_GFP_L4. Synchronized L4 larvae from C. elegans strain OP342 (a transgenic strain engineered to express a gene fusion between skn-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SKN-1 Combined (GFP ChIP)_ SKN1_L4 w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "SKN-1 Combined (GFP ChIP), SKN1_L4 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SKN-1 Combined (GFP ChIP)_ SKN1_L4 w peaks",
+ "description" : " Snyder_SKN-1_GFP_L4. Synchronized L4 larvae from C. elegans strain OP342 (a transgenic strain engineered to express a gene fusion between skn-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "displayId" : "SKN-1 Combined (GFP ChIP)_ SKN1_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay",
"maxScore" : 54.4602587792523,
- "minScore" : 0
+ "minScore" : 0,
+ "displayId" : "SKN-1 Combined (GFP ChIP)_ SKN1_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/17890.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SKN-1 Combined (GFP ChIP)_ SKN1_L4 w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/17913_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
"height" : 6,
"showDescriptions" : false,
- "color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "showLabels" : false
},
- "displayId" : "SKN-1 Combined (GFP ChIP)_ SKN1_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "displayId" : "SKN-1 Combined (GFP ChIP)_ SKN1_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
+ "description" : "Peak calls for SKN-1 Combined (GFP ChIP), SKN1_L4 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SKN-1 Combined (GFP ChIP)_ SKN1_L4 w peaks_bigbed_peaks",
"name" : "__SKN-1 Combined (GFP ChIP), SKN1_L4 peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/17913_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "description" : "Peak calls for SKN-1 Combined (GFP ChIP), SKN1_L4 w peaks"
- },
- {
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack"
+ },
+ {
+ "description" : " Snyder_SKN-1_GFP_L4. Synchronized L4 larvae from C. elegans strain OP342 (a transgenic strain engineered to express a gene fusion between skn-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "SKN-1 Combined (GFP ChIP), SKN1_L2 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SKN-1 Combined (GFP ChIP)_ SKN1_L2 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SKN-1 Combined (GFP ChIP)_ SKN1_L2 w peaks",
- "displays" : [
- {
- "displayId" : "SKN-1 Combined (GFP ChIP)_ SKN1_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 84.582991062196,
- "minScore" : 0
- }
- ],
"type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/20859.bw",
@@ -30090,35 +29475,41 @@
},
"type" : "BigWigAdapter"
},
- "name" : "SKN-1 Combined (GFP ChIP), SKN1_L2 w peaks",
- "description" : " Snyder_SKN-1_GFP_L4. Synchronized L4 larvae from C. elegans strain OP342 (a transgenic strain engineered to express a gene fusion between skn-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "displays" : [
+ {
+ "displayId" : "SKN-1 Combined (GFP ChIP)_ SKN1_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 84.582991062196,
+ "type" : "LinearWiggleDisplay"
+ }
+ ]
},
{
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Peak calls for SKN-1 Combined (GFP ChIP), SKN1_L2 w peaks",
+ "name" : "__SKN-1 Combined (GFP ChIP), SKN1_L2 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SKN-1 Combined (GFP ChIP)_ SKN1_L2 w peaks_bigbed_peaks",
"displays" : [
{
- "displayId" : "SKN-1 Combined (GFP ChIP)_ SKN1_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
"color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
"height" : 6,
- "showDescriptions" : false
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
},
+ "displayId" : "SKN-1 Combined (GFP ChIP)_ SKN1_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SKN-1 Combined (GFP ChIP)_ SKN1_L2 w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "description" : "Peak calls for SKN-1 Combined (GFP ChIP), SKN1_L2 w peaks",
- "name" : "__SKN-1 Combined (GFP ChIP), SKN1_L2 peaks",
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
@@ -30128,95 +29519,95 @@
}
},
{
- "displays" : [
- {
- "type" : "LinearWiggleDisplay",
- "maxScore" : 167.481757609363,
- "minScore" : 0,
- "displayId" : "SKN-1 Combined (GFP ChIP)_ SKN1_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SKN-1 Combined (GFP ChIP)_ SKN1_L3 w peaks",
"description" : " Snyder_SKN-1_GFP_L4. Synchronized L4 larvae from C. elegans strain OP342 (a transgenic strain engineered to express a gene fusion between skn-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "SKN-1 Combined (GFP ChIP), SKN1_L3 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SKN-1 Combined (GFP ChIP)_ SKN1_L3 w peaks",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 167.481757609363,
+ "minScore" : 0,
+ "displayId" : "SKN-1 Combined (GFP ChIP)_ SKN1_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18687.bw"
}
- },
- "type" : "QuantitativeTrack",
- "name" : "SKN-1 Combined (GFP ChIP), SKN1_L3 w peaks"
+ }
},
{
- "displays" : [
- {
- "displayId" : "SKN-1 Combined (GFP ChIP)_ SKN1_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- }
- }
- ],
+ "name" : "__SKN-1 Combined (GFP ChIP), SKN1_L3 peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SKN-1 Combined (GFP ChIP)_ SKN1_L3 w peaks_bigbed_peaks",
+ "description" : "Peak calls for SKN-1 Combined (GFP ChIP), SKN1_L3 w peaks",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : "Peak calls for SKN-1 Combined (GFP ChIP), SKN1_L3 w peaks",
- "name" : "__SKN-1 Combined (GFP ChIP), SKN1_L3 peaks",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18694_details.gff.bb",
- "locationType" : "UriLocation"
- }
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18694_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack"
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false
+ },
+ "displayId" : "SKN-1 Combined (GFP ChIP)_ SKN1_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
- "description" : " Identification of Dosage Compensation Complex Protein DPY-27::GFP Binding Regions in Embryos (Snyder project,Snyder subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "DPY-27 Combined (GFP ChIP) w peaks",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_DPY27_GFP_emb_combined_WS220.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_DPY27_GFP_emb_combined_WS220.bw"
+ }
},
- "type" : "QuantitativeTrack",
"displays" : [
{
+ "minScore" : 0,
"displayId" : "DPY-27 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"maxScore" : 35.6926441979147,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
+ "type" : "LinearWiggleDisplay"
}
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DPY-27 Combined (GFP ChIP) w peaks",
+ "name" : "DPY-27 Combined (GFP ChIP) w peaks",
+ "description" : " Identification of Dosage Compensation Complex Protein DPY-27::GFP Binding Regions in Embryos (Snyder project,Snyder subgroup)We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
]
},
{
@@ -30227,42 +29618,52 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4088_details.gff.bb"
}
},
- "type" : "FeatureTrack",
- "name" : "__DPY-27 Combined (GFP ChIP) peaks",
- "description" : "Peak calls for DPY-27 Combined (GFP ChIP) w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DPY-27 Combined (GFP ChIP) w peaks_bigbed_peaks",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
"height" : 6,
- "showDescriptions" : false
+ "showDescriptions" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
},
"displayId" : "DPY-27 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
+ ],
+ "name" : "__DPY-27 Combined (GFP ChIP) peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DPY-27 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "description" : "Peak calls for DPY-27 Combined (GFP ChIP) w peaks",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
]
},
{
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DVE-1 Combined (GFP ChIP)_ DVE-1_L4 w peaks",
+ "name" : "DVE-1 Combined (GFP ChIP), DVE-1_L4 w peaks",
+ "description" : " Snyder_DVE-1_GFP_L4. Synchronized L4 larvae from C. elegans strain OP398 (a transgenic strain engineered to express a gene fusion between dve-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DVE-1 Combined (GFP ChIP)_ DVE-1_L4 w peaks",
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18096.bw"
+ }
+ },
"displays" : [
{
"type" : "LinearWiggleDisplay",
@@ -30270,20 +29671,22 @@
"minScore" : 0,
"displayId" : "DVE-1 Combined (GFP ChIP)_ DVE-1_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
}
- ],
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18096.bw",
- "locationType" : "UriLocation"
- }
- },
- "name" : "DVE-1 Combined (GFP ChIP), DVE-1_L4 w peaks",
- "description" : " Snyder_DVE-1_GFP_L4. Synchronized L4 larvae from C. elegans strain OP398 (a transgenic strain engineered to express a gene fusion between dve-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ ]
},
{
- "description" : "Peak calls for DVE-1 Combined (GFP ChIP), DVE-1_L4 w peaks",
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
+ "height" : 6,
+ "showDescriptions" : false,
+ "showLabels" : false
+ },
+ "displayId" : "DVE-1 Combined (GFP ChIP)_ DVE-1_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
@@ -30292,133 +29695,111 @@
}
},
"type" : "FeatureTrack",
- "name" : "__DVE-1 Combined (GFP ChIP), DVE-1_L4 peaks",
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "height" : 6,
- "showDescriptions" : false
- },
- "displayId" : "DVE-1 Combined (GFP ChIP)_ DVE-1_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
- }
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DVE-1 Combined (GFP ChIP)_ DVE-1_L4 w peaks_bigbed_peaks"
+ "name" : "__DVE-1 Combined (GFP ChIP), DVE-1_L4 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DVE-1 Combined (GFP ChIP)_ DVE-1_L4 w peaks_bigbed_peaks",
+ "description" : "Peak calls for DVE-1 Combined (GFP ChIP), DVE-1_L4 w peaks"
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DVE-1 Combined (GFP ChIP)_ DVE-1_LEMB w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "description" : " Snyder_DVE-1_GFP_L4. Synchronized L4 larvae from C. elegans strain OP398 (a transgenic strain engineered to express a gene fusion between dve-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DVE-1 Combined (GFP ChIP)_ DVE-1_LEMB w peaks",
+ "name" : "DVE-1 Combined (GFP ChIP), DVE-1_LEMB w peaks",
"displays" : [
{
- "type" : "LinearWiggleDisplay",
"maxScore" : 133.157027843249,
+ "displayId" : "DVE-1 Combined (GFP ChIP)_ DVE-1_LEMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "displayId" : "DVE-1 Combined (GFP ChIP)_ DVE-1_LEMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
],
- "name" : "DVE-1 Combined (GFP ChIP), DVE-1_LEMB w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18197.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "description" : " Snyder_DVE-1_GFP_L4. Synchronized L4 larvae from C. elegans strain OP398 (a transgenic strain engineered to express a gene fusion between dve-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18197.bw"
+ }
+ }
},
{
- "name" : "__DVE-1 Combined (GFP ChIP), DVE-1_LEMB peaks",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18227_details.gff.bb",
"locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ }
},
- "description" : "Peak calls for DVE-1 Combined (GFP ChIP), DVE-1_LEMB w peaks",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DVE-1 Combined (GFP ChIP)_ DVE-1_LEMB w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
"displays" : [
{
"displayId" : "DVE-1 Combined (GFP ChIP)_ DVE-1_LEMB w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
+ "showLabels" : false,
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
+ "type" : "SvgFeatureRenderer"
},
"type" : "LinearBasicDisplay"
}
+ ],
+ "name" : "__DVE-1 Combined (GFP ChIP), DVE-1_LEMB peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_DVE-1 Combined (GFP ChIP)_ DVE-1_LEMB w peaks_bigbed_peaks",
+ "description" : "Peak calls for DVE-1 Combined (GFP ChIP), DVE-1_LEMB w peaks",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
]
},
{
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18589.bw"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "ELT-1 Combined (GFP ChIP), ELT-1_L3 w peaks",
"description" : " Snyder_ELT-1_GFP_L2. Synchronized L2 larvae from C. elegans strain OP354 (a transgenic strain engineered to express a gene fusion between elt-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "ELT-1 Combined (GFP ChIP), ELT-1_L3 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ELT-1 Combined (GFP ChIP)_ ELT-1_L3 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ELT-1 Combined (GFP ChIP)_ ELT-1_L3 w peaks",
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18589.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "minScore" : 0,
"maxScore" : 48.9834793727788,
- "type" : "LinearWiggleDisplay",
- "displayId" : "ELT-1 Combined (GFP ChIP)_ ELT-1_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "displayId" : "ELT-1 Combined (GFP ChIP)_ ELT-1_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
}
]
},
{
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18606_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "__ELT-1 Combined (GFP ChIP), ELT-1_L3 peaks",
- "description" : "Peak calls for ELT-1 Combined (GFP ChIP), ELT-1_L3 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -30427,178 +29808,195 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "description" : "Peak calls for ELT-1 Combined (GFP ChIP), ELT-1_L3 w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ELT-1 Combined (GFP ChIP)_ ELT-1_L3 w peaks_bigbed_peaks",
+ "name" : "__ELT-1 Combined (GFP ChIP), ELT-1_L3 peaks",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
+ "showLabels" : false,
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
+ "type" : "SvgFeatureRenderer"
},
"displayId" : "ELT-1 Combined (GFP ChIP)_ ELT-1_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18606_details.gff.bb"
+ }
+ }
},
{
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/17925.bw"
+ }
+ },
"displays" : [
{
- "displayId" : "ELT-1 Combined (GFP ChIP)_ ELT-1_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
"maxScore" : 50.7276944016709,
- "minScore" : 0
+ "displayId" : "ELT-1 Combined (GFP ChIP)_ ELT-1_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
}
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ELT-1 Combined (GFP ChIP)_ ELT-1_L2 w peaks",
+ "name" : "ELT-1 Combined (GFP ChIP), ELT-1_L2 w peaks",
+ "description" : " Snyder_ELT-1_GFP_L2. Synchronized L2 larvae from C. elegans strain OP354 (a transgenic strain engineered to express a gene fusion between elt-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ELT-1 Combined (GFP ChIP)_ ELT-1_L2 w peaks",
- "description" : " Snyder_ELT-1_GFP_L2. Synchronized L2 larvae from C. elegans strain OP354 (a transgenic strain engineered to express a gene fusion between elt-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/17925.bw"
- }
- },
- "name" : "ELT-1 Combined (GFP ChIP), ELT-1_L2 w peaks"
+ ]
},
{
- "description" : "Peak calls for ELT-1 Combined (GFP ChIP), ELT-1_L2 w peaks",
- "name" : "__ELT-1 Combined (GFP ChIP), ELT-1_L2 peaks",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/17947_details.gff.bb"
- }
- },
- "type" : "FeatureTrack",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "ELT-1 Combined (GFP ChIP)_ ELT-1_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
"color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
+ "showDescriptions" : false,
"height" : 6,
- "showDescriptions" : false
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "ELT-1 Combined (GFP ChIP)_ ELT-1_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ELT-1 Combined (GFP ChIP)_ ELT-1_L2 w peaks_bigbed_peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ]
- },
- {
- "type" : "QuantitativeTrack",
"adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/19760.bw",
- "locationType" : "UriLocation"
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/17947_details.gff.bb"
}
},
- "name" : "F23B12.7 Combined (GFP ChIP)",
- "description" : " Snyder_F23B12.7_GFP_YA. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ELT-1 Combined (GFP ChIP)_ ELT-1_L2 w peaks_bigbed_peaks",
+ "name" : "__ELT-1 Combined (GFP ChIP), ELT-1_L2 peaks",
+ "description" : "Peak calls for ELT-1 Combined (GFP ChIP), ELT-1_L2 w peaks"
+ },
+ {
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "description" : " Snyder_F23B12.7_GFP_YA. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_F23B12.7 Combined (GFP ChIP)",
+ "name" : "F23B12.7 Combined (GFP ChIP)",
"displays" : [
{
- "displayId" : "F23B12.7 Combined (GFP ChIP)_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 23.7434637867189,
"type" : "LinearWiggleDisplay",
- "maxScore" : 54.3877690506632
+ "maxScore" : 54.3877690506632,
+ "displayId" : "F23B12.7 Combined (GFP ChIP)_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 23.7434637867189
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/19760.bw"
+ }
+ }
},
{
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18593.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18593.bw"
}
},
+ "displays" : [
+ {
+ "maxScore" : 120.785643048413,
+ "minScore" : 0,
+ "displayId" : "F23F12.9 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_F23F12.9 Combined (GFP ChIP) w peaks",
"name" : "F23F12.9 Combined (GFP ChIP) w peaks",
"description" : " Identification of Transcription Factor F23F12.9::GFP Binding Regions in Embryos. Synchronized embryos from C. elegans strain OP327 (a transgenic strain engineered to express a gene fusion between F23F12.9 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_F23F12.9 Combined (GFP ChIP) w peaks",
- "displays" : [
- {
- "displayId" : "F23F12.9 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
- "maxScore" : 120.785643048413,
- "type" : "LinearWiggleDisplay"
- }
]
},
{
- "description" : "Peak calls for F23F12.9 Combined (GFP ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_F23F12.9 Combined (GFP ChIP) w peaks_bigbed_peaks",
"name" : "__F23F12.9 Combined (GFP ChIP) peaks",
+ "description" : "Peak calls for F23F12.9 Combined (GFP ChIP) w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18605_details.gff.bb"
- },
- "type" : "BigBedAdapter"
+ }
},
"displays" : [
{
"displayId" : "F23F12.9 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
"height" : 6,
- "showDescriptions" : false
- }
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_F23F12.9 Combined (GFP ChIP) w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
]
},
{
- "name" : "FKH-10 Combined (GFP ChIP), FKH-10_LEMB w peaks",
+ "displays" : [
+ {
+ "maxScore" : 98.7373158191035,
+ "minScore" : 0,
+ "displayId" : "FKH-10 Combined (GFP ChIP)_ FKH-10_LEMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
@@ -30606,124 +30004,125 @@
},
"type" : "BigWigAdapter"
},
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
- "description" : " Snyder_FKH-10_GFP_LEMB. Synchronized late embryos from C. elegans strain OP337 (a transgenic strain engineered to express a gene fusion between fkh-10 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_FKH-10 Combined (GFP ChIP)_ FKH-10_LEMB w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_FKH-10 Combined (GFP ChIP)_ FKH-10_LEMB w peaks",
+ "name" : "FKH-10 Combined (GFP ChIP), FKH-10_LEMB w peaks",
+ "description" : " Snyder_FKH-10_GFP_LEMB. Synchronized late embryos from C. elegans strain OP337 (a transgenic strain engineered to express a gene fusion between fkh-10 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ },
+ {
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "displays" : [
- {
- "type" : "LinearWiggleDisplay",
- "maxScore" : 98.7373158191035,
- "minScore" : 0,
- "displayId" : "FKH-10 Combined (GFP ChIP)_ FKH-10_LEMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
- ]
- },
- {
- "description" : "Peak calls for FKH-10 Combined (GFP ChIP), FKH-10_LEMB w peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
"name" : "__FKH-10 Combined (GFP ChIP), FKH-10_LEMB peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18332_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_FKH-10 Combined (GFP ChIP)_ FKH-10_LEMB w peaks_bigbed_peaks",
+ "description" : "Peak calls for FKH-10 Combined (GFP ChIP), FKH-10_LEMB w peaks",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "FKH-10 Combined (GFP ChIP)_ FKH-10_LEMB w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay"
+ "showDescriptions" : false,
+ "height" : 6,
+ "color1" : "deeppink"
+ }
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_FKH-10 Combined (GFP ChIP)_ FKH-10_LEMB w peaks_bigbed_peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ]
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18332_details.gff.bb"
+ }
+ }
},
{
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18239.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "minScore" : 0,
- "maxScore" : 87.7026035160005,
"type" : "LinearWiggleDisplay",
- "displayId" : "FKH-10 Combined (GFP ChIP)_ FKH-10_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "maxScore" : 87.7026035160005,
+ "displayId" : "FKH-10 Combined (GFP ChIP)_ FKH-10_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0
}
],
+ "description" : " Snyder_FKH-10_GFP_LEMB. Synchronized late embryos from C. elegans strain OP337 (a transgenic strain engineered to express a gene fusion between fkh-10 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "FKH-10 Combined (GFP ChIP), FKH-10_L4 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_FKH-10 Combined (GFP ChIP)_ FKH-10_L4 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_FKH-10 Combined (GFP ChIP)_ FKH-10_L4 w peaks",
- "description" : " Snyder_FKH-10_GFP_LEMB. Synchronized late embryos from C. elegans strain OP337 (a transgenic strain engineered to express a gene fusion between fkh-10 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18239.bw"
- },
- "type" : "BigWigAdapter"
- },
- "name" : "FKH-10 Combined (GFP ChIP), FKH-10_L4 w peaks"
+ ]
},
{
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18259_details.gff.bb",
"locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ }
},
- "type" : "FeatureTrack",
- "name" : "__FKH-10 Combined (GFP ChIP), FKH-10_L4 peaks",
- "description" : "Peak calls for FKH-10 Combined (GFP ChIP), FKH-10_L4 w peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_FKH-10 Combined (GFP ChIP)_ FKH-10_L4 w peaks_bigbed_peaks",
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
"color1" : "deeppink",
+ "showLabels" : false,
"showDescriptions" : false,
"height" : 6
},
- "displayId" : "FKH-10 Combined (GFP ChIP)_ FKH-10_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "displayId" : "FKH-10 Combined (GFP ChIP)_ FKH-10_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
+ ],
+ "description" : "Peak calls for FKH-10 Combined (GFP ChIP), FKH-10_L4 w peaks",
+ "name" : "__FKH-10 Combined (GFP ChIP), FKH-10_L4 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_FKH-10 Combined (GFP ChIP)_ FKH-10_L4 w peaks_bigbed_peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
]
},
{
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "displayId" : "FKH-2 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 31.7373292105291
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -30731,9 +30130,6 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18752.bw"
}
},
- "type" : "QuantitativeTrack",
- "name" : "FKH-2 Combined (GFP ChIP) w peaks",
- "description" : " Identification of Transcription Factor FKH-2::GFP Binding Regions in L3. Details Synchronized L3 larvae from C. elegans strain OP185 (a transgenic strain engineered to express a gene fusion between fkh-2 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -30742,60 +30138,53 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
+ "description" : " Identification of Transcription Factor FKH-2::GFP Binding Regions in L3. Details Synchronized L3 larvae from C. elegans strain OP185 (a transgenic strain engineered to express a gene fusion between fkh-2 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_FKH-2 Combined (GFP ChIP) w peaks",
- "displays" : [
- {
- "type" : "LinearWiggleDisplay",
- "maxScore" : 31.7373292105291,
- "minScore" : 0,
- "displayId" : "FKH-2 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
- ]
+ "name" : "FKH-2 Combined (GFP ChIP) w peaks"
},
{
"name" : "__FKH-2 Combined (GFP ChIP) peaks",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18767_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Peak calls for FKH-2 Combined (GFP ChIP) w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_FKH-2 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "description" : "Peak calls for FKH-2 Combined (GFP ChIP) w peaks",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18767_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
"height" : 6,
- "showDescriptions" : false
+ "showLabels" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
},
"displayId" : "FKH-2 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
]
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HAM-1 Combined (GFP ChIP)_ HAM-1_L4 w peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18622.bw",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
"type" : "LinearWiggleDisplay",
@@ -30804,157 +30193,183 @@
"displayId" : "HAM-1 Combined (GFP ChIP)_ HAM-1_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
}
],
+ "description" : " Identification of Transcription Factor HAM-1::GFP Binding Regions in L1. Details Synchronized fed L1 larvae from C. elegans strain OP102 (a transgenic strain engineered to express a gene fusion between ham-1 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"name" : "HAM-1 Combined (GFP ChIP), HAM-1_L4 w peaks",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18622.bw"
- }
- },
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HAM-1 Combined (GFP ChIP)_ HAM-1_L4 w peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
"type" : "QuantitativeTrack",
- "description" : " Identification of Transcription Factor HAM-1::GFP Binding Regions in L1. Details Synchronized fed L1 larvae from C. elegans strain OP102 (a transgenic strain engineered to express a gene fusion between ham-1 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ]
},
{
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
"color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false
},
- "type" : "LinearBasicDisplay",
"displayId" : "HAM-1 Combined (GFP ChIP)_ HAM-1_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HAM-1 Combined (GFP ChIP)_ HAM-1_L4 w peaks_bigbed_peaks",
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18643_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : "Peak calls for HAM-1 Combined (GFP ChIP), HAM-1_L4 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HAM-1 Combined (GFP ChIP)_ HAM-1_L4 w peaks_bigbed_peaks",
"name" : "__HAM-1 Combined (GFP ChIP), HAM-1_L4 peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18643_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- }
+ "description" : "Peak calls for HAM-1 Combined (GFP ChIP), HAM-1_L4 w peaks"
},
{
- "description" : " Identification of Transcription Factor HAM-1::GFP Binding Regions in L1. Details Synchronized fed L1 larvae from C. elegans strain OP102 (a transgenic strain engineered to express a gene fusion between ham-1 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18787.bw"
- },
- "type" : "BigWigAdapter"
- },
- "name" : "HAM-1 Combined (GFP ChIP), HAM-1_L1 w peaks",
"displays" : [
{
- "minScore" : 0,
- "maxScore" : 125.076599688201,
"type" : "LinearWiggleDisplay",
- "displayId" : "HAM-1 Combined (GFP ChIP)_ HAM-1_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "minScore" : 0,
+ "displayId" : "HAM-1 Combined (GFP ChIP)_ HAM-1_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 125.076599688201
}
],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18787.bw",
+ "locationType" : "UriLocation"
+ }
+ },
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HAM-1 Combined (GFP ChIP)_ HAM-1_L1 w peaks"
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HAM-1 Combined (GFP ChIP)_ HAM-1_L1 w peaks",
+ "name" : "HAM-1 Combined (GFP ChIP), HAM-1_L1 w peaks",
+ "description" : " Identification of Transcription Factor HAM-1::GFP Binding Regions in L1. Details Synchronized fed L1 larvae from C. elegans strain OP102 (a transgenic strain engineered to express a gene fusion between ham-1 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "displays" : [
- {
- "displayId" : "HAM-1 Combined (GFP ChIP)_ HAM-1_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
- }
- }
- ],
+ "description" : "Peak calls for HAM-1 Combined (GFP ChIP), HAM-1_L1 w peaks",
+ "name" : "__HAM-1 Combined (GFP ChIP), HAM-1_L1 peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HAM-1 Combined (GFP ChIP)_ HAM-1_L1 w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : "Peak calls for HAM-1 Combined (GFP ChIP), HAM-1_L1 w peaks",
- "name" : "__HAM-1 Combined (GFP ChIP), HAM-1_L1 peaks",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18799_details.gff.bb"
}
- }
+ },
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "HAM-1 Combined (GFP ChIP)_ HAM-1_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "renderer" : {
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ }
+ }
+ ]
},
{
- "name" : "HLH-30 Combined (GFP ChIP), HLH-30_LEMB w peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
"type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : " Snyder_HLH-30_GFP_L4. Synchronized L4 larvae from C. elegans strain OP433 (a transgenic strain engineered to express a gene fusion between hlh-30 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "HLH-30 Combined (GFP ChIP), HLH-30_LEMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HLH-30 Combined (GFP ChIP)_ HLH-30_LEMB w peaks",
+ "displays" : [
+ {
+ "maxScore" : 102.161591957652,
+ "displayId" : "HLH-30 Combined (GFP ChIP)_ HLH-30_LEMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18154.bw",
"locationType" : "UriLocation"
- }
- },
- "description" : " Snyder_HLH-30_GFP_L4. Synchronized L4 larvae from C. elegans strain OP433 (a transgenic strain engineered to express a gene fusion between hlh-30 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HLH-30 Combined (GFP ChIP)_ HLH-30_LEMB w peaks",
+ },
+ "type" : "BigWigAdapter"
+ }
+ },
+ {
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HLH-30 Combined (GFP ChIP)_ HLH-30_LEMB w peaks_bigbed_peaks",
+ "name" : "__HLH-30 Combined (GFP ChIP), HLH-30_LEMB peaks",
+ "description" : "Peak calls for HLH-30 Combined (GFP ChIP), HLH-30_LEMB w peaks",
"displays" : [
{
- "maxScore" : 102.161591957652,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0,
- "displayId" : "HLH-30 Combined (GFP ChIP)_ HLH-30_LEMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
- ]
- },
- {
- "displays" : [
- {
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
+ "showLabels" : false,
"showDescriptions" : false,
- "height" : 6
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "HLH-30 Combined (GFP ChIP)_ HLH-30_LEMB w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
],
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18166_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ }
+ },
+ {
+ "description" : " Snyder_HLH-30_GFP_L4. Synchronized L4 larvae from C. elegans strain OP433 (a transgenic strain engineered to express a gene fusion between hlh-30 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HLH-30 Combined (GFP ChIP)_ HLH-30_L4 w peaks",
+ "name" : "HLH-30 Combined (GFP ChIP), HLH-30_L4 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -30963,145 +30378,133 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HLH-30 Combined (GFP ChIP)_ HLH-30_LEMB w peaks_bigbed_peaks",
- "description" : "Peak calls for HLH-30 Combined (GFP ChIP), HLH-30_LEMB w peaks",
+ "type" : "QuantitativeTrack",
"adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18166_details.gff.bb",
- "locationType" : "UriLocation"
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18170.bw"
}
},
- "type" : "FeatureTrack",
- "name" : "__HLH-30 Combined (GFP ChIP), HLH-30_LEMB peaks"
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 168.183340014044,
+ "minScore" : 0,
+ "displayId" : "HLH-30 Combined (GFP ChIP)_ HLH-30_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ }
+ ]
},
{
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HLH-30 Combined (GFP ChIP)_ HLH-30_L4 w peaks_bigbed_peaks",
+ "name" : "__HLH-30 Combined (GFP ChIP), HLH-30_L4 peaks",
+ "description" : "Peak calls for HLH-30 Combined (GFP ChIP), HLH-30_L4 w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HLH-30 Combined (GFP ChIP)_ HLH-30_L4 w peaks",
- "displays" : [
- {
- "minScore" : 0,
- "maxScore" : 168.183340014044,
- "type" : "LinearWiggleDisplay",
- "displayId" : "HLH-30 Combined (GFP ChIP)_ HLH-30_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
- ],
"adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18170.bw"
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18176_details.gff.bb",
+ "locationType" : "UriLocation"
}
},
- "type" : "QuantitativeTrack",
- "name" : "HLH-30 Combined (GFP ChIP), HLH-30_L4 w peaks",
- "description" : " Snyder_HLH-30_GFP_L4. Synchronized L4 larvae from C. elegans strain OP433 (a transgenic strain engineered to express a gene fusion between hlh-30 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "HLH-30 Combined (GFP ChIP)_ HLH-30_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "height" : 6,
"showDescriptions" : false,
- "color1" : "deeppink",
+ "height" : 6,
"showLabels" : false,
+ "color1" : "deeppink",
"type" : "SvgFeatureRenderer"
},
- "displayId" : "HLH-30 Combined (GFP ChIP)_ HLH-30_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HLH-30 Combined (GFP ChIP)_ HLH-30_L4 w peaks_bigbed_peaks",
+ ]
+ },
+ {
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HPL-2 Combined (GFP ChIP)_ HPL-2_YL416_L1 w peaks",
+ "name" : "HPL-2 Combined (GFP ChIP), HPL-2_YL416_L1 w peaks",
+ "description" : "Identification of Transcription Factor HPL-2::GFP Binding Regions in L1. Synchronized L1 larvae from C. elegans strain YL416 (a transgenic strain engineered to express a gene fusion between hpl-2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "description" : "Peak calls for HLH-30 Combined (GFP ChIP), HLH-30_L4 w peaks",
- "name" : "__HLH-30 Combined (GFP ChIP), HLH-30_L4 peaks",
"adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18176_details.gff.bb",
- "locationType" : "UriLocation"
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/15092.bw"
},
- "type" : "BigBedAdapter"
+ "type" : "BigWigAdapter"
},
- "type" : "FeatureTrack"
- },
- {
"displays" : [
{
+ "minScore" : 0,
"displayId" : "HPL-2 Combined (GFP ChIP)_ HPL-2_YL416_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"maxScore" : 133.736663067938,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
+ "type" : "LinearWiggleDisplay"
}
+ ]
+ },
+ {
+ "name" : "__HPL-2 Combined (GFP ChIP), HPL-2_YL416_L1 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HPL-2 Combined (GFP ChIP)_ HPL-2_YL416_L1 w peaks_bigbed_peaks",
+ "description" : "Peak calls for HPL-2 Combined (GFP ChIP), HPL-2_YL416_L1 w peaks",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HPL-2 Combined (GFP ChIP)_ HPL-2_YL416_L1 w peaks",
- "description" : "Identification of Transcription Factor HPL-2::GFP Binding Regions in L1. Synchronized L1 larvae from C. elegans strain YL416 (a transgenic strain engineered to express a gene fusion between hpl-2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
"adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/15092.bw"
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/15112_details.gff.bb",
+ "locationType" : "UriLocation"
},
- "type" : "BigWigAdapter"
+ "type" : "BigBedAdapter"
},
- "name" : "HPL-2 Combined (GFP ChIP), HPL-2_YL416_L1 w peaks"
- },
- {
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "HPL-2 Combined (GFP ChIP)_ HPL-2_YL416_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
"type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6,
+ "color1" : "deeppink"
},
- "displayId" : "HPL-2 Combined (GFP ChIP)_ HPL-2_YL416_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
+ ]
+ },
+ {
+ "name" : "HPL-2 Combined (GFP ChIP), HPL-2_L1 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HPL-2 Combined (GFP ChIP)_ HPL-2_L1 w peaks",
+ "description" : "Identification of Transcription Factor HPL-2::GFP Binding Regions in L1. Synchronized L1 larvae from C. elegans strain YL416 (a transgenic strain engineered to express a gene fusion between hpl-2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HPL-2 Combined (GFP ChIP)_ HPL-2_YL416_L1 w peaks_bigbed_peaks",
- "description" : "Peak calls for HPL-2 Combined (GFP ChIP), HPL-2_YL416_L1 w peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/15112_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "__HPL-2 Combined (GFP ChIP), HPL-2_YL416_L1 peaks"
- },
- {
"adapter" : {
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18492.bw",
@@ -31109,164 +30512,166 @@
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "name" : "HPL-2 Combined (GFP ChIP), HPL-2_L1 w peaks",
- "description" : "Identification of Transcription Factor HPL-2::GFP Binding Regions in L1. Synchronized L1 larvae from C. elegans strain YL416 (a transgenic strain engineered to express a gene fusion between hpl-2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HPL-2 Combined (GFP ChIP)_ HPL-2_L1 w peaks",
"displays" : [
{
+ "minScore" : 0,
"displayId" : "HPL-2 Combined (GFP ChIP)_ HPL-2_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"maxScore" : 75.6030438822375,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
+ "type" : "LinearWiggleDisplay"
}
]
},
{
- "description" : "Peak calls for HPL-2 Combined (GFP ChIP), HPL-2_L1 w peaks",
- "name" : "__HPL-2 Combined (GFP ChIP), HPL-2_L1 peaks",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18512_details.gff.bb",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18512_details.gff.bb"
}
},
"displays" : [
{
- "displayId" : "HPL-2 Combined (GFP ChIP)_ HPL-2_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay",
+ "displayId" : "HPL-2 Combined (GFP ChIP)_ HPL-2_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false
}
}
],
+ "description" : "Peak calls for HPL-2 Combined (GFP ChIP), HPL-2_L1 w peaks",
+ "name" : "__HPL-2 Combined (GFP ChIP), HPL-2_L1 peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HPL-2 Combined (GFP ChIP)_ HPL-2_L1 w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
]
},
{
- "displays" : [
- {
- "minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 43.7508201537277,
- "displayId" : "HPL-2 Combined (GFP ChIP)_ Pmex-5_HPL-2_YL472_yAd w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HPL-2 Combined (GFP ChIP)_ Pmex-5_HPL-2_YL472_yAd w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"description" : "Identification of Transcription Factor HPL-2::GFP Binding Regions in L1. Synchronized L1 larvae from C. elegans strain YL416 (a transgenic strain engineered to express a gene fusion between hpl-2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HPL-2 Combined (GFP ChIP)_ Pmex-5_HPL-2_YL472_yAd w peaks",
+ "name" : "HPL-2 Combined (GFP ChIP), Pmex-5_HPL-2_YL472_yAd w peaks",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "minScore" : 0,
+ "displayId" : "HPL-2 Combined (GFP ChIP)_ Pmex-5_HPL-2_YL472_yAd w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 43.7508201537277
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18345.bw"
}
- },
- "type" : "QuantitativeTrack",
- "name" : "HPL-2 Combined (GFP ChIP), Pmex-5_HPL-2_YL472_yAd w peaks"
+ }
},
{
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18362_details.gff.bb"
+ }
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "HPL-2 Combined (GFP ChIP)_ Pmex-5_HPL-2_YL472_yAd w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
"height" : 6,
"showDescriptions" : false,
- "color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "showLabels" : false
},
- "displayId" : "HPL-2 Combined (GFP ChIP)_ Pmex-5_HPL-2_YL472_yAd w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
],
+ "description" : "Peak calls for HPL-2 Combined (GFP ChIP), Pmex-5_HPL-2_YL472_yAd w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_HPL-2 Combined (GFP ChIP)_ Pmex-5_HPL-2_YL472_yAd w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "__HPL-2 Combined (GFP ChIP), Pmex-5_HPL-2_YL472_yAd peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "description" : "Peak calls for HPL-2 Combined (GFP ChIP), Pmex-5_HPL-2_YL472_yAd w peaks",
- "name" : "__HPL-2 Combined (GFP ChIP), Pmex-5_HPL-2_YL472_yAd peaks",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18362_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack"
},
{
- "displays" : [
- {
- "minScore" : 0,
- "maxScore" : 106.181154513588,
- "type" : "LinearWiggleDisplay",
- "displayId" : "JUN-1 Combined (GFP ChIP)_ JUN-1_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_JUN-1 Combined (GFP ChIP)_ JUN-1_L4 w peaks",
+ "name" : "JUN-1 Combined (GFP ChIP), JUN-1_L4 w peaks",
+ "description" : " Identification of Transcription Factor JUN-1::GFP Binding Regions in L4. Synchronized L4 larvae from C. elegans strain OP234 (a transgenic strain engineered to express a gene fusion between jun-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_JUN-1 Combined (GFP ChIP)_ JUN-1_L4 w peaks",
- "description" : " Identification of Transcription Factor JUN-1::GFP Binding Regions in L4. Synchronized L4 larvae from C. elegans strain OP234 (a transgenic strain engineered to express a gene fusion between jun-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18060.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18060.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
- "name" : "JUN-1 Combined (GFP ChIP), JUN-1_L4 w peaks"
+ "displays" : [
+ {
+ "maxScore" : 106.181154513588,
+ "minScore" : 0,
+ "displayId" : "JUN-1 Combined (GFP ChIP)_ JUN-1_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
+ }
+ ]
},
{
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18079_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18079_details.gff.bb"
+ }
},
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false,
+ "color1" : "deeppink"
+ },
+ "displayId" : "JUN-1 Combined (GFP ChIP)_ JUN-1_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ }
+ ],
"name" : "__JUN-1 Combined (GFP ChIP), JUN-1_L4 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_JUN-1 Combined (GFP ChIP)_ JUN-1_L4 w peaks_bigbed_peaks",
"description" : "Peak calls for JUN-1 Combined (GFP ChIP), JUN-1_L4 w peaks",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -31274,212 +30679,199 @@
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_JUN-1 Combined (GFP ChIP)_ JUN-1_L4 w peaks_bigbed_peaks",
- "displays" : [
- {
- "displayId" : "JUN-1 Combined (GFP ChIP)_ JUN-1_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- }
- }
]
},
{
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"description" : " Identification of Transcription Factor JUN-1::GFP Binding Regions in L4. Synchronized L4 larvae from C. elegans strain OP234 (a transgenic strain engineered to express a gene fusion between jun-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_JUN-1 Combined (GFP ChIP)_ JUN-1_L3 w peaks",
"name" : "JUN-1 Combined (GFP ChIP), JUN-1_L3 w peaks",
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "maxScore" : 62.08863603953,
+ "minScore" : 0,
+ "displayId" : "JUN-1 Combined (GFP ChIP)_ JUN-1_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/17848.bw"
},
"type" : "BigWigAdapter"
- },
+ }
+ },
+ {
"displays" : [
{
- "displayId" : "JUN-1 Combined (GFP ChIP)_ JUN-1_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
- "maxScore" : 62.08863603953,
- "type" : "LinearWiggleDisplay"
+ "type" : "LinearBasicDisplay",
+ "displayId" : "JUN-1 Combined (GFP ChIP)_ JUN-1_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "renderer" : {
+ "color1" : "deeppink",
+ "height" : 6,
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_JUN-1 Combined (GFP ChIP)_ JUN-1_L3 w peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ]
- },
- {
- "name" : "__JUN-1 Combined (GFP ChIP), JUN-1_L3 peaks",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/17861_details.gff.bb",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/17861_details.gff.bb"
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "description" : "Peak calls for JUN-1 Combined (GFP ChIP), JUN-1_L3 w peaks",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_JUN-1 Combined (GFP ChIP)_ JUN-1_L3 w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "displays" : [
- {
- "renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "JUN-1 Combined (GFP ChIP)_ JUN-1_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
- }
- ]
+ "description" : "Peak calls for JUN-1 Combined (GFP ChIP), JUN-1_L3 w peaks",
+ "name" : "__JUN-1 Combined (GFP ChIP), JUN-1_L3 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_JUN-1 Combined (GFP ChIP)_ JUN-1_L3 w peaks_bigbed_peaks"
},
{
- "description" : " Identification of Transcription Factor JUN-1::GFP Binding Regions in L4. Synchronized L4 larvae from C. elegans strain OP234 (a transgenic strain engineered to express a gene fusion between jun-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"name" : "JUN-1 Combined (GFP ChIP), JUN-1_L1 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_JUN-1 Combined (GFP ChIP)_ JUN-1_L1 w peaks",
+ "description" : " Identification of Transcription Factor JUN-1::GFP Binding Regions in L4. Synchronized L4 larvae from C. elegans strain OP234 (a transgenic strain engineered to express a gene fusion between jun-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18013.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18013.bw"
}
},
"displays" : [
{
- "displayId" : "JUN-1 Combined (GFP ChIP)_ JUN-1_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay",
"maxScore" : 61.97019162921,
+ "displayId" : "JUN-1 Combined (GFP ChIP)_ JUN-1_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_JUN-1 Combined (GFP ChIP)_ JUN-1_L1 w peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
]
},
{
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "JUN-1 Combined (GFP ChIP)_ JUN-1_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ }
+ ],
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18025_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18025_details.gff.bb"
+ }
},
- "name" : "__JUN-1 Combined (GFP ChIP), JUN-1_L1 peaks",
- "description" : "Peak calls for JUN-1 Combined (GFP ChIP), JUN-1_L1 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_JUN-1 Combined (GFP ChIP)_ JUN-1_L1 w peaks_bigbed_peaks",
- "displays" : [
- {
- "displayId" : "JUN-1 Combined (GFP ChIP)_ JUN-1_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- }
- }
- ]
+ "description" : "Peak calls for JUN-1 Combined (GFP ChIP), JUN-1_L1 w peaks",
+ "name" : "__JUN-1 Combined (GFP ChIP), JUN-1_L1 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_JUN-1 Combined (GFP ChIP)_ JUN-1_L1 w peaks_bigbed_peaks"
},
{
- "displays" : [
- {
- "displayId" : "LIN-11 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "maxScore" : 75.4369828428075,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
- }
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-11 Combined (GFP ChIP) w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : "Identification of Transcription Factor LIN-11::GFP Binding Regions in L2 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. br/>
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"name" : "LIN-11 Combined (GFP ChIP) w peaks",
- "type" : "QuantitativeTrack",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-11 Combined (GFP ChIP) w peaks",
+ "description" : "Identification of Transcription Factor LIN-11::GFP Binding Regions in L2 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. br/>
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "maxScore" : 75.4369828428075,
+ "displayId" : "LIN-11 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_LIN-11_GFP_L2_combined_WS220.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_LIN-11_GFP_L2_combined_WS220.bw"
}
}
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-11 Combined (GFP ChIP) w peaks_bigbed_peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4264_details.gff.bb"
+ }
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "LIN-11 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "height" : 6,
+ "showLabels" : false,
"showDescriptions" : false,
+ "height" : 6,
"color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "LIN-11 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-11 Combined (GFP ChIP) w peaks_bigbed_peaks",
"name" : "__LIN-11 Combined (GFP ChIP) peaks",
+ "description" : "Peak calls for LIN-11 Combined (GFP ChIP) w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4264_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "description" : "Peak calls for LIN-11 Combined (GFP ChIP) w peaks"
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ]
},
{
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -31488,41 +30880,29 @@
"Transcription Factors",
"GFP ChIP"
],
+ "name" : "LIN-35 Combined (GFP ChIP), LIN-35_YL468_YAD w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-35 Combined (GFP ChIP)_ LIN-35_YL468_YAD w peaks",
+ "description" : " Identification of Transcription Factor LIN-35::GFP Binding Regions in yA. Synchronized young adults from C. elegans strain YL402 (a transgenic strain engineered to express a gene fusion between lin-35 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "minScore" : 0,
"type" : "LinearWiggleDisplay",
- "maxScore" : 48.7665687417336,
- "displayId" : "LIN-35 Combined (GFP ChIP)_ LIN-35_YL468_YAD w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "minScore" : 0,
+ "displayId" : "LIN-35 Combined (GFP ChIP)_ LIN-35_YL468_YAD w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 48.7665687417336
}
],
- "type" : "QuantitativeTrack",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18488.bw",
"locationType" : "UriLocation"
- }
- },
- "name" : "LIN-35 Combined (GFP ChIP), LIN-35_YL468_YAD w peaks",
- "description" : " Identification of Transcription Factor LIN-35::GFP Binding Regions in yA. Synchronized young adults from C. elegans strain YL402 (a transgenic strain engineered to express a gene fusion between lin-35 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
- "displays" : [
- {
- "displayId" : "LIN-35 Combined (GFP ChIP)_ LIN-35_YL468_YAD w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay"
- }
- ],
+ "description" : "Peak calls for LIN-35 Combined (GFP ChIP), LIN-35_YL468_YAD w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-35 Combined (GFP ChIP)_ LIN-35_YL468_YAD w peaks_bigbed_peaks",
+ "name" : "__LIN-35 Combined (GFP ChIP), LIN-35_YL468_YAD peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -31531,21 +30911,41 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : "Peak calls for LIN-35 Combined (GFP ChIP), LIN-35_YL468_YAD w peaks",
- "name" : "__LIN-35 Combined (GFP ChIP), LIN-35_YL468_YAD peaks",
+ "type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18496_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18496_details.gff.bb"
+ }
},
- "type" : "FeatureTrack"
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "height" : 6,
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "color1" : "deeppink"
+ },
+ "displayId" : "LIN-35 Combined (GFP ChIP)_ LIN-35_YL468_YAD w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
- "description" : " Identification of Transcription Factor LIN-35::GFP Binding Regions in yA. Synchronized young adults from C. elegans strain YL402 (a transgenic strain engineered to express a gene fusion between lin-35 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-35 Combined (GFP ChIP)_ LIN-35_YL402_yAd w peaks",
"name" : "LIN-35 Combined (GFP ChIP), LIN-35_YL402_yAd w peaks",
+ "description" : " Identification of Transcription Factor LIN-35::GFP Binding Regions in yA. Synchronized young adults from C. elegans strain YL402 (a transgenic strain engineered to express a gene fusion between lin-35 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
@@ -31555,120 +30955,118 @@
},
"displays" : [
{
- "displayId" : "LIN-35 Combined (GFP ChIP)_ LIN-35_YL402_yAd w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay",
- "maxScore" : 60.9104673880835,
- "minScore" : 0
+ "minScore" : 0,
+ "displayId" : "LIN-35 Combined (GFP ChIP)_ LIN-35_YL402_yAd w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 60.9104673880835
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-35 Combined (GFP ChIP)_ LIN-35_YL402_yAd w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
]
},
{
- "description" : "Peak calls for LIN-35 Combined (GFP ChIP), LIN-35_YL402_yAd w peaks",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/15101_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "__LIN-35 Combined (GFP ChIP), LIN-35_YL402_yAd peaks",
"displays" : [
{
+ "displayId" : "LIN-35 Combined (GFP ChIP)_ LIN-35_YL402_yAd w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
"color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "LIN-35 Combined (GFP ChIP)_ LIN-35_YL402_yAd w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/15101_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
+ },
+ "category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Peak calls for LIN-35 Combined (GFP ChIP), LIN-35_YL402_yAd w peaks",
+ "name" : "__LIN-35 Combined (GFP ChIP), LIN-35_YL402_yAd peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-35 Combined (GFP ChIP)_ LIN-35_YL402_yAd w peaks_bigbed_peaks"
},
{
- "name" : "LIN-35 Combined (GFP ChIP), LIN-35_YL398_L1 w peaks",
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "maxScore" : 263.098735578916,
+ "displayId" : "LIN-35 Combined (GFP ChIP)_ LIN-35_YL398_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/15116.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/15116.bw"
+ }
},
- "description" : " Identification of Transcription Factor LIN-35::GFP Binding Regions in yA. Synchronized young adults from C. elegans strain YL402 (a transgenic strain engineered to express a gene fusion between lin-35 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-35 Combined (GFP ChIP)_ LIN-35_YL398_L1 w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "displays" : [
- {
- "displayId" : "LIN-35 Combined (GFP ChIP)_ LIN-35_YL398_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 263.098735578916,
- "minScore" : 0
- }
- ]
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-35 Combined (GFP ChIP)_ LIN-35_YL398_L1 w peaks",
+ "name" : "LIN-35 Combined (GFP ChIP), LIN-35_YL398_L1 w peaks",
+ "description" : " Identification of Transcription Factor LIN-35::GFP Binding Regions in yA. Synchronized young adults from C. elegans strain YL402 (a transgenic strain engineered to express a gene fusion between lin-35 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
"displays" : [
{
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
"type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6,
+ "color1" : "deeppink"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "LIN-35 Combined (GFP ChIP)_ LIN-35_YL398_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "displayId" : "LIN-35 Combined (GFP ChIP)_ LIN-35_YL398_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-35 Combined (GFP ChIP)_ LIN-35_YL398_L1 w peaks_bigbed_peaks",
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/15126_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
+ },
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : "Peak calls for LIN-35 Combined (GFP ChIP), LIN-35_YL398_L1 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-35 Combined (GFP ChIP)_ LIN-35_YL398_L1 w peaks_bigbed_peaks",
"name" : "__LIN-35 Combined (GFP ChIP), LIN-35_YL398_L1 peaks",
+ "description" : "Peak calls for LIN-35 Combined (GFP ChIP), LIN-35_YL398_L1 w peaks"
+ },
+ {
"adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/15126_details.gff.bb",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18340.bw",
"locationType" : "UriLocation"
},
- "type" : "BigBedAdapter"
+ "type" : "BigWigAdapter"
},
- "type" : "FeatureTrack"
- },
- {
"displays" : [
{
"displayId" : "LIN-35 Combined (GFP ChIP)_ lin-35_n745_EFL-1_Ab_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
@@ -31678,27 +31076,23 @@
}
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-35 Combined (GFP ChIP)_ lin-35_n745_EFL-1_Ab_L1 w peaks",
+ "name" : "LIN-35 Combined (GFP ChIP), lin-35_n745_EFL-1_Ab_L1 w peaks",
+ "description" : " Identification of Transcription Factor LIN-35::GFP Binding Regions in yA. Synchronized young adults from C. elegans strain YL402 (a transgenic strain engineered to express a gene fusion between lin-35 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "description" : " Identification of Transcription Factor LIN-35::GFP Binding Regions in yA. Synchronized young adults from C. elegans strain YL402 (a transgenic strain engineered to express a gene fusion between lin-35 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "LIN-35 Combined (GFP ChIP), lin-35_n745_EFL-1_Ab_L1 w peaks",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18340.bw"
- }
- },
- "type" : "QuantitativeTrack"
+ ]
},
{
+ "name" : "__LIN-35 Combined (GFP ChIP), lin-35_n745_EFL-1_Ab_L1 peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-35 Combined (GFP ChIP)_ lin-35_n745_EFL-1_Ab_L1 w peaks_bigbed_peaks",
+ "description" : "Peak calls for LIN-35 Combined (GFP ChIP), lin-35_n745_EFL-1_Ab_L1 w peaks",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -31707,83 +31101,77 @@
"Transcription Factors",
"GFP ChIP"
],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18366_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6
},
"displayId" : "LIN-35 Combined (GFP ChIP)_ lin-35_n745_EFL-1_Ab_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
- ],
- "name" : "__LIN-35 Combined (GFP ChIP), lin-35_n745_EFL-1_Ab_L1 peaks",
- "type" : "FeatureTrack",
+ ]
+ },
+ {
"adapter" : {
- "bigBedLocation" : {
+ "bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18366_details.gff.bb"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18398.bw"
},
- "type" : "BigBedAdapter"
+ "type" : "BigWigAdapter"
},
- "description" : "Peak calls for LIN-35 Combined (GFP ChIP), lin-35_n745_EFL-1_Ab_L1 w peaks"
- },
- {
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-35 Combined (GFP ChIP)_ LIN-35_L1 w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
"displays" : [
{
- "maxScore" : 194.300519828703,
- "type" : "LinearWiggleDisplay",
+ "displayId" : "LIN-35 Combined (GFP ChIP)_ LIN-35_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "displayId" : "LIN-35 Combined (GFP ChIP)_ LIN-35_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "maxScore" : 194.300519828703,
+ "type" : "LinearWiggleDisplay"
}
],
+ "description" : " Identification of Transcription Factor LIN-35::GFP Binding Regions in yA. Synchronized young adults from C. elegans strain YL402 (a transgenic strain engineered to express a gene fusion between lin-35 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"name" : "LIN-35 Combined (GFP ChIP), LIN-35_L1 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-35 Combined (GFP ChIP)_ LIN-35_L1 w peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
"type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18398.bw",
- "locationType" : "UriLocation"
- }
- },
- "description" : " Identification of Transcription Factor LIN-35::GFP Binding Regions in yA. Synchronized young adults from C. elegans strain YL402 (a transgenic strain engineered to express a gene fusion between lin-35 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ]
},
{
- "description" : "Peak calls for LIN-35 Combined (GFP ChIP), LIN-35_L1 w peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18404_details.gff.bb"
- }
- },
- "name" : "__LIN-35 Combined (GFP ChIP), LIN-35_L1 peaks",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
+ "showLabels" : false,
"showDescriptions" : false,
"height" : 6
},
"displayId" : "LIN-35 Combined (GFP ChIP)_ LIN-35_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18404_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -31792,74 +31180,75 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-35 Combined (GFP ChIP)_ LIN-35_L1 w peaks_bigbed_peaks"
+ "type" : "FeatureTrack",
+ "description" : "Peak calls for LIN-35 Combined (GFP ChIP), LIN-35_L1 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LIN-35 Combined (GFP ChIP)_ LIN-35_L1 w peaks_bigbed_peaks",
+ "name" : "__LIN-35 Combined (GFP ChIP), LIN-35_L1 peaks"
},
{
- "displays" : [
- {
- "displayId" : "MED-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
- "maxScore" : 72.402581159135,
- "type" : "LinearWiggleDisplay"
- }
- ],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_MED-1 Combined (GFP ChIP) w peaks",
+ "name" : "MED-1 Combined (GFP ChIP) w peaks",
"description" : " Snyder_MED-1_GFP_MIDEMB. Synchronized embryos from C. elegans strain OP391 (a transgenic strain engineered to express a gene fusion between med-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "minScore" : 0,
+ "displayId" : "MED-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 72.402581159135,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18124.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18124.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "MED-1 Combined (GFP ChIP) w peaks"
+ }
},
{
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18137_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "MED-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
"color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "MED-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "showDescriptions" : false,
+ "height" : 6,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
+ }
}
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_MED-1 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "name" : "__MED-1 Combined (GFP ChIP) peaks",
+ "description" : "Peak calls for MED-1 Combined (GFP ChIP) w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_MED-1 Combined (GFP ChIP) w peaks_bigbed_peaks",
- "description" : "Peak calls for MED-1 Combined (GFP ChIP) w peaks",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18137_details.gff.bb",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "__MED-1 Combined (GFP ChIP) peaks"
+ ]
},
{
- "name" : "MML-1 Combined (GFP ChIP) w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
@@ -31867,69 +31256,80 @@
},
"type" : "BigWigAdapter"
},
- "description" : " Identification of Transcription Factor MML-1::GFP Binding Regions in L3. Synchronized L3 larvae from C. elegans strain OP198 (a transgenic strain engineered to express a gene fusion between mml-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 42.0586425244433,
+ "minScore" : 0,
+ "displayId" : "MML-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ }
+ ],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_MML-1 Combined (GFP ChIP) w peaks",
+ "name" : "MML-1 Combined (GFP ChIP) w peaks",
+ "description" : " Identification of Transcription Factor MML-1::GFP Binding Regions in L3. Synchronized L3 larvae from C. elegans strain OP198 (a transgenic strain engineered to express a gene fusion between mml-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "displays" : [
- {
- "displayId" : "MML-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "maxScore" : 42.0586425244433,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
- }
]
},
{
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "displayId" : "MML-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
- }
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_MML-1 Combined (GFP ChIP) w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : "Peak calls for MML-1 Combined (GFP ChIP) w peaks",
"name" : "__MML-1 Combined (GFP ChIP) peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_MML-1 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "description" : "Peak calls for MML-1 Combined (GFP ChIP) w peaks",
+ "displays" : [
+ {
+ "displayId" : "MML-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18740_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ }
+ },
+ {
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18740_details.gff.bb"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18882.bw"
}
},
- "type" : "FeatureTrack"
- },
- {
"displays" : [
{
- "maxScore" : 118.603975114277,
- "type" : "LinearWiggleDisplay",
+ "displayId" : "N2_POLIII_YA Combined (GFP ChIP)_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 45.4775117877116,
- "displayId" : "N2_POLIII_YA Combined (GFP ChIP)_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "maxScore" : 118.603975114277,
+ "type" : "LinearWiggleDisplay"
}
],
+ "description" : " Identification of Transcription Factor RPC-1::RPC-1 Binding Regions in Young Adults. Synchronized young adults from C. elegans strain N2 (a transgenic strain engineered to express a gene fusion between rpc-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_N2_POLIII_YA Combined (GFP ChIP)",
+ "name" : "N2_POLIII_YA Combined (GFP ChIP)",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -31938,57 +31338,38 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : " Identification of Transcription Factor RPC-1::RPC-1 Binding Regions in Young Adults. Synchronized young adults from C. elegans strain N2 (a transgenic strain engineered to express a gene fusion between rpc-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "N2_POLIII_YA Combined (GFP ChIP)",
- "type" : "QuantitativeTrack",
+ "type" : "QuantitativeTrack"
+ },
+ {
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18882.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18126.bw"
},
"type" : "BigWigAdapter"
- }
- },
- {
- "description" : " Snyder_NFYA-1_GFP_L3. Synchronized L3 larvae from C. elegans strain OP404 (a transgenic strain engineered to express a gene fusion between nfya-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18126.bw",
- "locationType" : "UriLocation"
- }
},
- "type" : "QuantitativeTrack",
- "name" : "NFYA-1 Combined (GFP ChIP), NFYA-1_L3 w peaks",
"displays" : [
{
"type" : "LinearWiggleDisplay",
"maxScore" : 271.535175501564,
- "minScore" : 0,
- "displayId" : "NFYA-1 Combined (GFP ChIP)_ NFYA-1_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "displayId" : "NFYA-1 Combined (GFP ChIP)_ NFYA-1_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0
}
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NFYA-1 Combined (GFP ChIP)_ NFYA-1_L3 w peaks",
+ "name" : "NFYA-1 Combined (GFP ChIP), NFYA-1_L3 w peaks",
+ "description" : " Snyder_NFYA-1_GFP_L3. Synchronized L3 larvae from C. elegans strain OP404 (a transgenic strain engineered to express a gene fusion between nfya-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NFYA-1 Combined (GFP ChIP)_ NFYA-1_L3 w peaks"
+ ]
},
{
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18144_details.gff.bb",
- "locationType" : "UriLocation"
- }
- },
- "name" : "__NFYA-1 Combined (GFP ChIP), NFYA-1_L3 peaks",
- "description" : "Peak calls for NFYA-1 Combined (GFP ChIP), NFYA-1_L3 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -31997,104 +31378,107 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "description" : "Peak calls for NFYA-1 Combined (GFP ChIP), NFYA-1_L3 w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NFYA-1 Combined (GFP ChIP)_ NFYA-1_L3 w peaks_bigbed_peaks",
+ "name" : "__NFYA-1 Combined (GFP ChIP), NFYA-1_L3 peaks",
"displays" : [
{
- "displayId" : "NFYA-1 Combined (GFP ChIP)_ NFYA-1_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
"showDescriptions" : false,
- "height" : 6
+ "height" : 6,
+ "showLabels" : false
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "NFYA-1 Combined (GFP ChIP)_ NFYA-1_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
- ]
+ ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18144_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ }
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "description" : " Snyder_NFYA-1_GFP_L3. Synchronized L3 larvae from C. elegans strain OP404 (a transgenic strain engineered to express a gene fusion between nfya-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NFYA-1 Combined (GFP ChIP)_ NFYA-1_YA w peaks",
+ "name" : "NFYA-1 Combined (GFP ChIP), NFYA-1_YA w peaks",
"displays" : [
{
+ "displayId" : "NFYA-1 Combined (GFP ChIP)_ NFYA-1_YA w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
"maxScore" : 91.5825962945105,
- "displayId" : "NFYA-1 Combined (GFP ChIP)_ NFYA-1_YA w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
],
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18149.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18149.bw",
+ "locationType" : "UriLocation"
}
- },
- "name" : "NFYA-1 Combined (GFP ChIP), NFYA-1_YA w peaks",
- "description" : " Snyder_NFYA-1_GFP_L3. Synchronized L3 larvae from C. elegans strain OP404 (a transgenic strain engineered to express a gene fusion between nfya-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
},
{
- "displays" : [
- {
- "renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "NFYA-1 Combined (GFP ChIP)_ NFYA-1_YA w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
- }
- ],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NFYA-1 Combined (GFP ChIP)_ NFYA-1_YA w peaks_bigbed_peaks",
+ "name" : "__NFYA-1 Combined (GFP ChIP), NFYA-1_YA peaks",
+ "description" : "Peak calls for NFYA-1 Combined (GFP ChIP), NFYA-1_YA w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "description" : "Peak calls for NFYA-1 Combined (GFP ChIP), NFYA-1_YA w peaks",
- "name" : "__NFYA-1 Combined (GFP ChIP), NFYA-1_YA peaks",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18161_details.gff.bb"
- }
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack"
- },
- {
"displays" : [
{
- "displayId" : "NFYA-1 Combined (GFP ChIP)_ NFYA-1_LEMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 190.761413755242
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "NFYA-1 Combined (GFP ChIP)_ NFYA-1_YA w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
- ],
+ ]
+ },
+ {
+ "description" : " Snyder_NFYA-1_GFP_L3. Synchronized L3 larvae from C. elegans strain OP404 (a transgenic strain engineered to express a gene fusion between nfya-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "NFYA-1 Combined (GFP ChIP), NFYA-1_LEMB w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NFYA-1 Combined (GFP ChIP)_ NFYA-1_LEMB w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : " Snyder_NFYA-1_GFP_L3. Synchronized L3 larvae from C. elegans strain OP404 (a transgenic strain engineered to express a gene fusion between nfya-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "NFYA-1 Combined (GFP ChIP), NFYA-1_LEMB w peaks",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -32102,54 +31486,51 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18095.bw"
}
},
- "type" : "QuantitativeTrack"
- },
- {
"displays" : [
{
- "displayId" : "NFYA-1 Combined (GFP ChIP)_ NFYA-1_LEMB w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay"
+ "minScore" : 0,
+ "displayId" : "NFYA-1 Combined (GFP ChIP)_ NFYA-1_LEMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 190.761413755242,
+ "type" : "LinearWiggleDisplay"
}
- ],
+ ]
+ },
+ {
+ "name" : "__NFYA-1 Combined (GFP ChIP), NFYA-1_LEMB peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NFYA-1 Combined (GFP ChIP)_ NFYA-1_LEMB w peaks_bigbed_peaks",
+ "description" : "Peak calls for NFYA-1 Combined (GFP ChIP), NFYA-1_LEMB w peaks",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : "Peak calls for NFYA-1 Combined (GFP ChIP), NFYA-1_LEMB w peaks",
- "name" : "__NFYA-1 Combined (GFP ChIP), NFYA-1_LEMB peaks",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18113_details.gff.bb",
"locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ }
},
- "type" : "FeatureTrack"
+ "displays" : [
+ {
+ "displayId" : "NFYA-1 Combined (GFP ChIP)_ NFYA-1_LEMB w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "renderer" : {
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
- "name" : "NHR-10 Combined (GFP ChIP) w peaks",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/17842.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
"type" : "QuantitativeTrack",
- "description" : " Snyder_NHR-10_GFP_L4. Synchronized L4 larvae from C. elegans strain OP239 (a transgenic strain engineered to express a gene fusion between nhr-10 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-10 Combined (GFP ChIP) w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -32158,97 +31539,89 @@
"Transcription Factors",
"GFP ChIP"
],
+ "name" : "NHR-10 Combined (GFP ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-10 Combined (GFP ChIP) w peaks",
+ "description" : " Snyder_NHR-10_GFP_L4. Synchronized L4 larvae from C. elegans strain OP239 (a transgenic strain engineered to express a gene fusion between nhr-10 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "displayId" : "NHR-10 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "maxScore" : 108.589534729013,
"type" : "LinearWiggleDisplay",
- "minScore" : 0
+ "maxScore" : 108.589534729013,
+ "minScore" : 0,
+ "displayId" : "NHR-10 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/17842.bw"
+ }
+ }
},
{
"description" : "Peak calls for NHR-10 Combined (GFP ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-10 Combined (GFP ChIP) w peaks_bigbed_peaks",
"name" : "__NHR-10 Combined (GFP ChIP) peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/17868_details.gff.bb"
- }
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
"displays" : [
{
"displayId" : "NHR-10 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
+ "showLabels" : false,
"showDescriptions" : false,
- "height" : 6
- }
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-10 Combined (GFP ChIP) w peaks_bigbed_peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
]
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-129 Combined (GFP ChIP)",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-129 Combined (GFP ChIP)",
+ "name" : "NHR-129 Combined (GFP ChIP)",
+ "description" : " Identification of Transcription Factor NHR-129::GFP Binding Regions in L2. Details Snyder_NHR-129_GFP_L2 (Snyder project, Snyder subgroup) Synchronized L2 larvae from C. elegans strain OP339 (a transgenic strain engineered to express a gene fusion between nhr-129 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
"type" : "LinearWiggleDisplay",
- "maxScore" : 279.774998842727,
+ "displayId" : "NHR-129 Combined (GFP ChIP)_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 110.6904496181,
- "displayId" : "NHR-129 Combined (GFP ChIP)_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "maxScore" : 279.774998842727
}
],
- "name" : "NHR-129 Combined (GFP ChIP)",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18933.bw"
- }
- },
- "type" : "QuantitativeTrack",
- "description" : " Identification of Transcription Factor NHR-129::GFP Binding Regions in L2. Details Snyder_NHR-129_GFP_L2 (Snyder project, Snyder subgroup) Synchronized L2 larvae from C. elegans strain OP339 (a transgenic strain engineered to express a gene fusion between nhr-129 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18933.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-21 Combined (GFP ChIP) w peaks",
- "displays" : [
- {
- "minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 233.024630477812,
- "displayId" : "NHR-21 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
- ],
- "type" : "QuantitativeTrack",
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
@@ -32256,33 +31629,52 @@
},
"type" : "BigWigAdapter"
},
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "displayId" : "NHR-21 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 233.024630477812
+ }
+ ],
+ "description" : " Snyder_NHR-21_GFP_L2. Synchronized L2 larvae from C. elegans strain OP361 (a transgenic strain engineered to express a gene fusion between nhr-21 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"name" : "NHR-21 Combined (GFP ChIP) w peaks",
- "description" : " Snyder_NHR-21_GFP_L2. Synchronized L2 larvae from C. elegans strain OP361 (a transgenic strain engineered to express a gene fusion between nhr-21 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-21 Combined (GFP ChIP) w peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ]
},
{
- "description" : "Peak calls for NHR-21 Combined (GFP ChIP) w peaks",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18001_details.gff.bb",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "name" : "__NHR-21 Combined (GFP ChIP) peaks",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "NHR-21 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
"type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
"showLabels" : false,
- "color1" : "deeppink"
+ "showDescriptions" : false,
+ "height" : 6
},
- "displayId" : "NHR-21 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
],
+ "name" : "__NHR-21 Combined (GFP ChIP) peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-21 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "description" : "Peak calls for NHR-21 Combined (GFP ChIP) w peaks",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -32290,74 +31682,72 @@
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-21 Combined (GFP ChIP) w peaks_bigbed_peaks"
+ ]
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "Identification of Transcription Factor NHR-237::GFP Binding Regions in Embryonic, L1 larvae, L2 larvae, and L3 larvae C. elegans. Details Synchronized C. elegans from various developmental stages of strain OP228 (a transgenic strain engineered to express a gene fusion between nhr-237 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "NHR-237 Combined (GFP ChIP), NHR-237 L3 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-237 Combined (GFP ChIP)_ NHR-237 L3 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-237 Combined (GFP ChIP)_ NHR-237 L3 w peaks",
- "displays" : [
- {
- "minScore" : 0,
- "maxScore" : 97.293170404925,
- "type" : "LinearWiggleDisplay",
- "displayId" : "NHR-237 Combined (GFP ChIP)_ NHR-237 L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
- ],
"type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18384.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18384.bw",
+ "locationType" : "UriLocation"
}
},
- "name" : "NHR-237 Combined (GFP ChIP), NHR-237 L3 w peaks",
- "description" : "Identification of Transcription Factor NHR-237::GFP Binding Regions in Embryonic, L1 larvae, L2 larvae, and L3 larvae C. elegans. Details Synchronized C. elegans from various developmental stages of strain OP228 (a transgenic strain engineered to express a gene fusion between nhr-237 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 97.293170404925,
+ "displayId" : "NHR-237 Combined (GFP ChIP)_ NHR-237 L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0
+ }
+ ]
},
{
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18392_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
- "displayId" : "NHR-237 Combined (GFP ChIP)_ NHR-237 L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
"height" : 6,
"showDescriptions" : false,
- "color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
- }
+ "showLabels" : false
+ },
+ "displayId" : "NHR-237 Combined (GFP ChIP)_ NHR-237 L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-237 Combined (GFP ChIP)_ NHR-237 L3 w peaks_bigbed_peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
+ "name" : "__NHR-237 Combined (GFP ChIP), NHR-237 L3 peaks",
+ "description" : "Peak calls for NHR-237 Combined (GFP ChIP), NHR-237 L3 w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : "Peak calls for NHR-237 Combined (GFP ChIP), NHR-237 L3 w peaks",
- "name" : "__NHR-237 Combined (GFP ChIP), NHR-237 L3 peaks",
"type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18392_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- }
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ]
},
{
- "name" : "NHR-237 Combined (GFP ChIP), NHR-237 L2 w peaks",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -32365,9 +31755,18 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18414.bw"
}
},
- "type" : "QuantitativeTrack",
- "description" : "Identification of Transcription Factor NHR-237::GFP Binding Regions in Embryonic, L1 larvae, L2 larvae, and L3 larvae C. elegans. Details Synchronized C. elegans from various developmental stages of strain OP228 (a transgenic strain engineered to express a gene fusion between nhr-237 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 94.8185216852015,
+ "minScore" : 0,
+ "displayId" : "NHR-237 Combined (GFP ChIP)_ NHR-237 L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ }
+ ],
+ "name" : "NHR-237 Combined (GFP ChIP), NHR-237 L2 w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-237 Combined (GFP ChIP)_ NHR-237 L2 w peaks",
+ "description" : "Identification of Transcription Factor NHR-237::GFP Binding Regions in Embryonic, L1 larvae, L2 larvae, and L3 larvae C. elegans. Details Synchronized C. elegans from various developmental stages of strain OP228 (a transgenic strain engineered to express a gene fusion between nhr-237 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -32375,52 +31774,59 @@
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "displays" : [
- {
- "maxScore" : 94.8185216852015,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0,
- "displayId" : "NHR-237 Combined (GFP ChIP)_ NHR-237 L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
]
},
{
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "displayId" : "NHR-237 Combined (GFP ChIP)_ NHR-237 L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
+ "showDescriptions" : false,
+ "height" : 6,
+ "showLabels" : false
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18430_details.gff.bb"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18430_details.gff.bb",
+ "locationType" : "UriLocation"
}
},
- "name" : "__NHR-237 Combined (GFP ChIP), NHR-237 L2 peaks",
- "description" : "Peak calls for NHR-237 Combined (GFP ChIP), NHR-237 L2 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-237 Combined (GFP ChIP)_ NHR-237 L2 w peaks_bigbed_peaks",
+ "description" : "Peak calls for NHR-237 Combined (GFP ChIP), NHR-237 L2 w peaks",
+ "name" : "__NHR-237 Combined (GFP ChIP), NHR-237 L2 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-237 Combined (GFP ChIP)_ NHR-237 L2 w peaks_bigbed_peaks"
+ },
+ {
"displays" : [
{
- "displayId" : "NHR-237 Combined (GFP ChIP)_ NHR-237 L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
- }
+ "displayId" : "NHR-237 Combined (GFP ChIP)_ NHR-237 EMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 182.320404789763,
+ "type" : "LinearWiggleDisplay"
}
- ]
- },
- {
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-237 Combined (GFP ChIP)_ NHR-237 EMB w peaks",
+ ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18623.bw",
+ "locationType" : "UriLocation"
+ }
+ },
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -32429,27 +31835,24 @@
"Transcription Factors",
"GFP ChIP"
],
- "displays" : [
- {
- "maxScore" : 182.320404789763,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0,
- "displayId" : "NHR-237 Combined (GFP ChIP)_ NHR-237 EMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
- ],
"name" : "NHR-237 Combined (GFP ChIP), NHR-237 EMB w peaks",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18623.bw"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-237 Combined (GFP ChIP)_ NHR-237 EMB w peaks",
"description" : "Identification of Transcription Factor NHR-237::GFP Binding Regions in Embryonic, L1 larvae, L2 larvae, and L3 larvae C. elegans. Details Synchronized C. elegans from various developmental stages of strain OP228 (a transgenic strain engineered to express a gene fusion between nhr-237 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "NHR-237 Combined (GFP ChIP)_ NHR-237 EMB w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
+ "showDescriptions" : false,
+ "height" : 6,
+ "showLabels" : false
+ }
+ }
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
@@ -32457,8 +31860,7 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18638_details.gff.bb"
}
},
- "name" : "__NHR-237 Combined (GFP ChIP), NHR-237 EMB peaks",
- "description" : "Peak calls for NHR-237 Combined (GFP ChIP), NHR-237 EMB w peaks",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -32467,75 +31869,64 @@
"Transcription Factors",
"GFP ChIP"
],
+ "name" : "__NHR-237 Combined (GFP ChIP), NHR-237 EMB peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-237 Combined (GFP ChIP)_ NHR-237 EMB w peaks_bigbed_peaks",
- "displays" : [
- {
- "displayId" : "NHR-237 Combined (GFP ChIP)_ NHR-237 EMB w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
- },
- "type" : "LinearBasicDisplay"
- }
- ]
+ "description" : "Peak calls for NHR-237 Combined (GFP ChIP), NHR-237 EMB w peaks"
},
{
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-237 Combined (GFP ChIP)_ NHR-237 L1 w peaks",
"displays" : [
{
"type" : "LinearWiggleDisplay",
"maxScore" : 129.787417741602,
- "minScore" : 0,
- "displayId" : "NHR-237 Combined (GFP ChIP)_ NHR-237 L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "displayId" : "NHR-237 Combined (GFP ChIP)_ NHR-237 L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0
}
],
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18676.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18676.bw"
+ }
},
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-237 Combined (GFP ChIP)_ NHR-237 L1 w peaks",
"name" : "NHR-237 Combined (GFP ChIP), NHR-237 L1 w peaks",
"description" : "Identification of Transcription Factor NHR-237::GFP Binding Regions in Embryonic, L1 larvae, L2 larvae, and L3 larvae C. elegans. Details Synchronized C. elegans from various developmental stages of strain OP228 (a transgenic strain engineered to express a gene fusion between nhr-237 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "description" : "Peak calls for NHR-237 Combined (GFP ChIP), NHR-237 L1 w peaks",
- "name" : "__NHR-237 Combined (GFP ChIP), NHR-237 L1 peaks",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18681_details.gff.bb"
- }
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18681_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "NHR-237 Combined (GFP ChIP)_ NHR-237 L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay",
"renderer" : {
+ "showLabels" : false,
"height" : 6,
"showDescriptions" : false,
"color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "NHR-237 Combined (GFP ChIP)_ NHR-237 L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
],
+ "name" : "__NHR-237 Combined (GFP ChIP), NHR-237 L1 peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-237 Combined (GFP ChIP)_ NHR-237 L1 w peaks_bigbed_peaks",
+ "description" : "Peak calls for NHR-237 Combined (GFP ChIP), NHR-237 L1 w peaks",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -32546,8 +31937,6 @@
]
},
{
- "name" : "NHR-25 Combined (GFP ChIP) w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -32555,63 +31944,62 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18530.bw"
}
},
+ "displays" : [
+ {
+ "minScore" : 0,
+ "displayId" : "NHR-25 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 170.968766268664,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"description" : " Identification of Transcription Factor NHR-25::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP33 (a transgenic strain engineered to express a gene fusion between nhr-25 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "NHR-25 Combined (GFP ChIP) w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-25 Combined (GFP ChIP) w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "displays" : [
- {
- "displayId" : "NHR-25 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 170.968766268664,
- "minScore" : 0
- }
]
},
{
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "NHR-25 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "renderer" : {
+ "color1" : "deeppink",
+ "height" : 6,
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
+ }
+ }
+ ],
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18540_details.gff.bb",
- "locationType" : "UriLocation"
- }
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18540_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "name" : "__NHR-25 Combined (GFP ChIP) peaks",
- "description" : "Peak calls for NHR-25 Combined (GFP ChIP) w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Peak calls for NHR-25 Combined (GFP ChIP) w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-25 Combined (GFP ChIP) w peaks_bigbed_peaks",
- "displays" : [
- {
- "displayId" : "NHR-25 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "height" : 6,
- "showDescriptions" : false
- }
- }
- ]
+ "name" : "__NHR-25 Combined (GFP ChIP) peaks"
},
{
- "description" : " Identification of Transcription Factor NHR-2::GFP Binding Regions in EMB. Synchronized embryos from C. elegans strain OP99 (a transgenic strain engineered to express a gene fusion between nhr-2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "NHR-2 Combined (GFP ChIP)",
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -32621,31 +32009,42 @@
},
"displays" : [
{
- "displayId" : "NHR-2 Combined (GFP ChIP)_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 47.4637286183608,
"type" : "LinearWiggleDisplay",
- "maxScore" : 106.756147328366
+ "maxScore" : 106.756147328366,
+ "displayId" : "NHR-2 Combined (GFP ChIP)_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 47.4637286183608
}
],
+ "description" : " Identification of Transcription Factor NHR-2::GFP Binding Regions in EMB. Synchronized embryos from C. elegans strain OP99 (a transgenic strain engineered to express a gene fusion between nhr-2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "NHR-2 Combined (GFP ChIP)",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-2 Combined (GFP ChIP)",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
+ ],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
]
},
{
"displays" : [
{
+ "type" : "LinearWiggleDisplay",
"displayId" : "NHR-67 Combined (GFP ChIP)_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 22.9553238901073,
- "maxScore" : 55.3697693639615,
- "type" : "LinearWiggleDisplay"
+ "maxScore" : 55.3697693639615
}
],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18288.bw"
+ }
+ },
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -32654,114 +32053,103 @@
"Transcription Factors",
"GFP ChIP"
],
+ "name" : "NHR-67 Combined (GFP ChIP)",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-67 Combined (GFP ChIP)",
- "description" : " Snyder_NHR-67_GFP_L3. Synchronized L3 larvae from C. elegans strain OP373 (a transgenic strain engineered to express a gene fusion between nhr-67 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18288.bw"
- }
- },
- "name" : "NHR-67 Combined (GFP ChIP)"
+ "description" : " Snyder_NHR-67_GFP_L3. Synchronized L3 larvae from C. elegans strain OP373 (a transgenic strain engineered to express a gene fusion between nhr-67 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "description" : " Identification of Transcription Factor NHR-6::GFP Binding Regions in L4. Synchronized L4 larvae from C. elegans strain OP90 (a transgenic strain engineered to express a gene fusion between nhr-6 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18549.bw"
- }
- },
- "name" : "NHR-6 Combined (GFP ChIP)",
"displays" : [
{
"minScore" : 45.4467932308337,
+ "displayId" : "NHR-6 Combined (GFP ChIP)_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"maxScore" : 124.98755524495,
- "type" : "LinearWiggleDisplay",
- "displayId" : "NHR-6 Combined (GFP ChIP)_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18549.bw",
+ "locationType" : "UriLocation"
+ }
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : " Identification of Transcription Factor NHR-6::GFP Binding Regions in L4. Synchronized L4 larvae from C. elegans strain OP90 (a transgenic strain engineered to express a gene fusion between nhr-6 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "NHR-6 Combined (GFP ChIP)",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-6 Combined (GFP ChIP)"
},
{
- "displays" : [
- {
- "displayId" : "NHR-76 Combined (GFP ChIP)_ NHR-76_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 51.2472343820124
- }
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-76 Combined (GFP ChIP)_ NHR-76_L3 w peaks",
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"description" : " Snyder_NHR-76_GFP_L4. Synchronized L4 larvae from C. elegans strain OP203 (a transgenic strain engineered to express a gene fusion between nhr-76 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "NHR-76 Combined (GFP ChIP), NHR-76_L3 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-76 Combined (GFP ChIP)_ NHR-76_L3 w peaks",
+ "displays" : [
+ {
+ "displayId" : "NHR-76 Combined (GFP ChIP)_ NHR-76_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 51.2472343820124,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18702.bw",
"locationType" : "UriLocation"
}
- },
- "type" : "QuantitativeTrack",
- "name" : "NHR-76 Combined (GFP ChIP), NHR-76_L3 w peaks"
+ }
},
{
+ "name" : "__NHR-76 Combined (GFP ChIP), NHR-76_L3 peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-76 Combined (GFP ChIP)_ NHR-76_L3 w peaks_bigbed_peaks",
+ "description" : "Peak calls for NHR-76 Combined (GFP ChIP), NHR-76_L3 w peaks",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18709_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
"displayId" : "NHR-76 Combined (GFP ChIP)_ NHR-76_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
"showDescriptions" : false,
- "height" : 6
- }
- }
- ],
- "name" : "__NHR-76 Combined (GFP ChIP), NHR-76_L3 peaks",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18709_details.gff.bb",
- "locationType" : "UriLocation"
+ "height" : 6,
+ "showLabels" : false
+ },
+ "type" : "LinearBasicDisplay"
}
- },
- "type" : "FeatureTrack",
- "description" : "Peak calls for NHR-76 Combined (GFP ChIP), NHR-76_L3 w peaks"
+ ]
},
{
- "description" : " Snyder_NHR-76_GFP_L4. Synchronized L4 larvae from C. elegans strain OP203 (a transgenic strain engineered to express a gene fusion between nhr-76 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "NHR-76 Combined (GFP ChIP), NHR-76_L4 w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/17982.bw",
@@ -32771,24 +32159,38 @@
},
"displays" : [
{
- "displayId" : "NHR-76 Combined (GFP ChIP)_ NHR-76_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay",
- "maxScore" : 110.867974197361,
- "minScore" : 0
+ "minScore" : 0,
+ "displayId" : "NHR-76 Combined (GFP ChIP)_ NHR-76_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 110.867974197361
}
],
+ "description" : " Snyder_NHR-76_GFP_L4. Synchronized L4 larvae from C. elegans strain OP203 (a transgenic strain engineered to express a gene fusion between nhr-76 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "NHR-76 Combined (GFP ChIP), NHR-76_L4 w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-76 Combined (GFP ChIP)_ NHR-76_L4 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
]
},
{
"description" : "Peak calls for NHR-76 Combined (GFP ChIP), NHR-76_L4 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-76 Combined (GFP ChIP)_ NHR-76_L4 w peaks_bigbed_peaks",
+ "name" : "__NHR-76 Combined (GFP ChIP), NHR-76_L4 peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
@@ -32796,105 +32198,87 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18012_details.gff.bb"
}
},
- "type" : "FeatureTrack",
- "name" : "__NHR-76 Combined (GFP ChIP), NHR-76_L4 peaks",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
"showLabels" : false,
- "color1" : "deeppink"
+ "height" : 6,
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
},
"displayId" : "NHR-76 Combined (GFP ChIP)_ NHR-76_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-76 Combined (GFP ChIP)_ NHR-76_L4 w peaks_bigbed_peaks"
+ ]
},
{
- "displays" : [
- {
- "displayId" : "NHR-116 Combined (GFP ChIP)_ NHR116_GFP_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 79.464739140087,
- "minScore" : 0
- }
- ],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-116 Combined (GFP ChIP)_ NHR116_GFP_L2 w peaks",
+ "name" : "NHR-116 Combined (GFP ChIP), NHR116_GFP_L2 w peaks",
+ "description" : " Identification of Transcription Factor NHR-116::GFP Binding Regions in L2. Synchronized L2 larvae from C. elegans strain OP226 (a transgenic strain engineered to express a gene fusion between nhr-116 and GFP) were treated with the cross-linking reagent formaldehyde. Place a submission-specific statement in here. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "description" : " Identification of Transcription Factor NHR-116::GFP Binding Regions in L2. Synchronized L2 larvae from C. elegans strain OP226 (a transgenic strain engineered to express a gene fusion between nhr-116 and GFP) were treated with the cross-linking reagent formaldehyde. Place a submission-specific statement in here. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "NHR-116 Combined (GFP ChIP), NHR116_GFP_L2 w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/14892.bw"
}
- }
+ },
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "displayId" : "NHR-116 Combined (GFP ChIP)_ NHR116_GFP_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 79.464739140087
+ }
+ ]
},
{
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/14904_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "__NHR-116 Combined (GFP ChIP), NHR116_GFP_L2 peaks",
- "description" : "Peak calls for NHR-116 Combined (GFP ChIP), NHR116_GFP_L2 w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-116 Combined (GFP ChIP)_ NHR116_GFP_L2 w peaks_bigbed_peaks",
+ "name" : "__NHR-116 Combined (GFP ChIP), NHR116_GFP_L2 peaks",
+ "description" : "Peak calls for NHR-116 Combined (GFP ChIP), NHR116_GFP_L2 w peaks",
"displays" : [
{
- "displayId" : "NHR-116 Combined (GFP ChIP)_ NHR116_GFP_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "deeppink",
+ "showLabels" : false,
"showDescriptions" : false,
- "height" : 6
- }
+ "height" : 6,
+ "color1" : "deeppink"
+ },
+ "displayId" : "NHR-116 Combined (GFP ChIP)_ NHR116_GFP_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
- ]
- },
- {
- "type" : "QuantitativeTrack",
+ ],
"adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/13527.bw",
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/14904_details.gff.bb",
"locationType" : "UriLocation"
}
- },
- "name" : "NHR-116 Combined (GFP ChIP), NHR116_GFP_L1 w peaks",
+ }
+ },
+ {
"description" : " Identification of Transcription Factor NHR-116::GFP Binding Regions in L2. Synchronized L2 larvae from C. elegans strain OP226 (a transgenic strain engineered to express a gene fusion between nhr-116 and GFP) were treated with the cross-linking reagent formaldehyde. Place a submission-specific statement in here. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-116 Combined (GFP ChIP)_ NHR116_GFP_L1 w peaks",
+ "name" : "NHR-116 Combined (GFP ChIP), NHR116_GFP_L1 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -32903,156 +32287,174 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-116 Combined (GFP ChIP)_ NHR116_GFP_L1 w peaks",
+ "type" : "QuantitativeTrack",
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/13527.bw",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "displayId" : "NHR-116 Combined (GFP ChIP)_ NHR116_GFP_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "maxScore" : 58.242623476321,
"type" : "LinearWiggleDisplay",
- "minScore" : 0
+ "minScore" : 0,
+ "displayId" : "NHR-116 Combined (GFP ChIP)_ NHR116_GFP_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 58.242623476321
}
]
},
{
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-116 Combined (GFP ChIP)_ NHR116_GFP_L1 w peaks_bigbed_peaks",
+ "name" : "__NHR-116 Combined (GFP ChIP), NHR116_GFP_L1 peaks",
+ "description" : "Peak calls for NHR-116 Combined (GFP ChIP), NHR116_GFP_L1 w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "displays" : [
- {
- "renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "NHR-116 Combined (GFP ChIP)_ NHR116_GFP_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
- }
- ],
- "name" : "__NHR-116 Combined (GFP ChIP), NHR116_GFP_L1 peaks",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/13554_details.gff.bb",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/13554_details.gff.bb"
}
},
- "description" : "Peak calls for NHR-116 Combined (GFP ChIP), NHR116_GFP_L1 w peaks"
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "NHR-116 Combined (GFP ChIP)_ NHR116_GFP_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6
+ }
+ }
+ ]
},
{
- "description" : " Identification of Transcription Factor NHR-77::GFP Binding Regions in L1. Synchronized L1 larvae from C. elegans strain OP353 (a transgenic strain engineered to express a gene fusion between nhr-77 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/13558.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "NHR-77 Combined (GFP ChIP), NHR77_GFP_L4 w peaks",
"displays" : [
{
- "displayId" : "NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "maxScore" : 85.0700560378305,
"type" : "LinearWiggleDisplay",
- "minScore" : 0
+ "maxScore" : 85.0700560378305,
+ "minScore" : 0,
+ "displayId" : "NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
}
],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/13558.bw",
+ "locationType" : "UriLocation"
+ }
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : " Identification of Transcription Factor NHR-77::GFP Binding Regions in L1. Synchronized L1 larvae from C. elegans strain OP353 (a transgenic strain engineered to express a gene fusion between nhr-77 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "NHR-77 Combined (GFP ChIP), NHR77_GFP_L4 w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L4 w peaks"
},
{
- "description" : "Peak calls for NHR-77 Combined (GFP ChIP), NHR77_GFP_L4 w peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/13563_details.gff.bb"
- }
- },
- "name" : "__NHR-77 Combined (GFP ChIP), NHR77_GFP_L4 peaks",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false
},
- "displayId" : "NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
],
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/13563_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "Peak calls for NHR-77 Combined (GFP ChIP), NHR77_GFP_L4 w peaks",
+ "name" : "__NHR-77 Combined (GFP ChIP), NHR77_GFP_L4 peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L4 w peaks_bigbed_peaks"
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L3 w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
"displays" : [
{
- "type" : "LinearWiggleDisplay",
"maxScore" : 51.6789207173152,
+ "displayId" : "NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "displayId" : "NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
],
- "name" : "NHR-77 Combined (GFP ChIP), NHR77_GFP_L3 w peaks",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/13481.bw",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigWigAdapter"
},
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L3 w peaks",
+ "name" : "NHR-77 Combined (GFP ChIP), NHR77_GFP_L3 w peaks",
"description" : " Identification of Transcription Factor NHR-77::GFP Binding Regions in L1. Synchronized L1 larvae from C. elegans strain OP353 (a transgenic strain engineered to express a gene fusion between nhr-77 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/13499_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
"showDescriptions" : false,
- "height" : 6
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "height" : 6,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
+ }
}
],
+ "name" : "__NHR-77 Combined (GFP ChIP), NHR77_GFP_L3 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L3 w peaks_bigbed_peaks",
+ "description" : "Peak calls for NHR-77 Combined (GFP ChIP), NHR77_GFP_L3 w peaks",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -33060,28 +32462,10 @@
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L3 w peaks_bigbed_peaks",
- "description" : "Peak calls for NHR-77 Combined (GFP ChIP), NHR77_GFP_L3 w peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/13499_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "__NHR-77 Combined (GFP ChIP), NHR77_GFP_L3 peaks"
+ ]
},
{
- "displays" : [
- {
- "type" : "LinearWiggleDisplay",
- "maxScore" : 133.076168135349,
- "minScore" : 0,
- "displayId" : "NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
- ],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -33090,104 +32474,101 @@
"Transcription Factors",
"GFP ChIP"
],
+ "name" : "NHR-77 Combined (GFP ChIP), NHR77_GFP_L1 w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L1 w peaks",
"description" : " Identification of Transcription Factor NHR-77::GFP Binding Regions in L1. Synchronized L1 larvae from C. elegans strain OP353 (a transgenic strain engineered to express a gene fusion between nhr-77 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "displayId" : "NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 133.076168135349
+ }
+ ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/14974.bw",
"locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "name" : "NHR-77 Combined (GFP ChIP), NHR77_GFP_L1 w peaks"
+ }
+ }
},
{
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/14981_details.gff.bb",
- "locationType" : "UriLocation"
- }
- },
- "name" : "__NHR-77 Combined (GFP ChIP), NHR77_GFP_L1 peaks",
- "description" : "Peak calls for NHR-77 Combined (GFP ChIP), NHR77_GFP_L1 w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L1 w peaks_bigbed_peaks",
+ "name" : "__NHR-77 Combined (GFP ChIP), NHR77_GFP_L1 peaks",
+ "description" : "Peak calls for NHR-77 Combined (GFP ChIP), NHR77_GFP_L1 w peaks",
"displays" : [
{
"displayId" : "NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
+ "type" : "SvgFeatureRenderer",
"showDescriptions" : false,
- "color1" : "deeppink",
+ "height" : 6,
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
- }
+ "color1" : "deeppink"
+ },
+ "type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/14981_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
+ "description" : " Identification of Transcription Factor NHR-77::GFP Binding Regions in L1. Synchronized L1 larvae from C. elegans strain OP353 (a transgenic strain engineered to express a gene fusion between nhr-77 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "NHR-77 Combined (GFP ChIP), NHR77_GFP_L2 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L2 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L2 w peaks",
- "displays" : [
- {
- "minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 44.4677180878473,
- "displayId" : "NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
- ],
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/13475.bw"
- },
- "type" : "BigWigAdapter"
+ }
},
- "name" : "NHR-77 Combined (GFP ChIP), NHR77_GFP_L2 w peaks",
- "description" : " Identification of Transcription Factor NHR-77::GFP Binding Regions in L1. Synchronized L1 larvae from C. elegans strain OP353 (a transgenic strain engineered to express a gene fusion between nhr-77 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "displayId" : "NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 44.4677180878473
+ }
+ ]
},
{
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L2 w peaks_bigbed_peaks",
+ "name" : "__NHR-77 Combined (GFP ChIP), NHR77_GFP_L2 peaks",
+ "description" : "Peak calls for NHR-77 Combined (GFP ChIP), NHR77_GFP_L2 w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L2 w peaks_bigbed_peaks",
- "displays" : [
- {
- "renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
- }
- ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
@@ -33195,414 +32576,426 @@
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "name" : "__NHR-77 Combined (GFP ChIP), NHR77_GFP_L2 peaks",
- "description" : "Peak calls for NHR-77 Combined (GFP ChIP), NHR77_GFP_L2 w peaks"
+ "displays" : [
+ {
+ "displayId" : "NHR-77 Combined (GFP ChIP)_ NHR77_GFP_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
- "name" : "PAX-1 Combined (GFP ChIP) w peaks",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18417.bw"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "description" : "Identification of Transcription Factor PAX-1::GFP Binding Regions in EMB. Details Synchronized embryos from C. elegans strain OP117 (a transgenic strain engineered to express a gene fusion between pax-1 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PAX-1 Combined (GFP ChIP) w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "description" : "Identification of Transcription Factor PAX-1::GFP Binding Regions in EMB. Details Synchronized embryos from C. elegans strain OP117 (a transgenic strain engineered to express a gene fusion between pax-1 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PAX-1 Combined (GFP ChIP) w peaks",
+ "name" : "PAX-1 Combined (GFP ChIP) w peaks",
"displays" : [
{
"displayId" : "PAX-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
+ "minScore" : 0,
"maxScore" : 98.0205710444285,
- "minScore" : 0
+ "type" : "LinearWiggleDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18417.bw"
+ }
+ }
},
{
- "name" : "__PAX-1 Combined (GFP ChIP) peaks",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18433_details.gff.bb",
"locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ }
},
- "description" : "Peak calls for PAX-1 Combined (GFP ChIP) w peaks",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PAX-1 Combined (GFP ChIP) w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
"displays" : [
{
+ "displayId" : "PAX-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"height" : 6,
"showDescriptions" : false
},
- "type" : "LinearBasicDisplay",
- "displayId" : "PAX-1 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
+ ],
+ "description" : "Peak calls for PAX-1 Combined (GFP ChIP) w peaks",
+ "name" : "__PAX-1 Combined (GFP ChIP) peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PAX-1 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
]
},
{
- "displays" : [
- {
- "minScore" : 28.8185112081759,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 67.127306691442,
- "displayId" : "PEB-1 Combined (GFP ChIP)_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
- ],
+ "description" : " Identification of Transcription Factor PEB-1::GFP Binding Regions in L2. Synchronized L2 larvae from C. elegans strain OP86 (a transgenic strain engineered to express a gene fusion between peb-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PEB-1 Combined (GFP ChIP)",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "PEB-1 Combined (GFP ChIP)",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "description" : " Identification of Transcription Factor PEB-1::GFP Binding Regions in L2. Synchronized L2 larvae from C. elegans strain OP86 (a transgenic strain engineered to express a gene fusion between peb-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "PEB-1 Combined (GFP ChIP)",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18908.bw"
- },
- "type" : "BigWigAdapter"
- }
- },
- {
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/15149.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18908.bw",
+ "locationType" : "UriLocation"
}
},
- "name" : "SEM-4 Combined (GFP ChIP)",
- "description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SEM-4 Combined (GFP ChIP)",
"displays" : [
{
- "maxScore" : 164.948915469042,
"type" : "LinearWiggleDisplay",
- "minScore" : 61.1063421047837,
- "displayId" : "SEM-4 Combined (GFP ChIP)_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "displayId" : "PEB-1 Combined (GFP ChIP)_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 28.8185112081759,
+ "maxScore" : 67.127306691442
}
]
},
{
- "name" : "SMA-9 Combined (GFP ChIP) w peaks",
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 164.948915469042,
+ "minScore" : 61.1063421047837,
+ "displayId" : "SEM-4 Combined (GFP ChIP)_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18472.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/15149.bw"
},
"type" : "BigWigAdapter"
},
- "description" : " Identification of Transcription Factor SMA-9::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP130 (a transgenic strain engineered to express a gene fusion between sma-9 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SMA-9 Combined (GFP ChIP) w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SEM-4 Combined (GFP ChIP)",
+ "name" : "SEM-4 Combined (GFP ChIP)",
+ "description" : " Identification of Transcription Factor SEM-4::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP57 (a transgenic strain engineered to express a gene fusion between sem-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ },
+ {
"displays" : [
{
+ "minScore" : 0,
"displayId" : "SMA-9 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"maxScore" : 82.611272511005,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
+ "type" : "LinearWiggleDisplay"
}
- ]
- },
- {
- "description" : "Peak calls for SMA-9 Combined (GFP ChIP) w peaks",
- "type" : "FeatureTrack",
+ ],
"adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18478_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "__SMA-9 Combined (GFP ChIP) peaks",
- "displays" : [
- {
- "displayId" : "SMA-9 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay"
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18472.bw"
}
- ],
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SMA-9 Combined (GFP ChIP) w peaks_bigbed_peaks"
+ "description" : " Identification of Transcription Factor SMA-9::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP130 (a transgenic strain engineered to express a gene fusion between sma-9 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "SMA-9 Combined (GFP ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SMA-9 Combined (GFP ChIP) w peaks"
},
{
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
+ "displays" : [
+ {
+ "renderer" : {
+ "showDescriptions" : false,
+ "height" : 6,
+ "showLabels" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "SMA-9 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18478_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "name" : "__SMA-9 Combined (GFP ChIP) peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SMA-9 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "description" : "Peak calls for SMA-9 Combined (GFP ChIP) w peaks"
+ },
+ {
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : " Identification of Transcription Factor SPTF-1::GFP Binding Regions in L1. Details Synchronized L1 larvae from C. elegans strain OP196 (a transgenic strain engineered to express a gene fusion between sptf-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "SPTF-1 Combined (GFP ChIP)",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_SPTF-1 Combined (GFP ChIP)",
"displays" : [
{
"minScore" : 54.8037643855614,
- "type" : "LinearWiggleDisplay",
+ "displayId" : "SPTF-1 Combined (GFP ChIP)_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"maxScore" : 124.572619350186,
- "displayId" : "SPTF-1 Combined (GFP ChIP)_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
],
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/14900.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/14900.bw"
}
- },
- "name" : "SPTF-1 Combined (GFP ChIP)",
- "description" : " Identification of Transcription Factor SPTF-1::GFP Binding Regions in L1. Details Synchronized L1 larvae from C. elegans strain OP196 (a transgenic strain engineered to express a gene fusion between sptf-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
},
{
- "description" : " Identification of Transcription Factor LSY-2::GFP Binding Regions in Starved. Synchronized starved L1 larvae from C. elegans strain OP367 (a transgenic strain engineered to express a gene fusion between lsy-2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "LSY-2 Combined (GFP ChIP), LSY-2_L4 w peaks",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/17923.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/17923.bw"
+ }
},
- "type" : "QuantitativeTrack",
"displays" : [
{
- "displayId" : "LSY-2 Combined (GFP ChIP)_ LSY-2_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"maxScore" : 187.368315659236,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
+ "minScore" : 0,
+ "displayId" : "LSY-2 Combined (GFP ChIP)_ LSY-2_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
],
+ "description" : " Identification of Transcription Factor LSY-2::GFP Binding Regions in Starved. Synchronized starved L1 larvae from C. elegans strain OP367 (a transgenic strain engineered to express a gene fusion between lsy-2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "LSY-2 Combined (GFP ChIP), LSY-2_L4 w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LSY-2 Combined (GFP ChIP)_ LSY-2_L4 w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
+ ],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
]
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LSY-2 Combined (GFP ChIP)_ LSY-2_L4 w peaks_bigbed_peaks",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "LSY-2 Combined (GFP ChIP)_ LSY-2_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
"type" : "SvgFeatureRenderer",
"showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6,
"color1" : "deeppink"
- },
- "displayId" : "LSY-2 Combined (GFP ChIP)_ LSY-2_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ }
}
],
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/17955_details.gff.bb"
- },
- "type" : "BigBedAdapter"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/17955_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
},
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LSY-2 Combined (GFP ChIP)_ LSY-2_L4 w peaks_bigbed_peaks",
"name" : "__LSY-2 Combined (GFP ChIP), LSY-2_L4 peaks",
"description" : "Peak calls for LSY-2 Combined (GFP ChIP), LSY-2_L4 w peaks"
},
{
- "description" : " Identification of Transcription Factor LSY-2::GFP Binding Regions in Starved. Synchronized starved L1 larvae from C. elegans strain OP367 (a transgenic strain engineered to express a gene fusion between lsy-2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "LSY-2 Combined (GFP ChIP), LSY-2_L2 w peaks",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/17883.bw",
"locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ }
},
- "type" : "QuantitativeTrack",
"displays" : [
{
- "displayId" : "LSY-2 Combined (GFP ChIP)_ LSY-2_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
"maxScore" : 191.423675153345,
- "minScore" : 0
+ "minScore" : 0,
+ "displayId" : "LSY-2 Combined (GFP ChIP)_ LSY-2_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
],
+ "description" : " Identification of Transcription Factor LSY-2::GFP Binding Regions in Starved. Synchronized starved L1 larvae from C. elegans strain OP367 (a transgenic strain engineered to express a gene fusion between lsy-2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "LSY-2 Combined (GFP ChIP), LSY-2_L2 w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LSY-2 Combined (GFP ChIP)_ LSY-2_L2 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
]
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LSY-2 Combined (GFP ChIP)_ LSY-2_L2 w peaks_bigbed_peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/17909_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
- "displayId" : "LSY-2 Combined (GFP ChIP)_ LSY-2_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
"height" : 6,
"showDescriptions" : false,
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
"showLabels" : false
},
+ "displayId" : "LSY-2 Combined (GFP ChIP)_ LSY-2_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay"
}
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LSY-2 Combined (GFP ChIP)_ LSY-2_L2 w peaks_bigbed_peaks",
"name" : "__LSY-2 Combined (GFP ChIP), LSY-2_L2 peaks",
+ "description" : "Peak calls for LSY-2 Combined (GFP ChIP), LSY-2_L2 w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/17909_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "description" : "Peak calls for LSY-2 Combined (GFP ChIP), LSY-2_L2 w peaks"
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ]
},
{
- "description" : " Identification of Transcription Factor LSY-2::GFP Binding Regions in Starved. Synchronized starved L1 larvae from C. elegans strain OP367 (a transgenic strain engineered to express a gene fusion between lsy-2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LSY-2 Combined (GFP ChIP)_ LSY-2_EMB w peaks",
"name" : "LSY-2 Combined (GFP ChIP), LSY-2_EMB w peaks",
+ "description" : " Identification of Transcription Factor LSY-2::GFP Binding Regions in Starved. Synchronized starved L1 larvae from C. elegans strain OP367 (a transgenic strain engineered to express a gene fusion between lsy-2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
"adapter" : {
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18596.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18596.bw"
},
"type" : "BigWigAdapter"
},
"displays" : [
{
- "type" : "LinearWiggleDisplay",
"maxScore" : 144.521363154923,
"minScore" : 0,
- "displayId" : "LSY-2 Combined (GFP ChIP)_ LSY-2_EMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "displayId" : "LSY-2 Combined (GFP ChIP)_ LSY-2_EMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LSY-2 Combined (GFP ChIP)_ LSY-2_EMB w peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
]
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LSY-2 Combined (GFP ChIP)_ LSY-2_EMB w peaks_bigbed_peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18613_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "LSY-2 Combined (GFP ChIP)_ LSY-2_EMB w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
- },
- "displayId" : "LSY-2 Combined (GFP ChIP)_ LSY-2_EMB w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "height" : 6,
+ "showDescriptions" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ }
}
],
"name" : "__LSY-2 Combined (GFP ChIP), LSY-2_EMB peaks",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18613_details.gff.bb",
- "locationType" : "UriLocation"
- }
- },
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_LSY-2 Combined (GFP ChIP)_ LSY-2_EMB w peaks_bigbed_peaks",
+ "description" : "Peak calls for LSY-2 Combined (GFP ChIP), LSY-2_EMB w peaks",
"type" : "FeatureTrack",
- "description" : "Peak calls for LSY-2 Combined (GFP ChIP), LSY-2_EMB w peaks"
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ]
},
{
+ "description" : " Identification of Transcription Factor NHR-12::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP318 (a transgenic strain engineered to express a gene fusion between nhr-12 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-12 Combined (GFP ChIP)_ NHR-12_EMB w peaks",
+ "name" : "NHR-12 Combined (GFP ChIP), NHR-12_EMB w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -33611,124 +33004,129 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "displays" : [
- {
- "minScore" : 0,
- "maxScore" : 87.6145885891875,
- "type" : "LinearWiggleDisplay",
- "displayId" : "NHR-12 Combined (GFP ChIP)_ NHR-12_EMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
- ],
- "name" : "NHR-12 Combined (GFP ChIP), NHR-12_EMB w peaks",
+ "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/17893.bw",
"locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ }
},
- "type" : "QuantitativeTrack",
- "description" : " Identification of Transcription Factor NHR-12::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP318 (a transgenic strain engineered to express a gene fusion between nhr-12 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "displays" : [
+ {
+ "maxScore" : 87.6145885891875,
+ "displayId" : "NHR-12 Combined (GFP ChIP)_ NHR-12_EMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
+ }
+ ]
},
{
- "description" : "Peak calls for NHR-12 Combined (GFP ChIP), NHR-12_EMB w peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/17927_details.gff.bb"
- }
- },
- "name" : "__NHR-12 Combined (GFP ChIP), NHR-12_EMB peaks",
"displays" : [
{
- "displayId" : "NHR-12 Combined (GFP ChIP)_ NHR-12_EMB w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
+ "showDescriptions" : false,
"height" : 6,
- "showDescriptions" : false
- }
+ "showLabels" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "NHR-12 Combined (GFP ChIP)_ NHR-12_EMB w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/17927_details.gff.bb"
+ }
+ },
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-12 Combined (GFP ChIP)_ NHR-12_EMB w peaks_bigbed_peaks"
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-12 Combined (GFP ChIP)_ NHR-12_EMB w peaks_bigbed_peaks",
+ "name" : "__NHR-12 Combined (GFP ChIP), NHR-12_EMB peaks",
+ "description" : "Peak calls for NHR-12 Combined (GFP ChIP), NHR-12_EMB w peaks"
},
{
- "displays" : [
- {
- "minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 120.955120815554,
- "displayId" : "NHR-12 Combined (GFP ChIP)_ NHR-12_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-12 Combined (GFP ChIP)_ NHR-12_L2 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : " Identification of Transcription Factor NHR-12::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP318 (a transgenic strain engineered to express a gene fusion between nhr-12 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"name" : "NHR-12 Combined (GFP ChIP), NHR-12_L2 w peaks",
- "type" : "QuantitativeTrack",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-12 Combined (GFP ChIP)_ NHR-12_L2 w peaks",
+ "description" : " Identification of Transcription Factor NHR-12::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP318 (a transgenic strain engineered to express a gene fusion between nhr-12 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "minScore" : 0,
+ "displayId" : "NHR-12 Combined (GFP ChIP)_ NHR-12_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 120.955120815554
+ }
+ ],
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18443.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18443.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
}
},
{
- "displays" : [
- {
- "displayId" : "NHR-12 Combined (GFP ChIP)_ NHR-12_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
- },
- "type" : "LinearBasicDisplay"
- }
- ],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-12 Combined (GFP ChIP)_ NHR-12_L2 w peaks_bigbed_peaks",
+ "name" : "__NHR-12 Combined (GFP ChIP), NHR-12_L2 peaks",
"description" : "Peak calls for NHR-12 Combined (GFP ChIP), NHR-12_L2 w peaks",
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "NHR-12 Combined (GFP ChIP)_ NHR-12_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "renderer" : {
+ "color1" : "deeppink",
+ "showDescriptions" : false,
+ "height" : 6,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
+ }
+ }
+ ],
"adapter" : {
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18450_details.gff.bb",
"locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
- },
- "name" : "__NHR-12 Combined (GFP ChIP), NHR-12_L2 peaks"
+ }
},
{
- "description" : " Identification of Transcription Factor NHR-12::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP318 (a transgenic strain engineered to express a gene fusion between nhr-12 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "displayId" : "NHR-12 Combined (GFP ChIP)_ NHR-12_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 147.142107485101,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -33736,62 +33134,62 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/17850.bw"
}
},
- "type" : "QuantitativeTrack",
- "name" : "NHR-12 Combined (GFP ChIP), NHR-12_L3 w peaks",
- "displays" : [
- {
- "maxScore" : 147.142107485101,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0,
- "displayId" : "NHR-12 Combined (GFP ChIP)_ NHR-12_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
- ],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-12 Combined (GFP ChIP)_ NHR-12_L3 w peaks"
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-12 Combined (GFP ChIP)_ NHR-12_L3 w peaks",
+ "name" : "NHR-12 Combined (GFP ChIP), NHR-12_L3 w peaks",
+ "description" : " Identification of Transcription Factor NHR-12::GFP Binding Regions in L2. Details Synchronized L2 larvae from C. elegans strain OP318 (a transgenic strain engineered to express a gene fusion between nhr-12 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "description" : "Peak calls for NHR-12 Combined (GFP ChIP), NHR-12_L3 w peaks",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/17878_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/17878_details.gff.bb"
+ }
},
- "name" : "__NHR-12 Combined (GFP ChIP), NHR-12_L3 peaks",
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
"type" : "SvgFeatureRenderer",
"showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false,
"color1" : "deeppink"
},
- "displayId" : "NHR-12 Combined (GFP ChIP)_ NHR-12_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "displayId" : "NHR-12 Combined (GFP ChIP)_ NHR-12_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
+ "name" : "__NHR-12 Combined (GFP ChIP), NHR-12_L3 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-12 Combined (GFP ChIP)_ NHR-12_L3 w peaks_bigbed_peaks",
+ "description" : "Peak calls for NHR-12 Combined (GFP ChIP), NHR-12_L3 w peaks",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-12 Combined (GFP ChIP)_ NHR-12_L3 w peaks_bigbed_peaks"
+ ]
},
{
- "description" : " Identification of Transcription Factor ZTF-7::GFP Binding Regions in L4. Details Synchronized L4 larvae from C. elegans strain OP332 (a transgenic strain engineered to express a gene fusion between ztf-7 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 306.993029848,
+ "minScore" : 0,
+ "displayId" : "ZTF-7 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18457.bw",
@@ -33799,51 +33197,40 @@
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "name" : "ZTF-7 Combined (GFP ChIP) w peaks",
- "displays" : [
- {
- "displayId" : "ZTF-7 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 306.993029848,
- "minScore" : 0
- }
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : " Identification of Transcription Factor ZTF-7::GFP Binding Regions in L4. Details Synchronized L4 larvae from C. elegans strain OP332 (a transgenic strain engineered to express a gene fusion between ztf-7 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "ZTF-7 Combined (GFP ChIP) w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-7 Combined (GFP ChIP) w peaks"
},
{
- "description" : "Peak calls for ZTF-7 Combined (GFP ChIP) w peaks",
- "name" : "__ZTF-7 Combined (GFP ChIP) peaks",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18462_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "ZTF-7 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
- }
+ "showDescriptions" : false,
+ "height" : 6
+ },
+ "displayId" : "ZTF-7 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-7 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18462_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -33851,103 +33238,117 @@
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Peak calls for ZTF-7 Combined (GFP ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-7 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "name" : "__ZTF-7 Combined (GFP ChIP) peaks"
},
{
- "displays" : [
- {
- "minScore" : 42.5911342719405,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 104.57858870285,
- "displayId" : "TLP-1 Combined (GFP ChIP)_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
- ],
+ "description" : " Identification of Transcription Factor TLP-1::GFP Binding Regions in L1. Synchronized L1 larvae from C. elegans strain OP321 (a transgenic strain engineered to express a gene fusion between tlp-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "TLP-1 Combined (GFP ChIP)",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_TLP-1 Combined (GFP ChIP)",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : " Identification of Transcription Factor TLP-1::GFP Binding Regions in L1. Synchronized L1 larvae from C. elegans strain OP321 (a transgenic strain engineered to express a gene fusion between tlp-1 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "TLP-1 Combined (GFP ChIP)",
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18850.bw"
- },
- "type" : "BigWigAdapter"
- }
- },
- {
- "description" : " Snyder_UNC-39_GFP_EMB. Synchronized embryos from C. elegans strain OP186 (a transgenic strain engineered to express a gene fusion between unc-39 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "UNC-39 Combined (GFP ChIP), UNC-39_L2 w peaks",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/17983.bw",
- "locationType" : "UriLocation"
}
},
"displays" : [
{
- "maxScore" : 138.495707983264,
+ "maxScore" : 104.57858870285,
+ "displayId" : "TLP-1 Combined (GFP ChIP)_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 42.5911342719405,
+ "type" : "LinearWiggleDisplay"
+ }
+ ]
+ },
+ {
+ "displays" : [
+ {
"type" : "LinearWiggleDisplay",
- "minScore" : 0,
- "displayId" : "UNC-39 Combined (GFP ChIP)_ UNC-39_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "maxScore" : 138.495707983264,
+ "displayId" : "UNC-39 Combined (GFP ChIP)_ UNC-39_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-39 Combined (GFP ChIP)_ UNC-39_L2 w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/17983.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ]
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "description" : " Snyder_UNC-39_GFP_EMB. Synchronized embryos from C. elegans strain OP186 (a transgenic strain engineered to express a gene fusion between unc-39 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-39 Combined (GFP ChIP)_ UNC-39_L2 w peaks",
+ "name" : "UNC-39 Combined (GFP ChIP), UNC-39_L2 w peaks"
},
{
- "description" : "Peak calls for UNC-39 Combined (GFP ChIP), UNC-39_L2 w peaks",
- "name" : "__UNC-39 Combined (GFP ChIP), UNC-39_L2 peaks",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18004_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "UNC-39 Combined (GFP ChIP)_ UNC-39_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay"
+ "color1" : "deeppink",
+ "height" : 6,
+ "showDescriptions" : false,
+ "showLabels" : false
+ }
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-39 Combined (GFP ChIP)_ UNC-39_L2 w peaks_bigbed_peaks",
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18004_details.gff.bb"
+ }
+ },
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ]
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-39 Combined (GFP ChIP)_ UNC-39_L2 w peaks_bigbed_peaks",
+ "name" : "__UNC-39 Combined (GFP ChIP), UNC-39_L2 peaks",
+ "description" : "Peak calls for UNC-39 Combined (GFP ChIP), UNC-39_L2 w peaks"
},
{
"description" : " Snyder_UNC-39_GFP_EMB. Synchronized embryos from C. elegans strain OP186 (a transgenic strain engineered to express a gene fusion between unc-39 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "UNC-39 Combined (GFP ChIP), UNC-39_EMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-39 Combined (GFP ChIP)_ UNC-39_EMB w peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
"type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18016.bw",
@@ -33955,205 +33356,184 @@
},
"type" : "BigWigAdapter"
},
- "name" : "UNC-39 Combined (GFP ChIP), UNC-39_EMB w peaks",
"displays" : [
{
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
+ "displayId" : "UNC-39 Combined (GFP ChIP)_ UNC-39_EMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"maxScore" : 164.546792046793,
- "displayId" : "UNC-39 Combined (GFP ChIP)_ UNC-39_EMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-39 Combined (GFP ChIP)_ UNC-39_EMB w peaks"
+ ]
},
{
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18038_details.gff.bb",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigBedAdapter"
},
- "name" : "__UNC-39 Combined (GFP ChIP), UNC-39_EMB peaks",
- "description" : "Peak calls for UNC-39 Combined (GFP ChIP), UNC-39_EMB w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-39 Combined (GFP ChIP)_ UNC-39_EMB w peaks_bigbed_peaks",
"displays" : [
{
- "displayId" : "UNC-39 Combined (GFP ChIP)_ UNC-39_EMB w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
"height" : 6,
- "showDescriptions" : false
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "UNC-39 Combined (GFP ChIP)_ UNC-39_EMB w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
- ]
- },
- {
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
],
+ "description" : "Peak calls for UNC-39 Combined (GFP ChIP), UNC-39_EMB w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-39 Combined (GFP ChIP)_ UNC-39_EMB w peaks_bigbed_peaks",
+ "name" : "__UNC-39 Combined (GFP ChIP), UNC-39_EMB peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-55 Combined (GFP ChIP)",
- "displays" : [
- {
- "type" : "LinearWiggleDisplay",
- "maxScore" : 1241.3793742861,
- "minScore" : 422.137293514411,
- "displayId" : "UNC-55 Combined (GFP ChIP)_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack"
+ },
+ {
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18917.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18917.bw"
}
},
- "type" : "QuantitativeTrack",
- "name" : "UNC-55 Combined (GFP ChIP)",
- "description" : " Identification of Transcription Factor RPC-1::RPC-1 Binding Regions in Young Adults. Synchronized L2 larvae from C. elegans strain NC1369 (a transgenic strain engineered to express a gene fusion between unc-55 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-130 Combined (GFP ChIP) w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
+ "displays" : [
+ {
+ "minScore" : 422.137293514411,
+ "displayId" : "UNC-55 Combined (GFP ChIP)_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 1241.3793742861,
+ "type" : "LinearWiggleDisplay"
+ }
],
+ "description" : " Identification of Transcription Factor RPC-1::RPC-1 Binding Regions in Young Adults. Synchronized L2 larvae from C. elegans strain NC1369 (a transgenic strain engineered to express a gene fusion between unc-55 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-55 Combined (GFP ChIP)",
+ "name" : "UNC-55 Combined (GFP ChIP)",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack"
+ },
+ {
"displays" : [
{
"displayId" : "UNC-130 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
+ "minScore" : 0,
"maxScore" : 61.2915800678,
- "minScore" : 0
+ "type" : "LinearWiggleDisplay"
}
],
- "name" : "UNC-130 Combined (GFP ChIP) w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_UNC-130_GFP_L1_combined_WS220.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "description" : " Identification of Transcription Factor UNC-130::GFP Binding Regions in L1 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
- "displays" : [
- {
- "renderer" : {
- "color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 6,
- "showDescriptions" : false
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "UNC-130 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_UNC-130_GFP_L1_combined_WS220.bw"
}
+ },
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
+ "description" : " Identification of Transcription Factor UNC-130::GFP Binding Regions in L1 (Snyder project,Snyder subgroup) General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-130 Combined (GFP ChIP) w peaks",
+ "name" : "UNC-130 Combined (GFP ChIP) w peaks"
+ },
+ {
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-130 Combined (GFP ChIP) w peaks_bigbed_peaks",
- "description" : "Peak calls for UNC-130 Combined (GFP ChIP) w peaks",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Peak calls for UNC-130 Combined (GFP ChIP) w peaks",
+ "name" : "__UNC-130 Combined (GFP ChIP) peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_UNC-130 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "displays" : [
+ {
+ "displayId" : "UNC-130 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "renderer" : {
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4254_details.gff.bb",
"locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
- },
- "name" : "__UNC-130 Combined (GFP ChIP) peaks"
+ }
},
{
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZIP-2 Combined (GFP ChIP) w peaks",
"displays" : [
{
+ "maxScore" : 466.052304168047,
"displayId" : "ZIP-2 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "maxScore" : 466.052304168047,
"type" : "LinearWiggleDisplay"
}
],
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18094.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18094.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
"type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
"name" : "ZIP-2 Combined (GFP ChIP) w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZIP-2 Combined (GFP ChIP) w peaks",
"description" : " Snyder_ZIP-2_GFP_L4. Synchronized L4 larvae from C. elegans strain OP432 (a transgenic strain engineered to express a gene fusion between zip-2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink",
"showDescriptions" : false,
- "height" : 6
+ "height" : 6,
+ "showLabels" : false,
+ "color1" : "deeppink"
},
- "type" : "LinearBasicDisplay",
"displayId" : "ZIP-2 Combined (GFP ChIP) w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZIP-2 Combined (GFP ChIP) w peaks_bigbed_peaks",
- "description" : "Peak calls for ZIP-2 Combined (GFP ChIP) w peaks",
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
@@ -34161,90 +33541,101 @@
},
"type" : "BigBedAdapter"
},
- "name" : "__ZIP-2 Combined (GFP ChIP) peaks"
- },
- {
- "name" : "ZK377.2 Combined (GFP ChIP), ZK377.2_GFP_L4 w peaks",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/13835.bw",
- "locationType" : "UriLocation"
- }
- },
- "type" : "QuantitativeTrack",
- "description" : " Identification of Transcription Factor ZK377.2::GFP Binding Regions in L1. Synchronized L1 larvae from C. elegans strain OP355 (a transgenic strain engineered to express a gene fusion between ZK377.2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L4 w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZIP-2 Combined (GFP ChIP) w peaks_bigbed_peaks",
+ "name" : "__ZIP-2 Combined (GFP ChIP) peaks",
+ "description" : "Peak calls for ZIP-2 Combined (GFP ChIP) w peaks"
+ },
+ {
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "description" : " Identification of Transcription Factor ZK377.2::GFP Binding Regions in L1. Synchronized L1 larvae from C. elegans strain OP355 (a transgenic strain engineered to express a gene fusion between ZK377.2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L4 w peaks",
+ "name" : "ZK377.2 Combined (GFP ChIP), ZK377.2_GFP_L4 w peaks",
"displays" : [
{
"displayId" : "ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
+ "minScore" : 0,
"maxScore" : 109.469782107746,
- "minScore" : 0
+ "type" : "LinearWiggleDisplay"
}
- ]
- },
- {
- "type" : "FeatureTrack",
+ ],
"adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/13845_details.gff.bb"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/13835.bw"
}
- },
- "name" : "__ZK377.2 Combined (GFP ChIP), ZK377.2_GFP_L4 peaks",
- "description" : "Peak calls for ZK377.2 Combined (GFP ChIP), ZK377.2_GFP_L4 w peaks",
+ }
+ },
+ {
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L4 w peaks_bigbed_peaks",
+ "name" : "__ZK377.2 Combined (GFP ChIP), ZK377.2_GFP_L4 peaks",
+ "description" : "Peak calls for ZK377.2 Combined (GFP ChIP), ZK377.2_GFP_L4 w peaks",
"displays" : [
{
- "displayId" : "ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
"type" : "SvgFeatureRenderer",
+ "height" : 6,
+ "showDescriptions" : false,
"showLabels" : false,
"color1" : "deeppink"
- }
+ },
+ "displayId" : "ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/13845_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
- "description" : " Identification of Transcription Factor ZK377.2::GFP Binding Regions in L1. Synchronized L1 larvae from C. elegans strain OP355 (a transgenic strain engineered to express a gene fusion between ZK377.2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/14936.bw"
- },
- "type" : "BigWigAdapter"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/14936.bw",
+ "locationType" : "UriLocation"
+ }
},
- "type" : "QuantitativeTrack",
- "name" : "ZK377.2 Combined (GFP ChIP), ZK377.2_GFP_L1 w peaks",
"displays" : [
{
- "displayId" : "ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
"maxScore" : 106.032971702696,
+ "minScore" : 0,
+ "displayId" : "ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay"
}
],
+ "description" : " Identification of Transcription Factor ZK377.2::GFP Binding Regions in L1. Synchronized L1 larvae from C. elegans strain OP355 (a transgenic strain engineered to express a gene fusion between ZK377.2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L1 w peaks",
+ "name" : "ZK377.2 Combined (GFP ChIP), ZK377.2_GFP_L1 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -34253,53 +33644,125 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L1 w peaks"
+ "type" : "QuantitativeTrack"
},
{
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/14942_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/14942_details.gff.bb"
+ }
},
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6
+ },
+ "displayId" : "ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"name" : "__ZK377.2 Combined (GFP ChIP), ZK377.2_GFP_L1 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L1 w peaks_bigbed_peaks",
"description" : "Peak calls for ZK377.2 Combined (GFP ChIP), ZK377.2_GFP_L1 w peaks",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ]
+ },
+ {
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L1 w peaks_bigbed_peaks",
+ "description" : " Identification of Transcription Factor ZK377.2::GFP Binding Regions in L1. Synchronized L1 larvae from C. elegans strain OP355 (a transgenic strain engineered to express a gene fusion between ZK377.2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "ZK377.2 Combined (GFP ChIP), ZK377.2_GFP_L2 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L2 w peaks",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 65.330709133205,
+ "displayId" : "ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0
+ }
+ ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/13514.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ }
+ },
+ {
"displays" : [
{
- "displayId" : "ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
+ "showDescriptions" : false,
"height" : 6,
- "showDescriptions" : false
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
},
+ "displayId" : "ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/13520_details.gff.bb"
+ },
+ "type" : "BigBedAdapter"
+ },
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L2 w peaks_bigbed_peaks",
+ "name" : "__ZK377.2 Combined (GFP ChIP), ZK377.2_GFP_L2 peaks",
+ "description" : "Peak calls for ZK377.2 Combined (GFP ChIP), ZK377.2_GFP_L2 w peaks"
},
{
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/13514.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/13831.bw",
"locationType" : "UriLocation"
}
},
- "name" : "ZK377.2 Combined (GFP ChIP), ZK377.2_GFP_L2 w peaks",
+ "displays" : [
+ {
+ "maxScore" : 35.6862864981083,
+ "displayId" : "ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
+ "name" : "ZK377.2 Combined (GFP ChIP), ZK377.2_GFP_L3 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L3 w peaks",
"description" : " Identification of Transcription Factor ZK377.2::GFP Binding Regions in L1. Synchronized L1 larvae from C. elegans strain OP355 (a transgenic strain engineered to express a gene fusion between ZK377.2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -34307,61 +33770,44 @@
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L2 w peaks",
- "displays" : [
- {
- "minScore" : 0,
- "maxScore" : 65.330709133205,
- "type" : "LinearWiggleDisplay",
- "displayId" : "ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
]
},
{
- "description" : "Peak calls for ZK377.2 Combined (GFP ChIP), ZK377.2_GFP_L2 w peaks",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/13520_details.gff.bb",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/13838_details.gff.bb",
"locationType" : "UriLocation"
}
},
- "name" : "__ZK377.2 Combined (GFP ChIP), ZK377.2_GFP_L2 peaks",
"displays" : [
{
- "displayId" : "ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
+ "displayId" : "ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
+ "showLabels" : false,
"showDescriptions" : false,
"height" : 6
- }
+ },
+ "type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "Peak calls for ZK377.2 Combined (GFP ChIP), ZK377.2_GFP_L3 w peaks",
+ "name" : "__ZK377.2 Combined (GFP ChIP), ZK377.2_GFP_L3 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L3 w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L2 w peaks_bigbed_peaks"
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ]
},
{
- "displays" : [
- {
- "displayId" : "ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
- "maxScore" : 35.6862864981083,
- "minScore" : 0
- }
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L3 w peaks",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -34370,63 +33816,63 @@
"Transcription Factors",
"GFP ChIP"
],
- "description" : " Identification of Transcription Factor ZK377.2::GFP Binding Regions in L1. Synchronized L1 larvae from C. elegans strain OP355 (a transgenic strain engineered to express a gene fusion between ZK377.2 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "ZK377.2 Combined (GFP ChIP), ZK377.2_GFP_L3 w peaks",
- "type" : "QuantitativeTrack",
+ "name" : "ZTF-11 Combined (GFP ChIP), ZTF-11_L4 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-11 Combined (GFP ChIP)_ ZTF-11_L4 w peaks",
+ "description" : " Snyder_ZTF-11_GFP_L3. Synchronized L3 larvae from C. elegans strain OP236 (a transgenic strain engineered to express a gene fusion between ztf-11 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 52.8813826600121,
+ "displayId" : "ZTF-11 Combined (GFP ChIP)_ ZTF-11_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0
+ }
+ ],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/13831.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/17949.bw",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigWigAdapter"
}
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L3 w peaks_bigbed_peaks",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
- "displayId" : "ZK377.2 Combined (GFP ChIP)_ ZK377.2_GFP_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
+ "color1" : "deeppink",
"height" : 6,
"showDescriptions" : false,
- "color1" : "deeppink",
"showLabels" : false,
"type" : "SvgFeatureRenderer"
},
+ "displayId" : "ZTF-11 Combined (GFP ChIP)_ ZTF-11_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay"
}
],
- "name" : "__ZK377.2 Combined (GFP ChIP), ZK377.2_GFP_L3 peaks",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/13838_details.gff.bb",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/17967_details.gff.bb",
"locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ }
},
"type" : "FeatureTrack",
- "description" : "Peak calls for ZK377.2 Combined (GFP ChIP), ZK377.2_GFP_L3 w peaks"
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "name" : "__ZTF-11 Combined (GFP ChIP), ZTF-11_L4 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-11 Combined (GFP ChIP)_ ZTF-11_L4 w peaks_bigbed_peaks",
+ "description" : "Peak calls for ZTF-11 Combined (GFP ChIP), ZTF-11_L4 w peaks"
},
{
- "name" : "ZTF-11 Combined (GFP ChIP), ZTF-11_L4 w peaks",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/17949.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
"description" : " Snyder_ZTF-11_GFP_L3. Synchronized L3 larvae from C. elegans strain OP236 (a transgenic strain engineered to express a gene fusion between ztf-11 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-11 Combined (GFP ChIP)_ ZTF-11_L4 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-11 Combined (GFP ChIP)_ ZTF-11_EMB w peaks",
+ "name" : "ZTF-11 Combined (GFP ChIP), ZTF-11_EMB w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -34435,155 +33881,171 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18125.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "displayId" : "ZTF-11 Combined (GFP ChIP)_ ZTF-11_L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "maxScore" : 52.8813826600121,
"type" : "LinearWiggleDisplay",
- "minScore" : 0
+ "displayId" : "ZTF-11 Combined (GFP ChIP)_ ZTF-11_EMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 86.105176819452
}
]
},
{
+ "description" : "Peak calls for ZTF-11 Combined (GFP ChIP), ZTF-11_EMB w peaks",
+ "name" : "__ZTF-11 Combined (GFP ChIP), ZTF-11_EMB peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-11 Combined (GFP ChIP)_ ZTF-11_EMB w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-11 Combined (GFP ChIP)_ ZTF-11_L4 w peaks_bigbed_peaks",
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18151_details.gff.bb"
+ }
+ },
"displays" : [
{
- "displayId" : "ZTF-11 Combined (GFP ChIP)_ ZTF-11_L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
"type" : "SvgFeatureRenderer",
"showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false,
"color1" : "deeppink"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "ZTF-11 Combined (GFP ChIP)_ ZTF-11_EMB w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
- ],
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/17967_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "__ZTF-11 Combined (GFP ChIP), ZTF-11_L4 peaks",
- "description" : "Peak calls for ZTF-11 Combined (GFP ChIP), ZTF-11_L4 w peaks"
+ ]
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-11 Combined (GFP ChIP)_ ZTF-11_EMB w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
+ "description" : " Snyder_ZTF-11_GFP_L3. Synchronized L3 larvae from C. elegans strain OP236 (a transgenic strain engineered to express a gene fusion between ztf-11 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-11 Combined (GFP ChIP)_ ZTF-11_L3 w peaks",
+ "name" : "ZTF-11 Combined (GFP ChIP), ZTF-11_L3 w peaks",
"displays" : [
{
- "maxScore" : 86.105176819452,
"type" : "LinearWiggleDisplay",
+ "displayId" : "ZTF-11 Combined (GFP ChIP)_ ZTF-11_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "displayId" : "ZTF-11 Combined (GFP ChIP)_ ZTF-11_EMB w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "maxScore" : 103.287606080516
}
],
- "name" : "ZTF-11 Combined (GFP ChIP), ZTF-11_EMB w peaks",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18125.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18071.bw",
"locationType" : "UriLocation"
- }
- },
- "type" : "QuantitativeTrack",
- "description" : " Snyder_ZTF-11_GFP_L3. Synchronized L3 larvae from C. elegans strain OP236 (a transgenic strain engineered to express a gene fusion between ztf-11 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-11 Combined (GFP ChIP)_ ZTF-11_EMB w peaks_bigbed_peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-11 Combined (GFP ChIP)_ ZTF-11_L3 w peaks_bigbed_peaks",
+ "name" : "__ZTF-11 Combined (GFP ChIP), ZTF-11_L3 peaks",
+ "description" : "Peak calls for ZTF-11 Combined (GFP ChIP), ZTF-11_L3 w peaks",
"displays" : [
{
- "displayId" : "ZTF-11 Combined (GFP ChIP)_ ZTF-11_EMB w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
+ "displayId" : "ZTF-11 Combined (GFP ChIP)_ ZTF-11_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
"type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "deeppink",
"showDescriptions" : false,
- "height" : 6
- }
+ "height" : 6,
+ "color1" : "deeppink"
+ },
+ "type" : "LinearBasicDisplay"
}
],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18151_details.gff.bb",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18086_details.gff.bb"
}
- },
- "type" : "FeatureTrack",
- "name" : "__ZTF-11 Combined (GFP ChIP), ZTF-11_EMB peaks",
- "description" : "Peak calls for ZTF-11 Combined (GFP ChIP), ZTF-11_EMB w peaks"
+ }
},
{
- "name" : "ZTF-11 Combined (GFP ChIP), ZTF-11_L3 w peaks",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18071.bw"
- },
- "type" : "BigWigAdapter"
- },
- "description" : " Snyder_ZTF-11_GFP_L3. Synchronized L3 larvae from C. elegans strain OP236 (a transgenic strain engineered to express a gene fusion between ztf-11 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-11 Combined (GFP ChIP)_ ZTF-11_L3 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-4 Combined (GFP ChIP)_ ZTF-4_L1 w peaks",
+ "name" : "ZTF-4 Combined (GFP ChIP), ZTF-4_L1 w peaks",
+ "description" : " Snyder_ZTF-4_GFP_L2. Synchronized L2 larvae from C. elegans strain OP322 (a transgenic strain engineered to express a gene fusion between ztf-4 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/17944.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "displayId" : "ZTF-11 Combined (GFP ChIP)_ ZTF-11_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
"type" : "LinearWiggleDisplay",
- "maxScore" : 103.287606080516
+ "maxScore" : 177.486681820052,
+ "minScore" : 0,
+ "displayId" : "ZTF-4 Combined (GFP ChIP)_ ZTF-4_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
}
]
},
{
"displays" : [
{
+ "displayId" : "ZTF-4 Combined (GFP ChIP)_ ZTF-4_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
+ "color1" : "deeppink",
"height" : 6,
"showDescriptions" : false,
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "ZTF-11 Combined (GFP ChIP)_ ZTF-11_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "type" : "LinearBasicDisplay"
}
],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/17992_details.gff.bb"
+ }
+ },
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -34592,143 +34054,72 @@
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-11 Combined (GFP ChIP)_ ZTF-11_L3 w peaks_bigbed_peaks",
- "description" : "Peak calls for ZTF-11 Combined (GFP ChIP), ZTF-11_L3 w peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18086_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "__ZTF-11 Combined (GFP ChIP), ZTF-11_L3 peaks"
+ "name" : "__ZTF-4 Combined (GFP ChIP), ZTF-4_L1 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-4 Combined (GFP ChIP)_ ZTF-4_L1 w peaks_bigbed_peaks",
+ "description" : "Peak calls for ZTF-4 Combined (GFP ChIP), ZTF-4_L1 w peaks"
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-4 Combined (GFP ChIP)_ ZTF-4_L1 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : " Snyder_ZTF-4_GFP_L2. Synchronized L2 larvae from C. elegans strain OP322 (a transgenic strain engineered to express a gene fusion between ztf-4 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "ZTF-4 Combined (GFP ChIP), ZTF-4_L3 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-4 Combined (GFP ChIP)_ ZTF-4_L3 w peaks",
"displays" : [
{
- "displayId" : "ZTF-4 Combined (GFP ChIP)_ ZTF-4_L1 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 61.062747811625,
+ "displayId" : "ZTF-4 Combined (GFP ChIP)_ ZTF-4_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "maxScore" : 177.486681820052,
"type" : "LinearWiggleDisplay"
}
],
- "name" : "ZTF-4 Combined (GFP ChIP), ZTF-4_L1 w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/17944.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/19078.bw",
"locationType" : "UriLocation"
}
- },
- "description" : " Snyder_ZTF-4_GFP_L2. Synchronized L2 larvae from C. elegans strain OP322 (a transgenic strain engineered to express a gene fusion between ztf-4 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
},
{
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "height" : 6,
- "showDescriptions" : false
- },
- "displayId" : "ZTF-4 Combined (GFP ChIP)_ ZTF-4_L1 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
- }
- ],
+ "description" : "Peak calls for ZTF-4 Combined (GFP ChIP), ZTF-4_L3 w peaks",
+ "name" : "__ZTF-4 Combined (GFP ChIP), ZTF-4_L3 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-4 Combined (GFP ChIP)_ ZTF-4_L3 w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-4 Combined (GFP ChIP)_ ZTF-4_L1 w peaks_bigbed_peaks",
- "description" : "Peak calls for ZTF-4 Combined (GFP ChIP), ZTF-4_L1 w peaks",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/17992_details.gff.bb"
- }
- },
- "type" : "FeatureTrack",
- "name" : "__ZTF-4 Combined (GFP ChIP), ZTF-4_L1 peaks"
- },
- {
- "description" : " Snyder_ZTF-4_GFP_L2. Synchronized L2 larvae from C. elegans strain OP322 (a transgenic strain engineered to express a gene fusion between ztf-4 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "ZTF-4 Combined (GFP ChIP), ZTF-4_L3 w peaks",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/19078.bw"
- }
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/19083_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
},
- "displays" : [
- {
- "minScore" : 0,
- "maxScore" : 61.062747811625,
- "type" : "LinearWiggleDisplay",
- "displayId" : "ZTF-4 Combined (GFP ChIP)_ ZTF-4_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-4 Combined (GFP ChIP)_ ZTF-4_L3 w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ]
- },
- {
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-4 Combined (GFP ChIP)_ ZTF-4_L3 w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "ZTF-4 Combined (GFP ChIP)_ ZTF-4_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
- },
- "displayId" : "ZTF-4 Combined (GFP ChIP)_ ZTF-4_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "showLabels" : false
+ }
}
- ],
- "name" : "__ZTF-4 Combined (GFP ChIP), ZTF-4_L3 peaks",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/19083_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "description" : "Peak calls for ZTF-4 Combined (GFP ChIP), ZTF-4_L3 w peaks"
+ ]
},
{
"category" : [
@@ -34736,65 +34127,68 @@
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : " Snyder_ZTF-4_GFP_L2. Synchronized L2 larvae from C. elegans strain OP322 (a transgenic strain engineered to express a gene fusion between ztf-4 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "ZTF-4 Combined (GFP ChIP), ZTF-4_L2 w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-4 Combined (GFP ChIP)_ ZTF-4_L2 w peaks",
"displays" : [
{
- "displayId" : "ZTF-4 Combined (GFP ChIP)_ ZTF-4_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "maxScore" : 155.882403859331,
"type" : "LinearWiggleDisplay",
- "minScore" : 0
+ "minScore" : 0,
+ "displayId" : "ZTF-4 Combined (GFP ChIP)_ ZTF-4_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 155.882403859331
}
],
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18015.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18015.bw"
}
- },
- "name" : "ZTF-4 Combined (GFP ChIP), ZTF-4_L2 w peaks",
- "description" : " Snyder_ZTF-4_GFP_L2. Synchronized L2 larvae from C. elegans strain OP322 (a transgenic strain engineered to express a gene fusion between ztf-4 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-4 Combined (GFP ChIP)_ ZTF-4_L2 w peaks_bigbed_peaks",
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18058_details.gff.bb"
+ }
+ },
"displays" : [
{
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
"type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6,
+ "color1" : "deeppink"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "ZTF-4 Combined (GFP ChIP)_ ZTF-4_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
+ "displayId" : "ZTF-4 Combined (GFP ChIP)_ ZTF-4_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
}
],
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18058_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
"name" : "__ZTF-4 Combined (GFP ChIP), ZTF-4_L2 peaks",
- "description" : "Peak calls for ZTF-4 Combined (GFP ChIP), ZTF-4_L2 w peaks"
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_ZTF-4 Combined (GFP ChIP)_ ZTF-4_L2 w peaks_bigbed_peaks",
+ "description" : "Peak calls for ZTF-4 Combined (GFP ChIP), ZTF-4_L2 w peaks",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ]
},
{
+ "name" : "NHR-23 Combined (GFP ChIP), NHR-23_L3 w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-23 Combined (GFP ChIP)_ NHR-23_L3 w peaks",
+ "description" : " Snyder_NHR-23_GFP_L2. Synchronized L2 larvae from C. elegans strain OP43 (a transgenic strain engineered to express a gene fusion between nhr-23 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -34803,15 +34197,6 @@
"Transcription Factors",
"GFP ChIP"
],
- "displays" : [
- {
- "type" : "LinearWiggleDisplay",
- "maxScore" : 134.527597185574,
- "minScore" : 0,
- "displayId" : "NHR-23 Combined (GFP ChIP)_ NHR-23_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
- ],
- "name" : "NHR-23 Combined (GFP ChIP), NHR-23_L3 w peaks",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -34819,74 +34204,92 @@
"locationType" : "UriLocation"
}
},
- "type" : "QuantitativeTrack",
- "description" : " Snyder_NHR-23_GFP_L2. Synchronized L2 larvae from C. elegans strain OP43 (a transgenic strain engineered to express a gene fusion between nhr-23 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "displays" : [
+ {
+ "minScore" : 0,
+ "displayId" : "NHR-23 Combined (GFP ChIP)_ NHR-23_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 134.527597185574,
+ "type" : "LinearWiggleDisplay"
+ }
+ ]
},
{
- "description" : "Peak calls for NHR-23 Combined (GFP ChIP), NHR-23_L3 w peaks",
"name" : "__NHR-23 Combined (GFP ChIP), NHR-23_L3 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-23 Combined (GFP ChIP)_ NHR-23_L3 w peaks_bigbed_peaks",
+ "description" : "Peak calls for NHR-23 Combined (GFP ChIP), NHR-23_L3 w peaks",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18671_details.gff.bb",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18671_details.gff.bb"
},
"type" : "BigBedAdapter"
},
"displays" : [
{
- "displayId" : "NHR-23 Combined (GFP ChIP)_ NHR-23_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay",
+ "displayId" : "NHR-23 Combined (GFP ChIP)_ NHR-23_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
"color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
"height" : 6,
- "showDescriptions" : false
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
}
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-23 Combined (GFP ChIP)_ NHR-23_L3 w peaks_bigbed_peaks",
+ ]
+ },
+ {
+ "description" : " Snyder_NHR-23_GFP_L2. Synchronized L2 larvae from C. elegans strain OP43 (a transgenic strain engineered to express a gene fusion between nhr-23 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "NHR-23 Combined (GFP ChIP), NHR-23_L2 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-23 Combined (GFP ChIP)_ NHR-23_L2 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
- },
- {
- "description" : " Snyder_NHR-23_GFP_L2. Synchronized L2 larvae from C. elegans strain OP43 (a transgenic strain engineered to express a gene fusion between nhr-23 and GFP) were treated with the cross-linking reagent formaldehyde. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "NHR-23 Combined (GFP ChIP), NHR-23_L2 w peaks",
+ ],
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18037.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18037.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
"displays" : [
{
+ "type" : "LinearWiggleDisplay",
"displayId" : "NHR-23 Combined (GFP ChIP)_ NHR-23_L2 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "maxScore" : 90.349917497134,
- "type" : "LinearWiggleDisplay"
+ "maxScore" : 90.349917497134
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-23 Combined (GFP ChIP)_ NHR-23_L2 w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
]
},
{
- "name" : "__NHR-23 Combined (GFP ChIP), NHR-23_L2 peaks",
+ "displays" : [
+ {
+ "renderer" : {
+ "showDescriptions" : false,
+ "height" : 6,
+ "showLabels" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "NHR-23 Combined (GFP ChIP)_ NHR-23_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
@@ -34894,106 +34297,99 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18066_details.gff.bb"
}
},
- "type" : "FeatureTrack",
- "description" : "Peak calls for NHR-23 Combined (GFP ChIP), NHR-23_L2 w peaks",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-23 Combined (GFP ChIP)_ NHR-23_L2 w peaks_bigbed_peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "displays" : [
- {
- "displayId" : "NHR-23 Combined (GFP ChIP)_ NHR-23_L2 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "renderer" : {
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "height" : 6,
- "showDescriptions" : false
- },
- "type" : "LinearBasicDisplay"
- }
- ]
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_NHR-23 Combined (GFP ChIP)_ NHR-23_L2 w peaks_bigbed_peaks",
+ "name" : "__NHR-23 Combined (GFP ChIP), NHR-23_L2 peaks",
+ "description" : "Peak calls for NHR-23 Combined (GFP ChIP), NHR-23_L2 w peaks"
},
{
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_N2_POLII_L1_combined_WS220.bw"
- },
- "type" : "BigWigAdapter"
- },
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_L1 w peaks",
"name" : "Pol II Combined (N2 ChIP), N2_POLII_L1 w peaks",
"description" : " Identification of Binding Regions for transcription factors in C. elegans. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Control N2 ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_L1 w peaks",
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_N2_POLII_L1_combined_WS220.bw"
+ }
+ },
"displays" : [
{
- "displayId" : "Pol II Combined (N2 ChIP)_ N2_POLII_L1 w peaks_Transcription Factors_Control N2 ChIP-LinearWiggleDisplay",
- "maxScore" : 74.3174335851365,
"type" : "LinearWiggleDisplay",
- "minScore" : 0
+ "minScore" : 0,
+ "displayId" : "Pol II Combined (N2 ChIP)_ N2_POLII_L1 w peaks_Transcription Factors_Control N2 ChIP-LinearWiggleDisplay",
+ "maxScore" : 74.3174335851365
}
]
},
{
- "description" : "Peak calls for Pol II Combined (N2 ChIP), N2_POLII_L1 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_L1 w peaks_bigbed_peaks",
"name" : "__Pol II Combined (N2 ChIP), N2_POLII_L1 peaks",
+ "description" : "Peak calls for Pol II Combined (N2 ChIP), N2_POLII_L1 w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Control N2 ChIP"
+ ],
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4325_details.gff.bb",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4325_details.gff.bb"
},
"type" : "BigBedAdapter"
},
"displays" : [
{
- "displayId" : "Pol II Combined (N2 ChIP)_ N2_POLII_L1 w peaks_Transcription Factors_Control N2 ChIP_bigbed_peaks",
"renderer" : {
"type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "deeppink",
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
+ "color1" : "deeppink"
},
+ "displayId" : "Pol II Combined (N2 ChIP)_ N2_POLII_L1 w peaks_Transcription Factors_Control N2 ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay"
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_L1 w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Control N2 ChIP"
]
},
{
- "name" : "Pol II Combined (N2 ChIP), N2_POLII_eemb w peaks",
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 93.901565726615,
+ "displayId" : "Pol II Combined (N2 ChIP)_ N2_POLII_eemb w peaks_Transcription Factors_Control N2 ChIP-LinearWiggleDisplay",
+ "minScore" : 0
+ }
+ ],
"adapter" : {
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_N2_POLII_eemb_combined_WS220.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_N2_POLII_eemb_combined_WS220.bw"
},
"type" : "BigWigAdapter"
},
- "description" : " Identification of Binding Regions for transcription factors in C. elegans. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_eemb w peaks",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -35002,19 +34398,24 @@
"Transcription Factors",
"Control N2 ChIP"
],
+ "name" : "Pol II Combined (N2 ChIP), N2_POLII_eemb w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_eemb w peaks",
+ "description" : " Identification of Binding Regions for transcription factors in C. elegans. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ },
+ {
"displays" : [
{
- "minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 93.901565726615,
- "displayId" : "Pol II Combined (N2 ChIP)_ N2_POLII_eemb w peaks_Transcription Factors_Control N2 ChIP-LinearWiggleDisplay"
+ "type" : "LinearBasicDisplay",
+ "displayId" : "Pol II Combined (N2 ChIP)_ N2_POLII_eemb w peaks_Transcription Factors_Control N2 ChIP_bigbed_peaks",
+ "renderer" : {
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ }
}
- ]
- },
- {
- "description" : "Peak calls for Pol II Combined (N2 ChIP), N2_POLII_eemb w peaks",
- "name" : "__Pol II Combined (N2 ChIP), N2_POLII_eemb peaks",
- "type" : "FeatureTrack",
+ ],
"adapter" : {
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4384_details.gff.bb",
@@ -35022,94 +34423,101 @@
},
"type" : "BigBedAdapter"
},
- "displays" : [
- {
- "renderer" : {
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "height" : 6,
- "showDescriptions" : false
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "Pol II Combined (N2 ChIP)_ N2_POLII_eemb w peaks_Transcription Factors_Control N2 ChIP_bigbed_peaks"
- }
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_eemb w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Control N2 ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ]
+ "name" : "__Pol II Combined (N2 ChIP), N2_POLII_eemb peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_eemb w peaks_bigbed_peaks",
+ "description" : "Peak calls for Pol II Combined (N2 ChIP), N2_POLII_eemb w peaks"
},
{
"description" : " Identification of Binding Regions for transcription factors in C. elegans. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Pol II Combined (N2 ChIP), N2_POLII_lemb w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_lemb w peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Control N2 ChIP"
+ ],
"type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_N2_POLII_lemb_combined_WS220.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_N2_POLII_lemb_combined_WS220.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
- "name" : "Pol II Combined (N2 ChIP), N2_POLII_lemb w peaks",
"displays" : [
{
- "maxScore" : 81.615285741175,
"type" : "LinearWiggleDisplay",
+ "displayId" : "Pol II Combined (N2 ChIP)_ N2_POLII_lemb w peaks_Transcription Factors_Control N2 ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "displayId" : "Pol II Combined (N2 ChIP)_ N2_POLII_lemb w peaks_Transcription Factors_Control N2 ChIP-LinearWiggleDisplay"
+ "maxScore" : 81.615285741175
}
- ],
+ ]
+ },
+ {
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Control N2 ChIP"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_lemb w peaks"
- },
- {
+ "description" : "Peak calls for Pol II Combined (N2 ChIP), N2_POLII_lemb w peaks",
+ "name" : "__Pol II Combined (N2 ChIP), N2_POLII_lemb peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_lemb w peaks_bigbed_peaks",
"displays" : [
{
- "displayId" : "Pol II Combined (N2 ChIP)_ N2_POLII_lemb w peaks_Transcription Factors_Control N2 ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
- "showDescriptions" : false,
- "height" : 6
- }
+ "showLabels" : false,
+ "height" : 6,
+ "showDescriptions" : false
+ },
+ "displayId" : "Pol II Combined (N2 ChIP)_ N2_POLII_lemb w peaks_Transcription Factors_Control N2 ChIP_bigbed_peaks"
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_lemb w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Control N2 ChIP"
- ],
- "description" : "Peak calls for Pol II Combined (N2 ChIP), N2_POLII_lemb w peaks",
- "name" : "__Pol II Combined (N2 ChIP), N2_POLII_lemb peaks",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4348_details.gff.bb"
- }
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4348_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
}
},
{
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_N2_POLII_L3_combined_WS220.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
+ "displays" : [
+ {
+ "maxScore" : 162.957168306926,
+ "minScore" : 0,
+ "displayId" : "Pol II Combined (N2 ChIP)_ N2_POLII_L3 w peaks_Transcription Factors_Control N2 ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
+ "description" : " Identification of Binding Regions for transcription factors in C. elegans. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_L3 w peaks",
+ "name" : "Pol II Combined (N2 ChIP), N2_POLII_L3 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -35118,27 +34526,9 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "displays" : [
- {
- "type" : "LinearWiggleDisplay",
- "maxScore" : 162.957168306926,
- "minScore" : 0,
- "displayId" : "Pol II Combined (N2 ChIP)_ N2_POLII_L3 w peaks_Transcription Factors_Control N2 ChIP-LinearWiggleDisplay"
- }
- ],
- "name" : "Pol II Combined (N2 ChIP), N2_POLII_L3 w peaks",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_N2_POLII_L3_combined_WS220.bw",
- "locationType" : "UriLocation"
- }
- },
- "description" : " Identification of Binding Regions for transcription factors in C. elegans. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "type" : "QuantitativeTrack"
},
{
- "name" : "__Pol II Combined (N2 ChIP), N2_POLII_L3 peaks",
"adapter" : {
"bigBedLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4336_details.gff.bb",
@@ -35146,51 +34536,65 @@
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "description" : "Peak calls for Pol II Combined (N2 ChIP), N2_POLII_L3 w peaks",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_L3 w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Control N2 ChIP"
- ],
"displays" : [
{
- "displayId" : "Pol II Combined (N2 ChIP)_ N2_POLII_L3 w peaks_Transcription Factors_Control N2 ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
"height" : 6,
- "showDescriptions" : false
- }
+ "showDescriptions" : false,
+ "color1" : "deeppink",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "Pol II Combined (N2 ChIP)_ N2_POLII_L3 w peaks_Transcription Factors_Control N2 ChIP_bigbed_peaks"
}
- ]
+ ],
+ "description" : "Peak calls for Pol II Combined (N2 ChIP), N2_POLII_L3 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_L3 w peaks_bigbed_peaks",
+ "name" : "__Pol II Combined (N2 ChIP), N2_POLII_L3 peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Control N2 ChIP"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack"
},
{
- "description" : " Identification of Binding Regions for transcription factors in C. elegans. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"name" : "Pol II Combined (N2 ChIP), N2_POLII_L4 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_L4 w peaks",
+ "description" : " Identification of Binding Regions for transcription factors in C. elegans. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Control N2 ChIP"
+ ],
"adapter" : {
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_N2_POLII_L4_combined_WS220.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_N2_POLII_L4_combined_WS220.bw"
},
"type" : "BigWigAdapter"
},
"displays" : [
{
"type" : "LinearWiggleDisplay",
- "maxScore" : 98.383983471616,
+ "displayId" : "Pol II Combined (N2 ChIP)_ N2_POLII_L4 w peaks_Transcription Factors_Control N2 ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "displayId" : "Pol II Combined (N2 ChIP)_ N2_POLII_L4 w peaks_Transcription Factors_Control N2 ChIP-LinearWiggleDisplay"
+ "maxScore" : 98.383983471616
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_L4 w peaks",
+ ]
+ },
+ {
+ "description" : "Peak calls for Pol II Combined (N2 ChIP), N2_POLII_L4 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_L4 w peaks_bigbed_peaks",
+ "name" : "__Pol II Combined (N2 ChIP), N2_POLII_L4 peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -35198,11 +34602,7 @@
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
- },
- {
- "description" : "Peak calls for Pol II Combined (N2 ChIP), N2_POLII_L4 w peaks",
- "name" : "__Pol II Combined (N2 ChIP), N2_POLII_L4 peaks",
+ ],
"type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
@@ -35213,29 +34613,19 @@
},
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "Pol II Combined (N2 ChIP)_ N2_POLII_L4 w peaks_Transcription Factors_Control N2 ChIP_bigbed_peaks",
"renderer" : {
+ "color1" : "deeppink",
+ "showLabels" : false,
"showDescriptions" : false,
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink"
- },
- "type" : "LinearBasicDisplay"
+ "type" : "SvgFeatureRenderer"
+ }
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_L4 w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Control N2 ChIP"
]
},
{
- "name" : "Pol II Combined (N2 ChIP), N2_POLII_YA w peaks",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -35243,80 +34633,81 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_N2_POLII_YA_combined_WS220.bw"
}
},
- "type" : "QuantitativeTrack",
- "description" : " Identification of Binding Regions for transcription factors in C. elegans. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "displays" : [
+ {
+ "displayId" : "Pol II Combined (N2 ChIP)_ N2_POLII_YA w peaks_Transcription Factors_Control N2 ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "maxScore" : 88.9537441549005,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
+ "name" : "Pol II Combined (N2 ChIP), N2_POLII_YA w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_YA w peaks",
+ "description" : " Identification of Binding Regions for transcription factors in C. elegans. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Control N2 ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "displays" : [
- {
- "maxScore" : 88.9537441549005,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0,
- "displayId" : "Pol II Combined (N2 ChIP)_ N2_POLII_YA w peaks_Transcription Factors_Control N2 ChIP-LinearWiggleDisplay"
- }
]
},
{
- "description" : "Peak calls for Pol II Combined (N2 ChIP), N2_POLII_YA w peaks",
"name" : "__Pol II Combined (N2 ChIP), N2_POLII_YA peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_YA w peaks_bigbed_peaks",
+ "description" : "Peak calls for Pol II Combined (N2 ChIP), N2_POLII_YA w peaks",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Control N2 ChIP"
+ ],
"adapter" : {
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4362_details.gff.bb"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4362_details.gff.bb",
+ "locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
"displays" : [
{
- "displayId" : "Pol II Combined (N2 ChIP)_ N2_POLII_YA w peaks_Transcription Factors_Control N2 ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "deeppink",
"showDescriptions" : false,
- "height" : 6
- }
+ "height" : 6,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "Pol II Combined (N2 ChIP)_ N2_POLII_YA w peaks_Transcription Factors_Control N2 ChIP_bigbed_peaks"
}
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_YA w peaks_bigbed_peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Control N2 ChIP"
]
},
{
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_L2 w peaks",
"name" : "Pol II Combined (N2 ChIP), N2_POLII_L2 w peaks",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_N2_POLII_L2_combined_WS220.bw"
- }
- },
- "type" : "QuantitativeTrack",
"description" : " Identification of Binding Regions for transcription factors in C. elegans. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_L2 w peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"Control N2 ChIP"
],
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_N2_POLII_L2_combined_WS220.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
"type" : "LinearWiggleDisplay",
@@ -35327,42 +34718,40 @@
]
},
{
- "description" : "Peak calls for Pol II Combined (N2 ChIP), N2_POLII_L2 w peaks",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "Control N2 ChIP"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4333_details.gff.bb"
- }
- },
+ "description" : "Peak calls for Pol II Combined (N2 ChIP), N2_POLII_L2 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_L2 w peaks_bigbed_peaks",
"name" : "__Pol II Combined (N2 ChIP), N2_POLII_L2 peaks",
"displays" : [
{
- "displayId" : "Pol II Combined (N2 ChIP)_ N2_POLII_L2 w peaks_Transcription Factors_Control N2 ChIP_bigbed_peaks",
"renderer" : {
- "showDescriptions" : false,
+ "color1" : "deeppink",
"height" : 6,
+ "showDescriptions" : false,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
+ "type" : "SvgFeatureRenderer"
},
+ "displayId" : "Pol II Combined (N2 ChIP)_ N2_POLII_L2 w peaks_Transcription Factors_Control N2 ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay"
}
],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "Control N2 ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_Control N2 ChIP_Pol II Combined (N2 ChIP)_ N2_POLII_L2 w peaks_bigbed_peaks"
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4333_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
- "name" : "PHA-4 Combined (GFP ChIP), PHA-4_L3 w peaks",
- "type" : "QuantitativeTrack",
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
@@ -35370,71 +34759,62 @@
},
"type" : "BigWigAdapter"
},
+ "displays" : [
+ {
+ "maxScore" : 134.495778335226,
+ "displayId" : "PHA-4 Combined (GFP ChIP)_ PHA-4_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
+ }
+ ],
"description" : "Identification of Transcription Factor PHA-4::GFP Binding Regions in Embryonic, L1 larvae, L2 larvae, L3 larvae, L4 larvae, and Young Adult C. elegans. Details Synchronized C. elegans from various developmental stages of strain OP37 (a transgenic strain engineered to express a gene fusion between pha-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "PHA-4 Combined (GFP ChIP), PHA-4_L3 w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA-4_L3 w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "displays" : [
- {
- "displayId" : "PHA-4 Combined (GFP ChIP)_ PHA-4_L3 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "minScore" : 0,
- "maxScore" : 134.495778335226,
- "type" : "LinearWiggleDisplay"
- }
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
]
},
{
- "displays" : [
- {
- "displayId" : "PHA-4 Combined (GFP ChIP)_ PHA-4_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "renderer" : {
- "color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "height" : 6,
- "showDescriptions" : false
- },
- "type" : "LinearBasicDisplay"
- }
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA-4_L3 w peaks_bigbed_peaks",
+ "name" : "__PHA-4 Combined (GFP ChIP), PHA-4_L3 peaks",
"description" : "Peak calls for PHA-4 Combined (GFP ChIP), PHA-4_L3 w peaks",
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "PHA-4 Combined (GFP ChIP)_ PHA-4_L3 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "deeppink",
+ "showDescriptions" : false,
+ "height" : 6,
+ "showLabels" : false
+ }
+ }
+ ],
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/19121_details.gff.bb"
- }
- },
- "name" : "__PHA-4 Combined (GFP ChIP), PHA-4_L3 peaks"
+ },
+ "type" : "BigBedAdapter"
+ }
},
{
- "name" : "PHA-4 Combined (GFP ChIP), PHA-4 L4 w peaks",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18725.bw"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "description" : "Identification of Transcription Factor PHA-4::GFP Binding Regions in Embryonic, L1 larvae, L2 larvae, L3 larvae, L4 larvae, and Young Adult C. elegans. Details Synchronized C. elegans from various developmental stages of strain OP37 (a transgenic strain engineered to express a gene fusion between pha-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA-4 L4 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -35443,59 +34823,76 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
+ "description" : "Identification of Transcription Factor PHA-4::GFP Binding Regions in Embryonic, L1 larvae, L2 larvae, L3 larvae, L4 larvae, and Young Adult C. elegans. Details Synchronized C. elegans from various developmental stages of strain OP37 (a transgenic strain engineered to express a gene fusion between pha-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA-4 L4 w peaks",
+ "name" : "PHA-4 Combined (GFP ChIP), PHA-4 L4 w peaks",
"displays" : [
{
"maxScore" : 29.2430927669257,
- "type" : "LinearWiggleDisplay",
+ "displayId" : "PHA-4 Combined (GFP ChIP)_ PHA-4 L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "displayId" : "PHA-4 Combined (GFP ChIP)_ PHA-4 L4 w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/18725.bw",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18732_details.gff.bb"
+ }
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
"showDescriptions" : false,
- "height" : 6
+ "height" : 6,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "PHA-4 Combined (GFP ChIP)_ PHA-4 L4 w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
],
+ "description" : "Peak calls for PHA-4 Combined (GFP ChIP), PHA-4 L4 w peaks",
+ "name" : "__PHA-4 Combined (GFP ChIP), PHA-4 L4 peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA-4 L4 w peaks_bigbed_peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA-4 L4 w peaks_bigbed_peaks",
- "description" : "Peak calls for PHA-4 Combined (GFP ChIP), PHA-4 L4 w peaks",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/18732_details.gff.bb",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "__PHA-4 Combined (GFP ChIP), PHA-4 L4 peaks"
+ ]
},
{
"displays" : [
{
- "displayId" : "PHA-4 Combined (GFP ChIP)_ PHA4_emb_GFP w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 106.948224194324,
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 106.948224194324
+ "displayId" : "PHA-4 Combined (GFP ChIP)_ PHA4_emb_GFP w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA4_emb_GFP w peaks",
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PHA4_GFP_emb_combined_WS220.bw"
+ }
+ },
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
@@ -35504,242 +34901,225 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"description" : "Identification of Transcription Factor PHA-4::GFP Binding Regions in Embryonic, L1 larvae, L2 larvae, L3 larvae, L4 larvae, and Young Adult C. elegans. Details Synchronized C. elegans from various developmental stages of strain OP37 (a transgenic strain engineered to express a gene fusion between pha-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "PHA-4 Combined (GFP ChIP), PHA4_emb_GFP w peaks",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PHA4_GFP_emb_combined_WS220.bw"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack"
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA4_emb_GFP w peaks",
+ "name" : "PHA-4 Combined (GFP ChIP), PHA4_emb_GFP w peaks"
},
{
- "description" : "Peak calls for PHA-4 Combined (GFP ChIP), PHA4_emb_GFP w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4241_details.gff.bb",
- "locationType" : "UriLocation"
- }
- },
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA4_emb_GFP w peaks_bigbed_peaks",
"name" : "__PHA-4 Combined (GFP ChIP), PHA4_emb_GFP peaks",
+ "description" : "Peak calls for PHA-4 Combined (GFP ChIP), PHA4_emb_GFP w peaks",
"displays" : [
{
- "displayId" : "PHA-4 Combined (GFP ChIP)_ PHA4_emb_GFP w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
"type" : "SvgFeatureRenderer",
"showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6,
"color1" : "deeppink"
- }
+ },
+ "displayId" : "PHA-4 Combined (GFP ChIP)_ PHA4_emb_GFP w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4241_details.gff.bb"
}
+ }
+ },
+ {
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA4_FedL1_GFP w peaks",
+ "name" : "PHA-4 Combined (GFP ChIP), PHA4_FedL1_GFP w peaks",
+ "description" : "Identification of Transcription Factor PHA-4::GFP Binding Regions in Embryonic, L1 larvae, L2 larvae, L3 larvae, L4 larvae, and Young Adult C. elegans. Details Synchronized C. elegans from various developmental stages of strain OP37 (a transgenic strain engineered to express a gene fusion between pha-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA4_emb_GFP w peaks_bigbed_peaks"
- },
- {
- "description" : "Identification of Transcription Factor PHA-4::GFP Binding Regions in Embryonic, L1 larvae, L2 larvae, L3 larvae, L4 larvae, and Young Adult C. elegans. Details Synchronized C. elegans from various developmental stages of strain OP37 (a transgenic strain engineered to express a gene fusion between pha-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PHA4_GFP_FedL1_combined_WS220.bw",
"locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ }
},
- "name" : "PHA-4 Combined (GFP ChIP), PHA4_FedL1_GFP w peaks",
"displays" : [
{
+ "type" : "LinearWiggleDisplay",
"displayId" : "PHA-4 Combined (GFP ChIP)_ PHA4_FedL1_GFP w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "maxScore" : 459.38990459688,
- "type" : "LinearWiggleDisplay"
+ "maxScore" : 459.38990459688
}
- ],
+ ]
+ },
+ {
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA4_FedL1_GFP w peaks"
- },
- {
"description" : "Peak calls for PHA-4 Combined (GFP ChIP), PHA4_FedL1_GFP w peaks",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4235_details.gff.bb",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
"name" : "__PHA-4 Combined (GFP ChIP), PHA4_FedL1_GFP peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA4_FedL1_GFP w peaks_bigbed_peaks",
"displays" : [
{
"displayId" : "PHA-4 Combined (GFP ChIP)_ PHA4_FedL1_GFP w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "deeppink",
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
+ "showLabels" : false,
+ "color1" : "deeppink"
},
"type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4235_details.gff.bb"
+ }
+ }
+ },
+ {
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA4_FedL1_GFP w peaks_bigbed_peaks"
- },
- {
- "description" : "Identification of Transcription Factor PHA-4::GFP Binding Regions in Embryonic, L1 larvae, L2 larvae, L3 larvae, L4 larvae, and Young Adult C. elegans. Details Synchronized C. elegans from various developmental stages of strain OP37 (a transgenic strain engineered to express a gene fusion between pha-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PHA4_GFP_lemb_combined_WS220.bw"
- },
- "type" : "BigWigAdapter"
- },
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "QuantitativeTrack",
+ "description" : "Identification of Transcription Factor PHA-4::GFP Binding Regions in Embryonic, L1 larvae, L2 larvae, L3 larvae, L4 larvae, and Young Adult C. elegans. Details Synchronized C. elegans from various developmental stages of strain OP37 (a transgenic strain engineered to express a gene fusion between pha-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA4_GFP_lemb w peaks",
"name" : "PHA-4 Combined (GFP ChIP), PHA4_GFP_lemb w peaks",
"displays" : [
{
- "displayId" : "PHA-4 Combined (GFP ChIP)_ PHA4_GFP_lemb w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 76.866209888004
+ "displayId" : "PHA-4 Combined (GFP ChIP)_ PHA4_GFP_lemb w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "maxScore" : 76.866209888004,
+ "type" : "LinearWiggleDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA4_GFP_lemb w peaks"
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PHA4_GFP_lemb_combined_WS220.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA4_GFP_lemb w peaks_bigbed_peaks",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA4_GFP_lemb w peaks_bigbed_peaks",
+ "name" : "__PHA-4 Combined (GFP ChIP), PHA4_GFP_lemb peaks",
+ "description" : "Peak calls for PHA-4 Combined (GFP ChIP), PHA4_GFP_lemb w peaks",
"displays" : [
{
- "displayId" : "PHA-4 Combined (GFP ChIP)_ PHA4_GFP_lemb w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
"type" : "SvgFeatureRenderer",
+ "height" : 6,
+ "showDescriptions" : false,
"showLabels" : false,
"color1" : "deeppink"
},
+ "displayId" : "PHA-4 Combined (GFP ChIP)_ PHA4_GFP_lemb w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"type" : "LinearBasicDisplay"
}
],
- "name" : "__PHA-4 Combined (GFP ChIP), PHA4_GFP_lemb peaks",
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/5401_details.gff.bb",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/5401_details.gff.bb"
},
"type" : "BigBedAdapter"
- },
- "description" : "Peak calls for PHA-4 Combined (GFP ChIP), PHA4_GFP_lemb w peaks"
+ }
},
{
- "type" : "QuantitativeTrack",
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 90.243374907619,
+ "minScore" : 0,
+ "displayId" : "PHA-4 Combined (GFP ChIP)_ PHA4_L2_GFP w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PHA4_GFP_L2_combined_WS220.bw"
- }
+ },
+ "type" : "BigWigAdapter"
},
- "name" : "PHA-4 Combined (GFP ChIP), PHA4_L2_GFP w peaks",
- "description" : "Identification of Transcription Factor PHA-4::GFP Binding Regions in Embryonic, L1 larvae, L2 larvae, L3 larvae, L4 larvae, and Young Adult C. elegans. Details Synchronized C. elegans from various developmental stages of strain OP37 (a transgenic strain engineered to express a gene fusion between pha-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA4_L2_GFP w peaks",
- "displays" : [
- {
- "minScore" : 0,
- "maxScore" : 90.243374907619,
- "type" : "LinearWiggleDisplay",
- "displayId" : "PHA-4 Combined (GFP ChIP)_ PHA4_L2_GFP w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
- }
- ]
+ "name" : "PHA-4 Combined (GFP ChIP), PHA4_L2_GFP w peaks",
+ "description" : "Identification of Transcription Factor PHA-4::GFP Binding Regions in Embryonic, L1 larvae, L2 larvae, L3 larvae, L4 larvae, and Young Adult C. elegans. Details Synchronized C. elegans from various developmental stages of strain OP37 (a transgenic strain engineered to express a gene fusion between pha-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
},
{
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7920_details.gff.bb"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/7920_details.gff.bb",
+ "locationType" : "UriLocation"
}
},
- "name" : "__PHA-4 Combined (GFP ChIP), PHA4_L2_GFP peaks",
- "description" : "Peak calls for PHA-4 Combined (GFP ChIP), PHA4_L2_GFP w peaks",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA4_L2_GFP w peaks_bigbed_peaks",
"displays" : [
{
"displayId" : "PHA-4 Combined (GFP ChIP)_ PHA4_L2_GFP w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showLabels" : false,
"height" : 6,
"showDescriptions" : false,
- "color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "color1" : "deeppink"
},
"type" : "LinearBasicDisplay"
}
- ]
- },
- {
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA4_GFP_YA w peaks",
+ ],
+ "name" : "__PHA-4 Combined (GFP ChIP), PHA4_L2_GFP peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA4_L2_GFP w peaks_bigbed_peaks",
+ "description" : "Peak calls for PHA-4 Combined (GFP ChIP), PHA4_L2_GFP w peaks",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -35747,183 +35127,194 @@
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
+ ]
+ },
+ {
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PHA4_GFP_YA_combined_WS220.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
"minScore" : 0,
- "type" : "LinearWiggleDisplay",
+ "displayId" : "PHA-4 Combined (GFP ChIP)_ PHA4_GFP_YA w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
"maxScore" : 67.0260031682595,
- "displayId" : "PHA-4 Combined (GFP ChIP)_ PHA4_GFP_YA w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
],
"name" : "PHA-4 Combined (GFP ChIP), PHA4_GFP_YA w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA4_GFP_YA w peaks",
+ "description" : "Identification of Transcription Factor PHA-4::GFP Binding Regions in Embryonic, L1 larvae, L2 larvae, L3 larvae, L4 larvae, and Young Adult C. elegans. Details Synchronized C. elegans from various developmental stages of strain OP37 (a transgenic strain engineered to express a gene fusion between pha-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP"
+ ]
+ },
+ {
"adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PHA4_GFP_YA_combined_WS220.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8012_details.gff.bb"
}
},
- "type" : "QuantitativeTrack",
- "description" : "Identification of Transcription Factor PHA-4::GFP Binding Regions in Embryonic, L1 larvae, L2 larvae, L3 larvae, L4 larvae, and Young Adult C. elegans. Details Synchronized C. elegans from various developmental stages of strain OP37 (a transgenic strain engineered to express a gene fusion between pha-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
"displays" : [
{
- "displayId" : "PHA-4 Combined (GFP ChIP)_ PHA4_GFP_YA w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "deeppink",
"type" : "SvgFeatureRenderer",
"showLabels" : false,
+ "showDescriptions" : false,
"height" : 6,
- "showDescriptions" : false
+ "color1" : "deeppink"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "PHA-4 Combined (GFP ChIP)_ PHA4_GFP_YA w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
}
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA4_GFP_YA w peaks_bigbed_peaks",
+ "name" : "__PHA-4 Combined (GFP ChIP), PHA4_GFP_YA peaks",
+ "description" : "Peak calls for PHA-4 Combined (GFP ChIP), PHA4_GFP_YA w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : "Peak calls for PHA-4 Combined (GFP ChIP), PHA4_GFP_YA w peaks",
- "name" : "__PHA-4 Combined (GFP ChIP), PHA4_GFP_YA peaks",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/8012_details.gff.bb"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack"
+ ]
},
{
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PHA4_GFP_Starved-L1_combined_WS220.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PHA4_GFP_Starved-L1_combined_WS220.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "name" : "PHA-4 Combined (GFP ChIP), PHA4_StarvedL1_GFP w peaks",
- "description" : "Identification of Transcription Factor PHA-4::GFP Binding Regions in Embryonic, L1 larvae, L2 larvae, L3 larvae, L4 larvae, and Young Adult C. elegans. Details Synchronized C. elegans from various developmental stages of strain OP37 (a transgenic strain engineered to express a gene fusion between pha-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
+ "displays" : [
+ {
+ "maxScore" : 310.053384854705,
+ "minScore" : 0,
+ "displayId" : "PHA-4 Combined (GFP ChIP)_ PHA4_StarvedL1_GFP w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
+ }
],
+ "description" : "Identification of Transcription Factor PHA-4::GFP Binding Regions in Embryonic, L1 larvae, L2 larvae, L3 larvae, L4 larvae, and Young Adult C. elegans. Details Synchronized C. elegans from various developmental stages of strain OP37 (a transgenic strain engineered to express a gene fusion between pha-4 and GFP) were treated with the cross-linking reagent formaldehyde. General Description We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "PHA-4 Combined (GFP ChIP), PHA4_StarvedL1_GFP w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA4_StarvedL1_GFP w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA4_StarvedL1_GFP w peaks",
- "displays" : [
- {
- "displayId" : "PHA-4 Combined (GFP ChIP)_ PHA4_StarvedL1_GFP w peaks_Transcription Factors_GFP ChIP-LinearWiggleDisplay",
- "maxScore" : 310.053384854705,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
- }
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
]
},
{
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "height" : 6,
- "showDescriptions" : false,
- "color1" : "deeppink",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
- },
- "displayId" : "PHA-4 Combined (GFP ChIP)_ PHA4_StarvedL1_GFP w peaks_Transcription Factors_GFP ChIP_bigbed_peaks"
- }
- ],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP_PHA-4 Combined (GFP ChIP)_ PHA4_StarvedL1_GFP w peaks_bigbed_peaks",
+ "name" : "__PHA-4 Combined (GFP ChIP), PHA4_StarvedL1_GFP peaks",
+ "description" : "Peak calls for PHA-4 Combined (GFP ChIP), PHA4_StarvedL1_GFP w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : "Peak calls for PHA-4 Combined (GFP ChIP), PHA4_StarvedL1_GFP w peaks",
- "name" : "__PHA-4 Combined (GFP ChIP), PHA4_StarvedL1_GFP peaks",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4240_details.gff.bb"
- }
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4240_details.gff.bb",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack"
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "PHA-4 Combined (GFP ChIP)_ PHA4_StarvedL1_GFP w peaks_Transcription Factors_GFP ChIP_bigbed_peaks",
+ "renderer" : {
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ }
+ }
+ ]
},
{
- "name" : "PHA-4 Combined (Pol II ChIP), PHA4_POLII_FedL1 w peaks",
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PHA4_POLII_FedL1_combined_WS220.bw"
- }
- },
- "description" : " Identification of Pol II Binding Regions in PHA-4::GFP Starved L1. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_PHA-4 Combined (Pol II ChIP)_ PHA4_POLII_FedL1 w peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"PolII ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : " Identification of Pol II Binding Regions in PHA-4::GFP Starved L1. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "PHA-4 Combined (Pol II ChIP), PHA4_POLII_FedL1 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_PHA-4 Combined (Pol II ChIP)_ PHA4_POLII_FedL1 w peaks",
"displays" : [
{
- "displayId" : "PHA-4 Combined (Pol II ChIP)_ PHA4_POLII_FedL1 w peaks_Transcription Factors_PolII ChIP-LinearWiggleDisplay",
"minScore" : 0,
+ "displayId" : "PHA-4 Combined (Pol II ChIP)_ PHA4_POLII_FedL1 w peaks_Transcription Factors_PolII ChIP-LinearWiggleDisplay",
"maxScore" : 386.423533926333,
"type" : "LinearWiggleDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PHA4_POLII_FedL1_combined_WS220.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "PolII ChIP"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_PHA-4 Combined (Pol II ChIP)_ PHA4_POLII_FedL1 w peaks_bigbed_peaks",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "deeppink",
+ "showLabels" : false,
+ "height" : 6,
"showDescriptions" : false,
- "height" : 6
+ "type" : "SvgFeatureRenderer"
},
"displayId" : "PHA-4 Combined (Pol II ChIP)_ PHA4_POLII_FedL1 w peaks_Transcription Factors_PolII ChIP_bigbed_peaks"
}
],
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4215_details.gff.bb",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4215_details.gff.bb"
+ }
},
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "PolII ChIP"
+ ],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_PHA-4 Combined (Pol II ChIP)_ PHA4_POLII_FedL1 w peaks_bigbed_peaks",
"name" : "__PHA-4 Combined (Pol II ChIP), PHA4_POLII_FedL1 peaks",
"description" : "Peak calls for PHA-4 Combined (Pol II ChIP), PHA4_POLII_FedL1 w peaks"
},
@@ -35933,164 +35324,160 @@
"Transcription Factors",
"PolII ChIP"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : " Identification of Pol II Binding Regions in PHA-4::GFP Starved L1. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "PHA-4 Combined (Pol II ChIP), PHA4_POLII_emb w peaks",
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_PHA-4 Combined (Pol II ChIP)_ PHA4_POLII_emb w peaks",
"displays" : [
{
- "minScore" : 0,
"maxScore" : 93.1053786284265,
- "type" : "LinearWiggleDisplay",
- "displayId" : "PHA-4 Combined (Pol II ChIP)_ PHA4_POLII_emb w peaks_Transcription Factors_PolII ChIP-LinearWiggleDisplay"
+ "minScore" : 0,
+ "displayId" : "PHA-4 Combined (Pol II ChIP)_ PHA4_POLII_emb w peaks_Transcription Factors_PolII ChIP-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
],
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PHA4_POLII_emb_combined_WS220.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "name" : "PHA-4 Combined (Pol II ChIP), PHA4_POLII_emb w peaks",
- "description" : " Identification of Pol II Binding Regions in PHA-4::GFP Starved L1. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PHA4_POLII_emb_combined_WS220.bw"
+ }
+ }
},
{
- "description" : "Peak calls for PHA-4 Combined (Pol II ChIP), PHA4_POLII_emb w peaks",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4221_details.gff.bb"
- }
+ },
+ "type" : "BigBedAdapter"
},
- "name" : "__PHA-4 Combined (Pol II ChIP), PHA4_POLII_emb peaks",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "PHA-4 Combined (Pol II ChIP)_ PHA4_POLII_emb w peaks_Transcription Factors_PolII ChIP_bigbed_peaks",
"renderer" : {
- "height" : 6,
+ "showLabels" : false,
"showDescriptions" : false,
+ "height" : 6,
"color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "PHA-4 Combined (Pol II ChIP)_ PHA4_POLII_emb w peaks_Transcription Factors_PolII ChIP_bigbed_peaks"
+ "type" : "SvgFeatureRenderer"
+ }
}
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_PHA-4 Combined (Pol II ChIP)_ PHA4_POLII_emb w peaks_bigbed_peaks",
+ "name" : "__PHA-4 Combined (Pol II ChIP), PHA4_POLII_emb peaks",
+ "description" : "Peak calls for PHA-4 Combined (Pol II ChIP), PHA4_POLII_emb w peaks",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"PolII ChIP"
- ],
+ ]
+ },
+ {
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_PHA-4 Combined (Pol II ChIP)_ PHA4_POLII_StarvedL1 w peaks",
+ "name" : "PHA-4 Combined (Pol II ChIP), PHA4_POLII_StarvedL1 w peaks",
+ "description" : " Identification of Pol II Binding Regions in PHA-4::GFP Starved L1. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_PHA-4 Combined (Pol II ChIP)_ PHA4_POLII_emb w peaks_bigbed_peaks"
- },
- {
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"PolII ChIP"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_PHA-4 Combined (Pol II ChIP)_ PHA4_POLII_StarvedL1 w peaks",
- "displays" : [
- {
- "displayId" : "PHA-4 Combined (Pol II ChIP)_ PHA4_POLII_StarvedL1 w peaks_Transcription Factors_PolII ChIP-LinearWiggleDisplay",
- "maxScore" : 370.735579924055,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
- }
- ],
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PHA4_POLII_Starved-L1_combined_WS220.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PHA4_POLII_Starved-L1_combined_WS220.bw",
+ "locationType" : "UriLocation"
}
},
- "name" : "PHA-4 Combined (Pol II ChIP), PHA4_POLII_StarvedL1 w peaks",
- "description" : " Identification of Pol II Binding Regions in PHA-4::GFP Starved L1. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "displays" : [
+ {
+ "maxScore" : 370.735579924055,
+ "displayId" : "PHA-4 Combined (Pol II ChIP)_ PHA4_POLII_StarvedL1 w peaks_Transcription Factors_PolII ChIP-LinearWiggleDisplay",
+ "minScore" : 0,
+ "type" : "LinearWiggleDisplay"
+ }
+ ]
},
{
- "description" : "Peak calls for PHA-4 Combined (Pol II ChIP), PHA4_POLII_StarvedL1 w peaks",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/4211_details.gff.bb"
- }
+ },
+ "type" : "BigBedAdapter"
},
- "name" : "__PHA-4 Combined (Pol II ChIP), PHA4_POLII_StarvedL1 peaks",
"displays" : [
{
- "displayId" : "PHA-4 Combined (Pol II ChIP)_ PHA4_POLII_StarvedL1 w peaks_Transcription Factors_PolII ChIP_bigbed_peaks",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
- "showDescriptions" : false,
"color1" : "deeppink",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "PHA-4 Combined (Pol II ChIP)_ PHA4_POLII_StarvedL1 w peaks_Transcription Factors_PolII ChIP_bigbed_peaks"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "Peak calls for PHA-4 Combined (Pol II ChIP), PHA4_POLII_StarvedL1 w peaks",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_PHA-4 Combined (Pol II ChIP)_ PHA4_POLII_StarvedL1 w peaks_bigbed_peaks",
+ "name" : "__PHA-4 Combined (Pol II ChIP), PHA4_POLII_StarvedL1 peaks",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"PolII ChIP"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_PolII ChIP_PHA-4 Combined (Pol II ChIP)_ PHA4_POLII_StarvedL1 w peaks_bigbed_peaks"
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack"
},
{
- "type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PHA4_GFP_L2_combined_WS220.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_PHA-4 Combined (GFP ChIP) recalled peaks_ L2",
"name" : "PHA-4 Combined (GFP ChIP) recalled peaks, L2",
"description" : "Identification of Transcription Factor PHA-4::GFP Binding Regions in Embryos. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_PHA-4 Combined (GFP ChIP) recalled peaks_ L2",
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PHA4_GFP_L2_combined_WS220.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
- "minScore" : 36.2257137195143,
- "maxScore" : 90.243374907619,
"type" : "LinearWiggleDisplay",
+ "maxScore" : 90.243374907619,
+ "minScore" : 36.2257137195143,
"displayId" : "PHA-4 Combined (GFP ChIP) recalled peaks_ L2_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay"
}
]
},
{
- "displays" : [
- {
- "displayId" : "PHA-4 Combined (GFP ChIP) recalled peaks_ Embryo_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
- "minScore" : 45.9191139841269,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 106.948224194324
- }
- ],
+ "name" : "PHA-4 Combined (GFP ChIP) recalled peaks, Embryo",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_PHA-4 Combined (GFP ChIP) recalled peaks_ Embryo",
+ "description" : "Identification of Transcription Factor PHA-4::GFP Binding Regions in Embryos. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -36099,9 +35486,6 @@
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_PHA-4 Combined (GFP ChIP) recalled peaks_ Embryo",
- "description" : "Identification of Transcription Factor PHA-4::GFP Binding Regions in Embryos. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
@@ -36109,9 +35493,24 @@
"locationType" : "UriLocation"
}
},
- "name" : "PHA-4 Combined (GFP ChIP) recalled peaks, Embryo"
+ "displays" : [
+ {
+ "displayId" : "PHA-4 Combined (GFP ChIP) recalled peaks_ Embryo_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
+ "minScore" : 45.9191139841269,
+ "maxScore" : 106.948224194324,
+ "type" : "LinearWiggleDisplay"
+ }
+ ]
},
{
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "maxScore" : 76.866209888004,
+ "minScore" : 31.7308492630413,
+ "displayId" : "PHA-4 Combined (GFP ChIP) recalled peaks_ Late embryo_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay"
+ }
+ ],
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
@@ -36119,169 +35518,161 @@
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack",
- "name" : "PHA-4 Combined (GFP ChIP) recalled peaks, Late embryo",
- "description" : "Identification of Transcription Factor PHA-4::GFP Binding Regions in Embryos. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
"trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_PHA-4 Combined (GFP ChIP) recalled peaks_ Late embryo",
+ "name" : "PHA-4 Combined (GFP ChIP) recalled peaks, Late embryo",
+ "description" : "Identification of Transcription Factor PHA-4::GFP Binding Regions in Embryos. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ },
+ {
+ "description" : "Identification of Transcription Factor PHA-4::GFP Binding Regions in Embryos. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "PHA-4 Combined (GFP ChIP) recalled peaks, YA",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_PHA-4 Combined (GFP ChIP) recalled peaks_ YA",
+ "category" : [
+ "modENCODE data (2014)",
+ "Transcription Factors",
+ "GFP ChIP (Peak Recall)"
+ ],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PHA4_GFP_YA_combined_WS220.bw"
+ }
+ },
"displays" : [
{
- "displayId" : "PHA-4 Combined (GFP ChIP) recalled peaks_ Late embryo_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
- "maxScore" : 76.866209888004,
"type" : "LinearWiggleDisplay",
- "minScore" : 31.7308492630413
+ "minScore" : 29.1937810455256,
+ "displayId" : "PHA-4 Combined (GFP ChIP) recalled peaks_ YA_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
+ "maxScore" : 67.0260031682595
}
]
},
{
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_PHA-4 Combined (GFP ChIP) recalled peaks_ YA",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_PHA-4 Combined (GFP ChIP) recalled peaks_ Starved L1",
+ "name" : "PHA-4 Combined (GFP ChIP) recalled peaks, Starved L1",
+ "description" : "Identification of Transcription Factor PHA-4::GFP Binding Regions in Embryos. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "displayId" : "PHA-4 Combined (GFP ChIP) recalled peaks_ YA_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay",
- "maxScore" : 67.0260031682595,
"type" : "LinearWiggleDisplay",
- "minScore" : 29.1937810455256
+ "maxScore" : 310.053384854705,
+ "minScore" : 126.725717002053,
+ "displayId" : "PHA-4 Combined (GFP ChIP) recalled peaks_ Starved L1_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay"
}
],
- "name" : "PHA-4 Combined (GFP ChIP) recalled peaks, YA",
"adapter" : {
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PHA4_GFP_YA_combined_WS220.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PHA4_GFP_Starved-L1_combined_WS220.bw"
},
"type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "description" : "Identification of Transcription Factor PHA-4::GFP Binding Regions in Embryos. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
},
{
- "name" : "PHA-4 Combined (GFP ChIP) recalled peaks, Starved L1",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PHA4_GFP_Starved-L1_combined_WS220.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
"description" : "Identification of Transcription Factor PHA-4::GFP Binding Regions in Embryos. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_PHA-4 Combined (GFP ChIP) recalled peaks_ Starved L1",
+ "name" : "PHA-4 Combined (GFP ChIP) recalled peaks, Fed L1",
+ "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_PHA-4 Combined (GFP ChIP) recalled peaks_ Fed L1",
"category" : [
"modENCODE data (2014)",
"Transcription Factors",
"GFP ChIP (Peak Recall)"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "displays" : [
- {
- "minScore" : 126.725717002053,
- "maxScore" : 310.053384854705,
- "type" : "LinearWiggleDisplay",
- "displayId" : "PHA-4 Combined (GFP ChIP) recalled peaks_ Starved L1_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay"
- }
- ]
- },
- {
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/snyder/Snyder_PHA4_GFP_FedL1_combined_WS220.bw",
"locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ }
},
- "type" : "QuantitativeTrack",
- "name" : "PHA-4 Combined (GFP ChIP) recalled peaks, Fed L1",
- "description" : "Identification of Transcription Factor PHA-4::GFP Binding Regions in Embryos. We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "category" : [
- "modENCODE data (2014)",
- "Transcription Factors",
- "GFP ChIP (Peak Recall)"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Transcription Factors_GFP ChIP (Peak Recall)_PHA-4 Combined (GFP ChIP) recalled peaks_ Fed L1",
"displays" : [
{
- "maxScore" : 459.38990459688,
"type" : "LinearWiggleDisplay",
+ "maxScore" : 459.38990459688,
"minScore" : 172.47586851697,
"displayId" : "PHA-4 Combined (GFP ChIP) recalled peaks_ Fed L1_Transcription Factors_GFP ChIP (Peak Recall)-LinearWiggleDisplay"
}
]
},
{
- "description" : "Synchronized C. elegans mixed stage embryos from strains YPT41, N2, and TY1072 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 methylated on lysine 20. The recovered DNA fragments (as well as a sample of input DNA) were sequenced on the Illumina GA-II platform. The signal graph data track shows the coverage of short reads in each sample. The alignment files were used to call binding peaks with the MACS algorithm to generate the track showing sequence features.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6210.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6210.bw"
+ }
},
- "type" : "QuantitativeTrack",
- "name" : "Histone Modifications in H4K20 (ChIP-seq), Mixed stage N2 embryos",
"displays" : [
{
- "minScore" : 36.8555452217659,
- "maxScore" : 77.046500672018,
"type" : "LinearWiggleDisplay",
- "displayId" : "Histone Modifications in H4K20 (ChIP-seq)_ Mixed stage N2 embryos_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "maxScore" : 77.046500672018,
+ "displayId" : "Histone Modifications in H4K20 (ChIP-seq)_ Mixed stage N2 embryos_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 36.8555452217659
}
],
+ "description" : "Synchronized C. elegans mixed stage embryos from strains YPT41, N2, and TY1072 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 methylated on lysine 20. The recovered DNA fragments (as well as a sample of input DNA) were sequenced on the Illumina GA-II platform. The signal graph data track shows the coverage of short reads in each sample. The alignment files were used to call binding peaks with the MACS algorithm to generate the track showing sequence features.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications in H4K20 (ChIP-seq), Mixed stage N2 embryos",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H4K20 (ChIP-seq)_ Mixed stage N2 embryos",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H4K20 (ChIP-seq)_ Mixed stage N2 embryos"
+ ]
},
{
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6211.bw"
- }
- },
- "name" : "Histone Modifications in H4K20 (ChIP-seq), Mixed stage TY1072 embryos",
"description" : "Synchronized C. elegans mixed stage embryos from strains YPT41, N2, and TY1072 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 methylated on lysine 20. The recovered DNA fragments (as well as a sample of input DNA) were sequenced on the Illumina GA-II platform. The signal graph data track shows the coverage of short reads in each sample. The alignment files were used to call binding peaks with the MACS algorithm to generate the track showing sequence features.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "Histone Modifications in H4K20 (ChIP-seq), Mixed stage TY1072 embryos",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H4K20 (ChIP-seq)_ Mixed stage TY1072 embryos",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H4K20 (ChIP-seq)_ Mixed stage TY1072 embryos",
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6211.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
"displays" : [
{
+ "displayId" : "Histone Modifications in H4K20 (ChIP-seq)_ Mixed stage TY1072 embryos_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"minScore" : 12.6330745450023,
- "type" : "LinearWiggleDisplay",
"maxScore" : 28.9426501363705,
- "displayId" : "Histone Modifications in H4K20 (ChIP-seq)_ Mixed stage TY1072 embryos_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
]
},
@@ -36291,16 +35682,19 @@
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "Synchronized C. elegans mixed stage embryos from strains YPT41, N2, and TY1072 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 methylated on lysine 20. The recovered DNA fragments (as well as a sample of input DNA) were sequenced on the Illumina GA-II platform. The signal graph data track shows the coverage of short reads in each sample. The alignment files were used to call bindin peaks with the MACS algorithm to generate the track showing sequence features.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications in H4K20 (ChIP-seq), Mixed stage YPT41 embryos",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications in H4K20 (ChIP-seq)_ Mixed stage YPT41 embryos",
"displays" : [
{
"maxScore" : 126.26061296394,
- "type" : "LinearWiggleDisplay",
+ "displayId" : "Histone Modifications in H4K20 (ChIP-seq)_ Mixed stage YPT41 embryos_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"minScore" : 53.7461022781,
- "displayId" : "Histone Modifications in H4K20 (ChIP-seq)_ Mixed stage YPT41 embryos_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
],
"adapter" : {
@@ -36309,66 +35703,63 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_6011.bw",
"locationType" : "UriLocation"
}
- },
- "type" : "QuantitativeTrack",
- "name" : "Histone Modifications in H4K20 (ChIP-seq), Mixed stage YPT41 embryos",
- "description" : "Synchronized C. elegans mixed stage embryos from strains YPT41, N2, and TY1072 were treated with the cross-linking reagent formaldehyde. Sonicated chromatin was prepared and immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 methylated on lysine 20. The recovered DNA fragments (as well as a sample of input DNA) were sequenced on the Illumina GA-II platform. The signal graph data track shows the coverage of short reads in each sample. The alignment files were used to call bindin peaks with the MACS algorithm to generate the track showing sequence features.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
},
{
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/henikoff/4432_SOH34_80g_WS220.mean.bw",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
"type" : "LinearWiggleDisplay",
"displayId" : "Mononucleosomes 80mM NaCl_ Adult Mononucleosomes_Chromatin Structure_Nucleosome Structure-LinearWiggleDisplay"
}
],
+ "name" : "Mononucleosomes 80mM NaCl, Adult Mononucleosomes",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Nucleosome Structure_Mononucleosomes 80mM NaCl_ Adult Mononucleosomes",
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Nucleosome Structure"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"description" : " Adult_Mononucleosomes. Staged C. elegans adults were prepared from a worm strain engineered to express biotin-tagged histone H3.3 (note that the transgene was not induced during this particular experiment). Chromatin isolated from these animals was digested with micrococcal nuclease and extracted with 80 mM NaCl, followed by gel electrophoresis. The gel-purified fraction was used in two-color hybridization experiments with NimbleGen genomic tiling microarrays. The hybridization signal from this fraction was compared to the signal from the input DNA. Scaled log2(ratios) are shown.
For more information, see modENCODE's track detail page ",
- "name" : "Mononucleosomes 80mM NaCl, Adult Mononucleosomes",
"type" : "QuantitativeTrack",
- "adapter" : {
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/henikoff/4432_SOH34_80g_WS220.mean.bw"
- },
- "type" : "BigWigAdapter"
- }
- },
- {
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
- "Histone Modifications and Variants"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-Seq_ ab9048_H3K36me1:206009_N2_L3",
+ "Nucleosome Structure"
+ ]
+ },
+ {
"displays" : [
{
"displayId" : "Histone Modifications (H3K36) ChIP-Seq_ ab9048_H3K36me1:206009_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"minScore" : 35.788722290607,
- "type" : "LinearWiggleDisplay",
- "maxScore" : 76.940370577597
+ "maxScore" : 76.940370577597,
+ "type" : "LinearWiggleDisplay"
}
],
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5049.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5049.bw"
}
},
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"name" : "Histone Modifications (H3K36) ChIP-Seq, ab9048_H3K36me1:206009_N2_L3",
- "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-Seq_ ab9048_H3K36me1:206009_N2_L3"
},
{
"category" : [
@@ -36376,68 +35767,63 @@
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications (H3K36) ChIP-Seq, NB211254_H3K36ac_N2_L3",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-Seq_ NB211254_H3K36ac_N2_L3",
"displays" : [
{
- "maxScore" : 172.325139576463,
- "type" : "LinearWiggleDisplay",
+ "displayId" : "Histone Modifications (H3K36) ChIP-Seq_ NB211254_H3K36ac_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"minScore" : 73.597196060233,
- "displayId" : "Histone Modifications (H3K36) ChIP-Seq_ NB211254_H3K36ac_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "maxScore" : 172.325139576463,
+ "type" : "LinearWiggleDisplay"
}
],
- "type" : "QuantitativeTrack",
"adapter" : {
"type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5043.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5043.bw",
+ "locationType" : "UriLocation"
}
- },
- "name" : "Histone Modifications (H3K36) ChIP-Seq, NB211254_H3K36ac_N2_L3",
- "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ }
},
{
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-Seq_ HK00012_H3K36me2:2C3_N2_L3",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-Seq_ HK00012_H3K36me2:2C3_N2_L3",
+ "name" : "Histone Modifications (H3K36) ChIP-Seq, HK00012_H3K36me2:2C3_N2_L3",
+ "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "minScore" : 99.9409281740504,
"maxScore" : 224.887661133486,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Histone Modifications (H3K36) ChIP-Seq_ HK00012_H3K36me2:2C3_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "displayId" : "Histone Modifications (H3K36) ChIP-Seq_ HK00012_H3K36me2:2C3_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 99.9409281740504,
+ "type" : "LinearWiggleDisplay"
}
],
- "name" : "Histone Modifications (H3K36) ChIP-Seq, HK00012_H3K36me2:2C3_N2_L3",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5041.bw"
- }
- },
- "type" : "QuantitativeTrack",
- "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5041.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
- "displays" : [
- {
- "maxScore" : 273.523176024916,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0,
- "displayId" : "Histone Modifications (H3K36) ChIP-Seq_ AB9050_H3K36me3_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
- }
- ],
+ "name" : "Histone Modifications (H3K36) ChIP-Seq, AB9050_H3K36me3_N2_L3 w peaks",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-Seq_ AB9050_H3K36me3_N2_L3 w peaks",
+ "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -36446,28 +35832,23 @@
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "description" : "H3K36 modifications (Lieb project, Strome subgroup). Synchronized C. elegans L1 larvae from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H3 methylated on lysine 36. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is set to zero and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "name" : "Histone Modifications (H3K36) ChIP-Seq, AB9050_H3K36me3_N2_L3 w peaks",
"adapter" : {
"bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-AB9050_H3K36me3_N2_L3_merged.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/seq-AB9050_H3K36me3_N2_L3_merged.bw",
+ "locationType" : "UriLocation"
},
"type" : "BigWigAdapter"
},
- "type" : "QuantitativeTrack"
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "minScore" : 0,
+ "displayId" : "Histone Modifications (H3K36) ChIP-Seq_ AB9050_H3K36me3_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "maxScore" : 273.523176024916
+ }
+ ]
},
{
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10258_details.gff.bb"
- }
- },
- "type" : "FeatureTrack",
- "name" : "__Histone Modifications (H3K36) ChIP-Seq, AB9050_H3K36me3_N2_L3 peaks",
- "description" : "Peak calls for Histone Modifications (H3K36) ChIP-Seq, AB9050_H3K36me3_N2_L3 w peaks",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -36476,90 +35857,62 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "description" : "Peak calls for Histone Modifications (H3K36) ChIP-Seq, AB9050_H3K36me3_N2_L3 w peaks",
"trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K36) ChIP-Seq_ AB9050_H3K36me3_N2_L3 w peaks_bigbed_peaks",
+ "name" : "__Histone Modifications (H3K36) ChIP-Seq, AB9050_H3K36me3_N2_L3 peaks",
"displays" : [
{
"displayId" : "Histone Modifications (H3K36) ChIP-Seq_ AB9050_H3K36me3_N2_L3 w peaks_Chromatin Structure_Histone Modifications and Variants_bigbed_peaks",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 6,
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
- }
+ "color1" : "deeppink",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 6
+ },
+ "type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/bigbed_binaries/10258_details.gff.bb",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications (H3K9) ChIP-Seq, AB8898_H3K9me3:33990_N2_L3",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K9) ChIP-Seq_ AB8898_H3K9me3:33990_N2_L3",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K9) ChIP-Seq_ AB8898_H3K9me3:33990_N2_L3",
- "displays" : [
- {
- "displayId" : "Histone Modifications (H3K9) ChIP-Seq_ AB8898_H3K9me3:33990_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "maxScore" : 1049.42341739636,
- "type" : "LinearWiggleDisplay",
- "minScore" : 368.928927740799
- }
- ],
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5037.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
- "name" : "Histone Modifications (H3K9) ChIP-Seq, AB8898_H3K9me3:33990_N2_L3",
- "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less."
- },
- {
- "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5036.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5037.bw"
},
"type" : "BigWigAdapter"
},
- "name" : "Histone Modifications (H3K9) ChIP-Seq, AB8896_H3K9me1_104560_N2_L3",
"displays" : [
{
"type" : "LinearWiggleDisplay",
- "maxScore" : 140.685992539981,
- "minScore" : 62.4058775381939,
- "displayId" : "Histone Modifications (H3K9) ChIP-Seq_ AB8896_H3K9me1_104560_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "minScore" : 368.928927740799,
+ "displayId" : "Histone Modifications (H3K9) ChIP-Seq_ AB8898_H3K9me3:33990_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "maxScore" : 1049.42341739636
}
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modENCODE data (2014)",
- "Chromatin Structure",
- "Histone Modifications and Variants"
- ],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K9) ChIP-Seq_ AB8896_H3K9me1_104560_N2_L3"
+ ]
},
{
"type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5040.bw"
- }
- },
- "name" : "Histone Modifications (H3K9) ChIP-Seq, HK00009_H3K9me3:2F3_N2_L3",
- "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -36568,27 +35921,41 @@
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K9) ChIP-Seq_ HK00009_H3K9me3:2F3_N2_L3",
+ "name" : "Histone Modifications (H3K9) ChIP-Seq, AB8896_H3K9me1_104560_N2_L3",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K9) ChIP-Seq_ AB8896_H3K9me1_104560_N2_L3",
+ "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "displayId" : "Histone Modifications (H3K9) ChIP-Seq_ HK00009_H3K9me3:2F3_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
"type" : "LinearWiggleDisplay",
- "maxScore" : 313.319096765096,
- "minScore" : 112.828901932482
+ "maxScore" : 140.685992539981,
+ "minScore" : 62.4058775381939,
+ "displayId" : "Histone Modifications (H3K9) ChIP-Seq_ AB8896_H3K9me1_104560_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5036.bw"
+ }
+ }
},
{
+ "displays" : [
+ {
+ "type" : "LinearWiggleDisplay",
+ "minScore" : 112.828901932482,
+ "displayId" : "Histone Modifications (H3K9) ChIP-Seq_ HK00009_H3K9me3:2F3_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "maxScore" : 313.319096765096
+ }
+ ],
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5050.bw",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5040.bw",
"locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ }
},
- "type" : "QuantitativeTrack",
- "name" : "Histone Modifications (H3K9) ChIP-Seq, HK00008_H3K9me2:6D11_N2_L3",
- "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
@@ -36597,76 +35964,99 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K9) ChIP-Seq_ HK00008_H3K9me2:6D11_N2_L3",
+ "type" : "QuantitativeTrack",
+ "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K9) ChIP-Seq_ HK00009_H3K9me3:2F3_N2_L3",
+ "name" : "Histone Modifications (H3K9) ChIP-Seq, HK00009_H3K9me3:2F3_N2_L3"
+ },
+ {
"displays" : [
{
- "minScore" : 287.666029966308,
"maxScore" : 773.164333231235,
- "type" : "LinearWiggleDisplay",
- "displayId" : "Histone Modifications (H3K9) ChIP-Seq_ HK00008_H3K9me2:6D11_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "displayId" : "Histone Modifications (H3K9) ChIP-Seq_ HK00008_H3K9me2:6D11_N2_L3_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "minScore" : 287.666029966308,
+ "type" : "LinearWiggleDisplay"
}
- ]
- },
- {
- "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
- "type" : "QuantitativeTrack",
+ ],
"adapter" : {
"bigWigLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5039.bw"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5050.bw"
},
"type" : "BigWigAdapter"
},
- "name" : "Histone Modifications (H4K20) ChIP-Seq",
- "displays" : [
- {
- "displayId" : "Histone Modifications (H4K20) ChIP-Seq_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
- "maxScore" : 234.065382330125,
- "type" : "LinearWiggleDisplay",
- "minScore" : 107.317876168941
- }
- ],
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4K20) ChIP-Seq"
+ "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "name" : "Histone Modifications (H3K9) ChIP-Seq, HK00008_H3K9me2:6D11_N2_L3",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K9) ChIP-Seq_ HK00008_H3K9me2:6D11_N2_L3"
},
{
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5046.bw",
- "locationType" : "UriLocation"
- }
- },
- "type" : "QuantitativeTrack",
- "name" : "Histone Modifications (H3K18) ChIP-Seq",
- "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"modENCODE data (2014)",
"Chromatin Structure",
"Histone Modifications and Variants"
],
- "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K18) ChIP-Seq",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H4K20) ChIP-Seq",
+ "name" : "Histone Modifications (H4K20) ChIP-Seq",
+ "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
"displays" : [
{
- "maxScore" : 123.755287284323,
"type" : "LinearWiggleDisplay",
+ "minScore" : 107.317876168941,
+ "displayId" : "Histone Modifications (H4K20) ChIP-Seq_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "maxScore" : 234.065382330125
+ }
+ ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5039.bw"
+ },
+ "type" : "BigWigAdapter"
+ }
+ },
+ {
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/lieb/modencode_5046.bw",
+ "locationType" : "UriLocation"
+ }
+ },
+ "displays" : [
+ {
+ "maxScore" : 123.755287284323,
"minScore" : 58.4602448038268,
- "displayId" : "Histone Modifications (H3K18) ChIP-Seq_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay"
+ "displayId" : "Histone Modifications (H3K18) ChIP-Seq_Chromatin Structure_Histone Modifications and Variants-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
- ]
+ ],
+ "description" : "H4 modifications (Lieb project, Strome subgroup). Synchronized C. elegans early embryos from strain N2. Immunoprecipitated with an affinity-purified polyclonal antibody that recognizes histone H4 acetylated on lysine 8. The focus of our analysis will be elements that specify nucleosome positioning and occupancy, control domains of gene expression, induce repression of the X chromosome, guide mitotic segregation and genome duplication, govern homolog pairing and recombination during meiosis, and organize chromosome positioning within the nucleus. 126 strategically selected targets include key histone modifications, histone variants, RNA polymerase II isoforms, dosage-compensation proteins, centromere components, homolog-pairing facilitators, recombination markers, and nuclear-envelope constituents.
For more information, see modENCODE's track detail page
Note that the default minimum for the graph is the mean plus 1.65 times the standard deviation of the data set and the default maximum is the mean plus 5 times the standard deviation or the data set maximum value, whichever is less.",
+ "trackId" : "c_elegans_PRJNA13758__Chromatin Structure_Histone Modifications and Variants_Histone Modifications (H3K18) ChIP-Seq",
+ "name" : "Histone Modifications (H3K18) ChIP-Seq",
+ "category" : [
+ "modENCODE data (2014)",
+ "Chromatin Structure",
+ "Histone Modifications and Variants"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack"
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for eyg-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF172ORC/ and for more information on this eyg-1 experiment, see https://www.encodeproject.org/experiments/ENCSR604KUU/.",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
@@ -36674,27 +36064,28 @@
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "name" : "eyg-1",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "eyg-1-ENCFF172ORC-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"type" : "SvgFeatureRenderer",
- "color1" : "blue"
- },
- "displayId" : "eyg-1-ENCFF172ORC-LinearBasicDisplay"
+ "color1" : "blue",
+ "height" : 6
+ }
}
],
+ "name" : "eyg-1",
+ "trackId" : "c_elegans_PRJNA13758_eyg-1-ENCFF172ORC",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for eyg-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF172ORC/ and for more information on this eyg-1 experiment, see https://www.encodeproject.org/experiments/ENCSR604KUU/.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"modERN",
"late embryonic"
- ],
- "trackId" : "c_elegans_PRJNA13758_eyg-1-ENCFF172ORC"
+ ]
},
{
"displays" : [
@@ -36708,27 +36099,26 @@
"displayId" : "unc-86-ENCFF361ROR-LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_unc-86-ENCFF361ROR",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF361ROR/@@download/ENCFF361ROR.bigBed"
+ }
+ },
"category" : [
"modERN",
"late embryonic"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for unc-86 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF361ROR/ and for more information on this unc-86 experiment, see https://www.encodeproject.org/experiments/ENCSR693VPE/.",
"name" : "unc-86",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF361ROR/@@download/ENCFF361ROR.bigBed",
- "locationType" : "UriLocation"
- }
- }
+ "trackId" : "c_elegans_PRJNA13758_unc-86-ENCFF361ROR"
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for lin-14 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF693ZCG/ and for more information on this lin-14 experiment, see https://www.encodeproject.org/experiments/ENCSR714ALL/.",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
@@ -36736,19 +36126,20 @@
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "name" : "lin-14",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "lin-14-ENCFF693ZCG-LinearBasicDisplay",
"renderer" : {
"height" : 6,
"color1" : "blue",
"type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay"
+ }
}
],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for lin-14 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF693ZCG/ and for more information on this lin-14 experiment, see https://www.encodeproject.org/experiments/ENCSR714ALL/.",
+ "trackId" : "c_elegans_PRJNA13758_lin-14-ENCFF693ZCG",
+ "name" : "lin-14",
"category" : [
"modERN",
"L1 larva"
@@ -36756,19 +36147,16 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_lin-14-ENCFF693ZCG"
+ "type" : "FeatureTrack"
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F57A8.1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF450VLL/ and for more information on this F57A8.1 experiment, see https://www.encodeproject.org/experiments/ENCSR857HWD/.",
- "name" : "F57A8.1",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF450VLL/@@download/ENCFF450VLL.bigBed"
- },
- "type" : "BigBedAdapter"
+ "uri" : "https://www.encodeproject.org/files/ENCFF450VLL/@@download/ENCFF450VLL.bigBed",
+ "locationType" : "UriLocation"
+ }
},
- "type" : "FeatureTrack",
"displays" : [
{
"displayId" : "F57A8.1-ENCFF450VLL-LinearBasicDisplay",
@@ -36781,56 +36169,53 @@
}
],
"trackId" : "c_elegans_PRJNA13758_F57A8.1-ENCFF450VLL",
+ "name" : "F57A8.1",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F57A8.1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF450VLL/ and for more information on this F57A8.1 experiment, see https://www.encodeproject.org/experiments/ENCSR857HWD/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
"young adult"
]
},
{
- "trackId" : "c_elegans_PRJNA13758_lsl-1-ENCFF427HQJ",
- "category" : [
- "modERN",
- "young adult"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "lsl-1-ENCFF427HQJ-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"color1" : "blue",
- "height" : 6
- },
- "type" : "LinearBasicDisplay"
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "name" : "lsl-1",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF427HQJ/@@download/ENCFF427HQJ.bigBed",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF427HQJ/@@download/ENCFF427HQJ.bigBed"
}
},
+ "category" : [
+ "modERN",
+ "young adult"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for lsl-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF427HQJ/ and for more information on this lsl-1 experiment, see https://www.encodeproject.org/experiments/ENCSR969MNX/."
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for lsl-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF427HQJ/ and for more information on this lsl-1 experiment, see https://www.encodeproject.org/experiments/ENCSR969MNX/.",
+ "trackId" : "c_elegans_PRJNA13758_lsl-1-ENCFF427HQJ",
+ "name" : "lsl-1"
},
{
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF694KVR/@@download/ENCFF694KVR.bigBed",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
"name" : "elt-2",
+ "trackId" : "c_elegans_PRJNA13758_elt-2-ENCFF694KVR",
"description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for elt-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF694KVR/ and for more information on this elt-2 experiment, see https://www.encodeproject.org/experiments/ENCSR955ZJN/.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -36838,16 +36223,22 @@
"modERN",
"L3 larva"
],
- "trackId" : "c_elegans_PRJNA13758_elt-2-ENCFF694KVR",
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF694KVR/@@download/ENCFF694KVR.bigBed",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
+ "displayId" : "elt-2-ENCFF694KVR-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
+ "type" : "SvgFeatureRenderer",
"color1" : "blue",
- "type" : "SvgFeatureRenderer"
+ "height" : 6
},
- "type" : "LinearBasicDisplay",
- "displayId" : "elt-2-ENCFF694KVR-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
]
},
@@ -36856,137 +36247,82 @@
{
"displayId" : "let-607-ENCFF069WTX-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"color1" : "blue",
+ "height" : 6,
"type" : "SvgFeatureRenderer"
},
"type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_let-607-ENCFF069WTX",
- "category" : [
- "modERN",
- "young adult"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for let-607 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF069WTX/ and for more information on this let-607 experiment, see https://www.encodeproject.org/experiments/ENCSR914MJK/.",
- "name" : "let-607",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://www.encodeproject.org/files/ENCFF069WTX/@@download/ENCFF069WTX.bigBed",
"locationType" : "UriLocation"
}
- }
- },
- {
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "height" : 6,
- "color1" : "blue",
- "type" : "SvgFeatureRenderer"
- },
- "displayId" : "tbx-8-ENCFF002ILG-LinearBasicDisplay"
- }
- ],
- "category" : [
- "modERN",
- "mixed stage (embryonic)"
- ],
+ },
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_tbx-8-ENCFF002ILG",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for tbx-8 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF002ILG/ and for more information on this tbx-8 experiment, see https://www.encodeproject.org/experiments/ENCSR549VKC/.",
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF002ILG/@@download/ENCFF002ILG.bigBed"
- }
- },
- "name" : "tbx-8"
+ "category" : [
+ "modERN",
+ "young adult"
+ ],
+ "trackId" : "c_elegans_PRJNA13758_let-607-ENCFF069WTX",
+ "name" : "let-607",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for let-607 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF069WTX/ and for more information on this let-607 experiment, see https://www.encodeproject.org/experiments/ENCSR914MJK/."
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-19 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF644ZEN/ and for more information on this ceh-19 experiment, see https://www.encodeproject.org/experiments/ENCSR281LRS/.",
- "name" : "ceh-19",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF644ZEN/@@download/ENCFF644ZEN.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF002ILG/@@download/ENCFF002ILG.bigBed"
}
},
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "ceh-19-ENCFF644ZEN-LinearBasicDisplay",
+ "displayId" : "tbx-8-ENCFF002ILG-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "color1" : "blue",
+ "height" : 6
},
"type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_ceh-19-ENCFF644ZEN",
- "category" : [
- "modERN",
- "late embryonic"
- ],
+ "name" : "tbx-8",
+ "trackId" : "c_elegans_PRJNA13758_tbx-8-ENCFF002ILG",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for tbx-8 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF002ILG/ and for more information on this tbx-8 experiment, see https://www.encodeproject.org/experiments/ENCSR549VKC/.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modERN",
+ "mixed stage (embryonic)"
]
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for pax-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF713SRM/ and for more information on this pax-3 experiment, see https://www.encodeproject.org/experiments/ENCSR518WKG/.",
- "name" : "pax-3",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF713SRM/@@download/ENCFF713SRM.bigBed",
- "locationType" : "UriLocation"
- }
- },
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "color1" : "blue",
+ "height" : 6
},
- "displayId" : "pax-3-ENCFF713SRM-LinearBasicDisplay"
+ "displayId" : "ceh-19-ENCFF644ZEN-LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_pax-3-ENCFF713SRM",
- "category" : [
- "modERN",
- "L1 larva"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ]
- },
- {
- "name" : "ttx-3",
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF738TXH/@@download/ENCFF738TXH.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF644ZEN/@@download/ENCFF644ZEN.bigBed",
"locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ttx-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF738TXH/ and for more information on this ttx-3 experiment, see https://www.encodeproject.org/experiments/ENCSR233MSN/.",
- "trackId" : "c_elegans_PRJNA13758_ttx-3-ENCFF738TXH",
"category" : [
"modERN",
"late embryonic"
@@ -36994,205 +36330,230 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-19 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF644ZEN/ and for more information on this ceh-19 experiment, see https://www.encodeproject.org/experiments/ENCSR281LRS/.",
+ "trackId" : "c_elegans_PRJNA13758_ceh-19-ENCFF644ZEN",
+ "name" : "ceh-19"
+ },
+ {
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF713SRM/@@download/ENCFF713SRM.bigBed"
+ }
+ },
"displays" : [
{
- "displayId" : "ttx-3-ENCFF738TXH-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "color1" : "blue",
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "pax-3-ENCFF713SRM-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ]
- },
- {
+ ],
+ "name" : "pax-3",
+ "trackId" : "c_elegans_PRJNA13758_pax-3-ENCFF713SRM",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for pax-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF713SRM/ and for more information on this pax-3 experiment, see https://www.encodeproject.org/experiments/ENCSR518WKG/.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"modERN",
- "late embryonic"
- ],
- "trackId" : "c_elegans_PRJNA13758_ahr-1-ENCFF224RLI",
+ "L1 larva"
+ ]
+ },
+ {
"displays" : [
{
- "displayId" : "ahr-1-ENCFF224RLI-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "ttx-3-ENCFF738TXH-LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
- "height" : 6
+ "height" : 6,
+ "color1" : "blue"
}
}
],
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF224RLI/@@download/ENCFF224RLI.bigBed",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF738TXH/@@download/ENCFF738TXH.bigBed"
+ }
},
"type" : "FeatureTrack",
- "name" : "ahr-1",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ahr-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF224RLI/ and for more information on this ahr-1 experiment, see https://www.encodeproject.org/experiments/ENCSR050PRW/."
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modERN",
+ "late embryonic"
+ ],
+ "name" : "ttx-3",
+ "trackId" : "c_elegans_PRJNA13758_ttx-3-ENCFF738TXH",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ttx-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF738TXH/ and for more information on this ttx-3 experiment, see https://www.encodeproject.org/experiments/ENCSR233MSN/."
},
{
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "ahr-1-ENCFF224RLI-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"color1" : "blue",
+ "height" : 6,
"type" : "SvgFeatureRenderer"
- },
- "displayId" : "somi-1-ENCFF552MLZ-LinearBasicDisplay"
+ }
+ }
+ ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF224RLI/@@download/ENCFF224RLI.bigBed",
+ "locationType" : "UriLocation"
}
+ },
+ "category" : [
+ "modERN",
+ "late embryonic"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ahr-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF224RLI/ and for more information on this ahr-1 experiment, see https://www.encodeproject.org/experiments/ENCSR050PRW/.",
+ "name" : "ahr-1",
+ "trackId" : "c_elegans_PRJNA13758_ahr-1-ENCFF224RLI"
+ },
+ {
"category" : [
"modERN",
"young adult"
],
- "trackId" : "c_elegans_PRJNA13758_somi-1-ENCFF552MLZ",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for somi-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF552MLZ/ and for more information on this somi-1 experiment, see https://www.encodeproject.org/experiments/ENCSR360VOG/.",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF552MLZ/@@download/ENCFF552MLZ.bigBed"
- },
- "type" : "BigBedAdapter"
- },
"type" : "FeatureTrack",
- "name" : "somi-1"
- },
- {
- "name" : "hmg-4",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for somi-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF552MLZ/ and for more information on this somi-1 experiment, see https://www.encodeproject.org/experiments/ENCSR360VOG/.",
+ "name" : "somi-1",
+ "trackId" : "c_elegans_PRJNA13758_somi-1-ENCFF552MLZ",
+ "displays" : [
+ {
+ "displayId" : "somi-1-ENCFF552MLZ-LinearBasicDisplay",
+ "renderer" : {
+ "height" : 6,
+ "color1" : "blue",
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF909GPQ/@@download/ENCFF909GPQ.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF552MLZ/@@download/ENCFF552MLZ.bigBed",
+ "locationType" : "UriLocation"
}
- },
+ }
+ },
+ {
"type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hmg-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF909GPQ/ and for more information on this hmg-4 experiment, see https://www.encodeproject.org/experiments/ENCSR306UKE/.",
- "trackId" : "c_elegans_PRJNA13758_hmg-4-ENCFF909GPQ",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modERN",
"early embryonic"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "hmg-4",
+ "trackId" : "c_elegans_PRJNA13758_hmg-4-ENCFF909GPQ",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hmg-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF909GPQ/ and for more information on this hmg-4 experiment, see https://www.encodeproject.org/experiments/ENCSR306UKE/.",
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
+ "color1" : "blue",
"height" : 6
},
- "displayId" : "hmg-4-ENCFF909GPQ-LinearBasicDisplay"
+ "displayId" : "hmg-4-ENCFF909GPQ-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ]
- },
- {
- "type" : "FeatureTrack",
+ ],
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF927WYT/@@download/ENCFF927WYT.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF909GPQ/@@download/ENCFF909GPQ.bigBed",
"locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
- },
+ }
+ },
+ {
+ "trackId" : "c_elegans_PRJNA13758_unc-3-ENCFF927WYT",
"name" : "unc-3",
"description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for unc-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF927WYT/ and for more information on this unc-3 experiment, see https://www.encodeproject.org/experiments/ENCSR246TDY/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
"late embryonic"
],
- "trackId" : "c_elegans_PRJNA13758_unc-3-ENCFF927WYT",
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "height" : 6,
- "color1" : "blue",
- "type" : "SvgFeatureRenderer"
- },
- "displayId" : "unc-3-ENCFF927WYT-LinearBasicDisplay"
- }
- ]
- },
- {
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-13 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF163BSC/ and for more information on this ceh-13 experiment, see https://www.encodeproject.org/experiments/ENCSR389SSP/.",
- "name" : "ceh-13",
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF163BSC/@@download/ENCFF163BSC.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF927WYT/@@download/ENCFF927WYT.bigBed"
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "ceh-13-ENCFF163BSC-LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 6,
- "color1" : "blue",
- "type" : "SvgFeatureRenderer"
+ "color1" : "blue"
},
+ "displayId" : "unc-3-ENCFF927WYT-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
- ],
- "trackId" : "c_elegans_PRJNA13758_ceh-13-ENCFF163BSC",
- "category" : [
- "modERN",
- "early embryonic"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
]
},
{
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF994HKK/@@download/ENCFF994HKK.bigBed",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
"type" : "FeatureTrack",
- "name" : "alr-1",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for alr-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF994HKK/ and for more information on this alr-1 experiment, see https://www.encodeproject.org/experiments/ENCSR961TXR/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"modERN",
- "L1 larva"
+ "early embryonic"
],
- "trackId" : "c_elegans_PRJNA13758_alr-1-ENCFF994HKK",
+ "name" : "ceh-13",
+ "trackId" : "c_elegans_PRJNA13758_ceh-13-ENCFF163BSC",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-13 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF163BSC/ and for more information on this ceh-13 experiment, see https://www.encodeproject.org/experiments/ENCSR389SSP/.",
"displays" : [
{
+ "displayId" : "ceh-13-ENCFF163BSC-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "alr-1-ENCFF994HKK-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF163BSC/@@download/ENCFF163BSC.bigBed"
+ }
+ }
},
{
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -37200,226 +36561,249 @@
"modERN",
"L1 larva"
],
- "trackId" : "c_elegans_PRJNA13758_efl-3-ENCFF224KZR",
+ "name" : "alr-1",
+ "trackId" : "c_elegans_PRJNA13758_alr-1-ENCFF994HKK",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for alr-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF994HKK/ and for more information on this alr-1 experiment, see https://www.encodeproject.org/experiments/ENCSR961TXR/.",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "alr-1-ENCFF994HKK-LinearBasicDisplay",
"renderer" : {
+ "color1" : "blue",
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "efl-3-ENCFF224KZR-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF224KZR/@@download/ENCFF224KZR.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF994HKK/@@download/ENCFF994HKK.bigBed",
+ "locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
- },
- "name" : "efl-3",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for efl-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF224KZR/ and for more information on this efl-3 experiment, see https://www.encodeproject.org/experiments/ENCSR209ZYI/."
+ }
},
{
- "trackId" : "c_elegans_PRJNA13758_ceh-8-ENCFF960PMB",
- "category" : [
- "modERN",
- "L1 larva"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
+ "color1" : "blue",
"height" : 6
},
- "type" : "LinearBasicDisplay",
- "displayId" : "ceh-8-ENCFF960PMB-LinearBasicDisplay"
+ "displayId" : "efl-3-ENCFF224KZR-LinearBasicDisplay"
}
],
- "name" : "ceh-8",
"adapter" : {
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF960PMB/@@download/ENCFF960PMB.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF224KZR/@@download/ENCFF224KZR.bigBed",
+ "locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
"type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-8 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF960PMB/ and for more information on this ceh-8 experiment, see https://www.encodeproject.org/experiments/ENCSR953PJS/."
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modERN",
+ "L1 larva"
+ ],
+ "name" : "efl-3",
+ "trackId" : "c_elegans_PRJNA13758_efl-3-ENCFF224KZR",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for efl-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF224KZR/ and for more information on this efl-3 experiment, see https://www.encodeproject.org/experiments/ENCSR209ZYI/."
},
{
+ "name" : "ceh-8",
+ "trackId" : "c_elegans_PRJNA13758_ceh-8-ENCFF960PMB",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-8 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF960PMB/ and for more information on this ceh-8 experiment, see https://www.encodeproject.org/experiments/ENCSR953PJS/.",
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF188GID/@@download/ENCFF188GID.bigBed"
- }
- },
- "name" : "elt-2",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for elt-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF188GID/ and for more information on this elt-2 experiment, see https://www.encodeproject.org/experiments/ENCSR266NAT/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"modERN",
- "late embryonic"
+ "L1 larva"
],
- "trackId" : "c_elegans_PRJNA13758_elt-2-ENCFF188GID",
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF960PMB/@@download/ENCFF960PMB.bigBed"
+ }
+ },
"displays" : [
{
- "displayId" : "elt-2-ENCFF188GID-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "color1" : "blue",
- "height" : 6
+ "height" : 6,
+ "color1" : "blue"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "ceh-8-ENCFF960PMB-LinearBasicDisplay"
}
]
},
{
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "elt-2-ENCFF188GID-LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
+ "color1" : "blue",
"height" : 6
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "tlf-1-ENCFF213LJM-LinearBasicDisplay"
+ }
}
],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF188GID/@@download/ENCFF188GID.bigBed"
+ },
+ "type" : "BigBedAdapter"
+ },
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modERN",
+ "late embryonic"
+ ],
+ "name" : "elt-2",
+ "trackId" : "c_elegans_PRJNA13758_elt-2-ENCFF188GID",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for elt-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF188GID/ and for more information on this elt-2 experiment, see https://www.encodeproject.org/experiments/ENCSR266NAT/."
+ },
+ {
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for tlf-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF213LJM/ and for more information on this tlf-1 experiment, see https://www.encodeproject.org/experiments/ENCSR049FHU/.",
+ "name" : "tlf-1",
"trackId" : "c_elegans_PRJNA13758_tlf-1-ENCFF213LJM",
"category" : [
"modERN",
"young adult"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for tlf-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF213LJM/ and for more information on this tlf-1 experiment, see https://www.encodeproject.org/experiments/ENCSR049FHU/.",
- "name" : "tlf-1",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF213LJM/@@download/ENCFF213LJM.bigBed",
- "locationType" : "UriLocation"
- }
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF213LJM/@@download/ENCFF213LJM.bigBed"
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack"
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "height" : 6,
+ "color1" : "blue"
+ },
+ "displayId" : "tlf-1-ENCFF213LJM-LinearBasicDisplay"
+ }
+ ]
},
{
"displays" : [
{
- "displayId" : "hlh-13-ENCFF631NJO-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "color1" : "blue",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "hlh-13-ENCFF631NJO-LinearBasicDisplay"
}
],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF631NJO/@@download/ENCFF631NJO.bigBed"
+ }
+ },
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
"late embryonic"
],
"trackId" : "c_elegans_PRJNA13758_hlh-13-ENCFF631NJO",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hlh-13 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF631NJO/ and for more information on this hlh-13 experiment, see https://www.encodeproject.org/experiments/ENCSR457RNA/.",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF631NJO/@@download/ENCFF631NJO.bigBed"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "hlh-13"
+ "name" : "hlh-13",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hlh-13 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF631NJO/ and for more information on this hlh-13 experiment, see https://www.encodeproject.org/experiments/ENCSR457RNA/."
},
{
- "name" : "lin-32",
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "blue",
+ "height" : 6
+ },
+ "displayId" : "lin-32-ENCFF624RSH-LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF624RSH/@@download/ENCFF624RSH.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF624RSH/@@download/ENCFF624RSH.bigBed",
+ "locationType" : "UriLocation"
}
},
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for lin-32 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF624RSH/ and for more information on this lin-32 experiment, see https://www.encodeproject.org/experiments/ENCSR264HFB/.",
- "trackId" : "c_elegans_PRJNA13758_lin-32-ENCFF624RSH",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modERN",
"mixed stage (embryonic)"
],
+ "name" : "lin-32",
+ "trackId" : "c_elegans_PRJNA13758_lin-32-ENCFF624RSH",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for lin-32 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF624RSH/ and for more information on this lin-32 experiment, see https://www.encodeproject.org/experiments/ENCSR264HFB/."
+ },
+ {
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "displays" : [
- {
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "blue",
- "height" : 6
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "lin-32-ENCFF624RSH-LinearBasicDisplay"
- }
- ]
- },
- {
+ "type" : "FeatureTrack",
+ "category" : [
+ "modERN",
+ "L1 larva"
+ ],
+ "trackId" : "c_elegans_PRJNA13758_elt-2-ENCFF801JKF",
+ "name" : "elt-2",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for elt-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF801JKF/ and for more information on this elt-2 experiment, see https://www.encodeproject.org/experiments/ENCSR697MUB/.",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "elt-2-ENCFF801JKF-LinearBasicDisplay",
"renderer" : {
"height" : 6,
"color1" : "blue",
"type" : "SvgFeatureRenderer"
- },
- "displayId" : "elt-2-ENCFF801JKF-LinearBasicDisplay"
+ }
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "L1 larva"
- ],
- "trackId" : "c_elegans_PRJNA13758_elt-2-ENCFF801JKF",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for elt-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF801JKF/ and for more information on this elt-2 experiment, see https://www.encodeproject.org/experiments/ENCSR697MUB/.",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF801JKF/@@download/ENCFF801JKF.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF801JKF/@@download/ENCFF801JKF.bigBed",
+ "locationType" : "UriLocation"
}
- },
- "name" : "elt-2"
+ }
},
{
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF709ESK/@@download/ENCFF709ESK.bigBed"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "F57C9.4",
"description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F57C9.4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF709ESK/ and for more information on this F57C9.4 experiment, see https://www.encodeproject.org/experiments/ENCSR823IAC/.",
+ "trackId" : "c_elegans_PRJNA13758_F57C9.4-ENCFF709ESK",
+ "name" : "F57C9.4",
"category" : [
"modERN",
"young adult"
@@ -37427,41 +36811,28 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_F57C9.4-ENCFF709ESK",
- "displays" : [
- {
- "displayId" : "F57C9.4-ENCFF709ESK-LinearBasicDisplay",
- "renderer" : {
- "color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
- },
- "type" : "LinearBasicDisplay"
- }
- ]
- },
- {
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for tra-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF100SUQ/ and for more information on this tra-4 experiment, see https://www.encodeproject.org/experiments/ENCSR928FFW/.",
+ "type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF100SUQ/@@download/ENCFF100SUQ.bigBed"
- },
- "type" : "BigBedAdapter"
+ "uri" : "https://www.encodeproject.org/files/ENCFF709ESK/@@download/ENCFF709ESK.bigBed"
+ }
},
- "type" : "FeatureTrack",
- "name" : "tra-4",
"displays" : [
{
- "displayId" : "tra-4-ENCFF100SUQ-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
- }
+ "color1" : "blue",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "F57C9.4-ENCFF709ESK-LinearBasicDisplay"
}
- ],
+ ]
+ },
+ {
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -37469,61 +36840,81 @@
"modERN",
"early embryonic"
],
- "trackId" : "c_elegans_PRJNA13758_tra-4-ENCFF100SUQ"
- },
- {
+ "name" : "tra-4",
+ "trackId" : "c_elegans_PRJNA13758_tra-4-ENCFF100SUQ",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for tra-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF100SUQ/ and for more information on this tra-4 experiment, see https://www.encodeproject.org/experiments/ENCSR928FFW/.",
"displays" : [
{
- "displayId" : "K02D7.2-ENCFF155VRT-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
+ "displayId" : "tra-4-ENCFF100SUQ-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"color1" : "blue",
- "height" : 6
- },
- "type" : "LinearBasicDisplay"
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ }
}
],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF100SUQ/@@download/ENCFF100SUQ.bigBed",
+ "locationType" : "UriLocation"
+ }
+ }
+ },
+ {
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
"late embryonic"
],
"trackId" : "c_elegans_PRJNA13758_K02D7.2-ENCFF155VRT",
+ "name" : "K02D7.2",
"description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for K02D7.2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF155VRT/ and for more information on this K02D7.2 experiment, see https://www.encodeproject.org/experiments/ENCSR565YWG/.",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "K02D7.2-ENCFF155VRT-LinearBasicDisplay",
+ "renderer" : {
+ "height" : 6,
+ "color1" : "blue",
+ "type" : "SvgFeatureRenderer"
+ }
+ }
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF155VRT/@@download/ENCFF155VRT.bigBed",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF155VRT/@@download/ENCFF155VRT.bigBed"
}
- },
- "type" : "FeatureTrack",
- "name" : "K02D7.2"
+ }
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ztf-26 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF545QTX/ and for more information on this ztf-26 experiment, see https://www.encodeproject.org/experiments/ENCSR869PRN/.",
"adapter" : {
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF545QTX/@@download/ENCFF545QTX.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF545QTX/@@download/ENCFF545QTX.bigBed",
+ "locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "name" : "ztf-26",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "ztf-26-ENCFF545QTX-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"color1" : "blue",
+ "height" : 6,
"type" : "SvgFeatureRenderer"
},
- "displayId" : "ztf-26-ENCFF545QTX-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ztf-26 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF545QTX/ and for more information on this ztf-26 experiment, see https://www.encodeproject.org/experiments/ENCSR869PRN/.",
+ "trackId" : "c_elegans_PRJNA13758_ztf-26-ENCFF545QTX",
+ "name" : "ztf-26",
"category" : [
"modERN",
"young adult"
@@ -37531,19 +36922,9 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_ztf-26-ENCFF545QTX"
+ "type" : "FeatureTrack"
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for repo-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF224YHJ/ and for more information on this repo-1 experiment, see https://www.encodeproject.org/experiments/ENCSR809IFM/.",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF224YHJ/@@download/ENCFF224YHJ.bigBed",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "repo-1",
"displays" : [
{
"renderer" : {
@@ -37551,40 +36932,30 @@
"color1" : "blue",
"height" : 6
},
- "type" : "LinearBasicDisplay",
- "displayId" : "repo-1-ENCFF224YHJ-LinearBasicDisplay"
+ "displayId" : "repo-1-ENCFF224YHJ-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF224YHJ/@@download/ENCFF224YHJ.bigBed",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
"young adult"
],
- "trackId" : "c_elegans_PRJNA13758_repo-1-ENCFF224YHJ"
+ "trackId" : "c_elegans_PRJNA13758_repo-1-ENCFF224YHJ",
+ "name" : "repo-1",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for repo-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF224YHJ/ and for more information on this repo-1 experiment, see https://www.encodeproject.org/experiments/ENCSR809IFM/."
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "young adult"
- ],
- "trackId" : "c_elegans_PRJNA13758_atf-7-ENCFF660RQT",
- "displays" : [
- {
- "displayId" : "atf-7-ENCFF660RQT-LinearBasicDisplay",
- "renderer" : {
- "height" : 6,
- "color1" : "blue",
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay"
- }
- ],
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
@@ -37592,111 +36963,139 @@
"uri" : "https://www.encodeproject.org/files/ENCFF660RQT/@@download/ENCFF660RQT.bigBed"
}
},
- "name" : "atf-7",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for atf-7 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF660RQT/ and for more information on this atf-7 experiment, see https://www.encodeproject.org/experiments/ENCSR411OOP/."
- },
- {
"displays" : [
{
- "displayId" : "C34B4.2-ENCFF194JSG-LinearBasicDisplay",
+ "displayId" : "atf-7-ENCFF660RQT-LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 6,
- "color1" : "blue",
- "type" : "SvgFeatureRenderer"
+ "color1" : "blue"
},
"type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_C34B4.2-ENCFF194JSG",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for atf-7 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF660RQT/ and for more information on this atf-7 experiment, see https://www.encodeproject.org/experiments/ENCSR411OOP/.",
+ "name" : "atf-7",
+ "trackId" : "c_elegans_PRJNA13758_atf-7-ENCFF660RQT",
"category" : [
"modERN",
- "L1 larva"
+ "young adult"
],
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for C34B4.2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF194JSG/ and for more information on this C34B4.2 experiment, see https://www.encodeproject.org/experiments/ENCSR180ETP/.",
- "name" : "C34B4.2",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ]
+ },
+ {
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://www.encodeproject.org/files/ENCFF194JSG/@@download/ENCFF194JSG.bigBed",
"locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- }
+ }
+ },
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "blue",
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "C34B4.2-ENCFF194JSG-LinearBasicDisplay"
+ }
+ ],
+ "name" : "C34B4.2",
+ "trackId" : "c_elegans_PRJNA13758_C34B4.2-ENCFF194JSG",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for C34B4.2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF194JSG/ and for more information on this C34B4.2 experiment, see https://www.encodeproject.org/experiments/ENCSR180ETP/.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modERN",
+ "L1 larva"
+ ]
},
{
+ "name" : "vab-15",
"trackId" : "c_elegans_PRJNA13758_vab-15-ENCFF628XNQ",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for vab-15 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF628XNQ/ and for more information on this vab-15 experiment, see https://www.encodeproject.org/experiments/ENCSR757OPC/.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modERN",
"L1 larva"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF628XNQ/@@download/ENCFF628XNQ.bigBed",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
"displayId" : "vab-15-ENCFF628XNQ-LinearBasicDisplay",
+ "renderer" : {
+ "height" : 6,
+ "color1" : "blue",
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ]
+ },
+ {
+ "displays" : [
+ {
"type" : "LinearBasicDisplay",
+ "displayId" : "ceh-79-ENCFF583KQW-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"color1" : "blue",
- "height" : 6
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
}
}
],
- "name" : "vab-15",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF628XNQ/@@download/ENCFF628XNQ.bigBed",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF583KQW/@@download/ENCFF583KQW.bigBed"
},
"type" : "BigBedAdapter"
},
"type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for vab-15 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF628XNQ/ and for more information on this vab-15 experiment, see https://www.encodeproject.org/experiments/ENCSR757OPC/."
- },
- {
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-79 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF583KQW/ and for more information on this ceh-79 experiment, see https://www.encodeproject.org/experiments/ENCSR388MJH/.",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF583KQW/@@download/ENCFF583KQW.bigBed",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "ceh-79",
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
- },
- "displayId" : "ceh-79-ENCFF583KQW-LinearBasicDisplay"
- }
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
"category" : [
"modERN",
"young adult"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_ceh-79-ENCFF583KQW"
+ "name" : "ceh-79",
+ "trackId" : "c_elegans_PRJNA13758_ceh-79-ENCFF583KQW",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-79 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF583KQW/ and for more information on this ceh-79 experiment, see https://www.encodeproject.org/experiments/ENCSR388MJH/."
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for dpff-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF723NIR/ and for more information on this dpff-1 experiment, see https://www.encodeproject.org/experiments/ENCSR447OYJ/.",
"name" : "dpff-1",
+ "trackId" : "c_elegans_PRJNA13758_dpff-1-ENCFF723NIR",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for dpff-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF723NIR/ and for more information on this dpff-1 experiment, see https://www.encodeproject.org/experiments/ENCSR447OYJ/.",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modERN",
+ "young adult"
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF723NIR/@@download/ENCFF723NIR.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF723NIR/@@download/ENCFF723NIR.bigBed",
+ "locationType" : "UriLocation"
}
},
"displays" : [
@@ -37709,141 +37108,136 @@
},
"type" : "LinearBasicDisplay"
}
- ],
- "trackId" : "c_elegans_PRJNA13758_dpff-1-ENCFF723NIR",
- "category" : [
- "modERN",
- "young adult"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
]
},
{
- "name" : "hif-1",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF629RSP/@@download/ENCFF629RSP.bigBed"
- }
- },
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hif-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF629RSP/ and for more information on this hif-1 experiment, see https://www.encodeproject.org/experiments/ENCSR991HIA/.",
- "trackId" : "c_elegans_PRJNA13758_hif-1-ENCFF629RSP",
"category" : [
"modERN",
"L4 larva"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hif-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF629RSP/ and for more information on this hif-1 experiment, see https://www.encodeproject.org/experiments/ENCSR991HIA/.",
+ "name" : "hif-1",
+ "trackId" : "c_elegans_PRJNA13758_hif-1-ENCFF629RSP",
"displays" : [
{
- "displayId" : "hif-1-ENCFF629RSP-LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
+ "color1" : "blue",
"height" : 6
},
+ "displayId" : "hif-1-ENCFF629RSP-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF629RSP/@@download/ENCFF629RSP.bigBed"
+ }
+ }
},
{
- "trackId" : "c_elegans_PRJNA13758_ccch-3-ENCFF837OBP",
- "category" : [
- "modERN",
- "young adult"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF837OBP/@@download/ENCFF837OBP.bigBed",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "ccch-3-ENCFF837OBP-LinearBasicDisplay",
"renderer" : {
+ "height" : 6,
"color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "ccch-3-ENCFF837OBP-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
"name" : "ccch-3",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF837OBP/@@download/ENCFF837OBP.bigBed"
- },
- "type" : "BigBedAdapter"
- },
+ "trackId" : "c_elegans_PRJNA13758_ccch-3-ENCFF837OBP",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ccch-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF837OBP/ and for more information on this ccch-3 experiment, see https://www.encodeproject.org/experiments/ENCSR514BBN/.",
"type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ccch-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF837OBP/ and for more information on this ccch-3 experiment, see https://www.encodeproject.org/experiments/ENCSR514BBN/."
- },
- {
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"modERN",
- "late embryonic"
- ],
- "trackId" : "c_elegans_PRJNA13758_pha-2-ENCFF897MUW",
+ "young adult"
+ ]
+ },
+ {
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "pha-2-ENCFF897MUW-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "color1" : "blue",
+ "height" : 6
},
- "displayId" : "pha-2-ENCFF897MUW-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://www.encodeproject.org/files/ENCFF897MUW/@@download/ENCFF897MUW.bigBed"
- }
+ },
+ "type" : "BigBedAdapter"
},
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modERN",
+ "late embryonic"
+ ],
"name" : "pha-2",
+ "trackId" : "c_elegans_PRJNA13758_pha-2-ENCFF897MUW",
"description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for pha-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF897MUW/ and for more information on this pha-2 experiment, see https://www.encodeproject.org/experiments/ENCSR164CYL/."
},
{
"description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for sox-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF183LPX/ and for more information on this sox-4 experiment, see https://www.encodeproject.org/experiments/ENCSR204WOO/.",
+ "name" : "sox-4",
+ "trackId" : "c_elegans_PRJNA13758_sox-4-ENCFF183LPX",
+ "category" : [
+ "modERN",
+ "late embryonic"
+ ],
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF183LPX/@@download/ENCFF183LPX.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF183LPX/@@download/ENCFF183LPX.bigBed",
+ "locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
- "name" : "sox-4",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "sox-4-ENCFF183LPX-LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
- "height" : 6
+ "height" : 6,
+ "color1" : "blue"
},
- "displayId" : "sox-4-ENCFF183LPX-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "late embryonic"
- ],
- "trackId" : "c_elegans_PRJNA13758_sox-4-ENCFF183LPX"
+ ]
},
{
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for spr-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF791MYR/ and for more information on this spr-3 experiment, see https://www.encodeproject.org/experiments/ENCSR810BRE/.",
+ "trackId" : "c_elegans_PRJNA13758_spr-3-ENCFF791MYR",
+ "name" : "spr-3",
"category" : [
"modERN",
"L4 larva"
@@ -37851,278 +37245,276 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_spr-3-ENCFF791MYR",
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF791MYR/@@download/ENCFF791MYR.bigBed"
+ }
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "spr-3-ENCFF791MYR-LinearBasicDisplay",
"renderer" : {
+ "height" : 6,
"color1" : "blue",
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ]
+ },
+ {
+ "displays" : [
+ {
+ "displayId" : "hlh-17-ENCFF784HDR-LinearBasicDisplay",
+ "renderer" : {
"type" : "SvgFeatureRenderer",
+ "color1" : "blue",
"height" : 6
},
- "displayId" : "spr-3-ENCFF791MYR-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF791MYR/@@download/ENCFF791MYR.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF784HDR/@@download/ENCFF784HDR.bigBed",
+ "locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
- "name" : "spr-3",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for spr-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF791MYR/ and for more information on this spr-3 experiment, see https://www.encodeproject.org/experiments/ENCSR810BRE/."
- },
- {
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modERN",
"L1 larva"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "hlh-17",
"trackId" : "c_elegans_PRJNA13758_hlh-17-ENCFF784HDR",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hlh-17 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF784HDR/ and for more information on this hlh-17 experiment, see https://www.encodeproject.org/experiments/ENCSR895KXK/."
+ },
+ {
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF700GAN/@@download/ENCFF700GAN.bigBed",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
- "displayId" : "hlh-17-ENCFF784HDR-LinearBasicDisplay",
"renderer" : {
+ "height" : 6,
"color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
+ "type" : "SvgFeatureRenderer"
},
+ "displayId" : "mxl-3-ENCFF700GAN-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
+ "name" : "mxl-3",
+ "trackId" : "c_elegans_PRJNA13758_mxl-3-ENCFF700GAN",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for mxl-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF700GAN/ and for more information on this mxl-3 experiment, see https://www.encodeproject.org/experiments/ENCSR416GJW/.",
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF784HDR/@@download/ENCFF784HDR.bigBed"
- }
- },
- "name" : "hlh-17",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hlh-17 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF784HDR/ and for more information on this hlh-17 experiment, see https://www.encodeproject.org/experiments/ENCSR895KXK/."
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modERN",
+ "L4 larva"
+ ]
},
{
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F13C5.2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF072XKZ/ and for more information on this F13C5.2 experiment, see https://www.encodeproject.org/experiments/ENCSR387HSD/.",
+ "name" : "F13C5.2",
+ "trackId" : "c_elegans_PRJNA13758_F13C5.2-ENCFF072XKZ",
"category" : [
"modERN",
- "L4 larva"
+ "early embryonic"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_mxl-3-ENCFF700GAN",
- "displays" : [
- {
- "renderer" : {
- "color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "mxl-3-ENCFF700GAN-LinearBasicDisplay"
- }
- ],
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF700GAN/@@download/ENCFF700GAN.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF072XKZ/@@download/ENCFF072XKZ.bigBed",
"locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ }
},
- "name" : "mxl-3",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for mxl-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF700GAN/ and for more information on this mxl-3 experiment, see https://www.encodeproject.org/experiments/ENCSR416GJW/."
- },
- {
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"color1" : "blue",
+ "height" : 6,
"type" : "SvgFeatureRenderer"
},
"displayId" : "F13C5.2-ENCFF072XKZ-LinearBasicDisplay"
}
- ],
- "trackId" : "c_elegans_PRJNA13758_F13C5.2-ENCFF072XKZ",
+ ]
+ },
+ {
+ "trackId" : "c_elegans_PRJNA13758_athp-1-ENCFF087FOX",
+ "name" : "athp-1",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for athp-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF087FOX/ and for more information on this athp-1 experiment, see https://www.encodeproject.org/experiments/ENCSR875XJL/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
- "early embryonic"
+ "young adult"
],
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F13C5.2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF072XKZ/ and for more information on this F13C5.2 experiment, see https://www.encodeproject.org/experiments/ENCSR387HSD/.",
- "name" : "F13C5.2",
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF072XKZ/@@download/ENCFF072XKZ.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF087FOX/@@download/ENCFF087FOX.bigBed",
+ "locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
- }
+ },
+ "displays" : [
+ {
+ "displayId" : "athp-1-ENCFF087FOX-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "blue",
+ "height" : 6
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for athp-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF087FOX/ and for more information on this athp-1 experiment, see https://www.encodeproject.org/experiments/ENCSR875XJL/.",
- "name" : "athp-1",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF087FOX/@@download/ENCFF087FOX.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF760UFU/@@download/ENCFF760UFU.bigBed",
+ "locationType" : "UriLocation"
}
},
"displays" : [
{
+ "displayId" : "K12H6.12-ENCFF760UFU-LinearBasicDisplay",
"renderer" : {
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "color1" : "blue",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "athp-1-ENCFF087FOX-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_athp-1-ENCFF087FOX",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for K12H6.12 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF760UFU/ and for more information on this K12H6.12 experiment, see https://www.encodeproject.org/experiments/ENCSR500LPZ/.",
+ "name" : "K12H6.12",
+ "trackId" : "c_elegans_PRJNA13758_K12H6.12-ENCFF760UFU",
"category" : [
"modERN",
"young adult"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
]
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for K12H6.12 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF760UFU/ and for more information on this K12H6.12 experiment, see https://www.encodeproject.org/experiments/ENCSR500LPZ/.",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for sdz-12 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF887VOL/ and for more information on this sdz-12 experiment, see https://www.encodeproject.org/experiments/ENCSR122TLF/.",
+ "trackId" : "c_elegans_PRJNA13758_sdz-12-ENCFF887VOL",
+ "name" : "sdz-12",
+ "category" : [
+ "modERN",
+ "L4 larva"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF760UFU/@@download/ENCFF760UFU.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF887VOL/@@download/ENCFF887VOL.bigBed"
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "name" : "K12H6.12",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
+ "color1" : "blue",
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "K12H6.12-ENCFF760UFU-LinearBasicDisplay"
+ "displayId" : "sdz-12-ENCFF887VOL-LinearBasicDisplay"
}
- ],
- "category" : [
- "modERN",
- "young adult"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_K12H6.12-ENCFF760UFU"
+ ]
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "L4 larva"
- ],
- "trackId" : "c_elegans_PRJNA13758_sdz-12-ENCFF887VOL",
"displays" : [
{
- "displayId" : "sdz-12-ENCFF887VOL-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "color1" : "blue",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "Y55F3AM.14-ENCFF668OZF-LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF887VOL/@@download/ENCFF887VOL.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF668OZF/@@download/ENCFF668OZF.bigBed",
+ "locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
- "name" : "sdz-12",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for sdz-12 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF887VOL/ and for more information on this sdz-12 experiment, see https://www.encodeproject.org/experiments/ENCSR122TLF/."
+ "category" : [
+ "modERN",
+ "L2 larva"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for Y55F3AM.14 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF668OZF/ and for more information on this Y55F3AM.14 experiment, see https://www.encodeproject.org/experiments/ENCSR872HBZ/.",
+ "name" : "Y55F3AM.14",
+ "trackId" : "c_elegans_PRJNA13758_Y55F3AM.14-ENCFF668OZF"
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for Y55F3AM.14 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF668OZF/ and for more information on this Y55F3AM.14 experiment, see https://www.encodeproject.org/experiments/ENCSR872HBZ/.",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF668OZF/@@download/ENCFF668OZF.bigBed",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF617WQM/@@download/ENCFF617WQM.bigBed"
}
},
- "name" : "Y55F3AM.14",
"displays" : [
{
- "displayId" : "Y55F3AM.14-ENCFF668OZF-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "hlh-15-ENCFF617WQM-LinearBasicDisplay",
"renderer" : {
"color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
}
}
],
- "category" : [
- "modERN",
- "L2 larva"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_Y55F3AM.14-ENCFF668OZF"
- },
- {
+ "name" : "hlh-15",
+ "trackId" : "c_elegans_PRJNA13758_hlh-15-ENCFF617WQM",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hlh-15 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF617WQM/ and for more information on this hlh-15 experiment, see https://www.encodeproject.org/experiments/ENCSR155UEF/.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"modERN",
"late embryonic"
- ],
- "trackId" : "c_elegans_PRJNA13758_hlh-15-ENCFF617WQM",
- "displays" : [
- {
- "displayId" : "hlh-15-ENCFF617WQM-LinearBasicDisplay",
- "renderer" : {
- "color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
- },
- "type" : "LinearBasicDisplay"
- }
- ],
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF617WQM/@@download/ENCFF617WQM.bigBed"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "hlh-15",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hlh-15 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF617WQM/ and for more information on this hlh-15 experiment, see https://www.encodeproject.org/experiments/ENCSR155UEF/."
+ ]
},
{
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -38130,112 +37522,102 @@
"modERN",
"young adult"
],
+ "name" : "ztf-22",
"trackId" : "c_elegans_PRJNA13758_ztf-22-ENCFF214PKJ",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ztf-22 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF214PKJ/ and for more information on this ztf-22 experiment, see https://www.encodeproject.org/experiments/ENCSR684PHU/.",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
+ "height" : 6,
"color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
+ "type" : "SvgFeatureRenderer"
},
"displayId" : "ztf-22-ENCFF214PKJ-LinearBasicDisplay"
}
],
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"uri" : "https://www.encodeproject.org/files/ENCFF214PKJ/@@download/ENCFF214PKJ.bigBed",
"locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "ztf-22",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ztf-22 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF214PKJ/ and for more information on this ztf-22 experiment, see https://www.encodeproject.org/experiments/ENCSR684PHU/."
+ },
+ "type" : "BigBedAdapter"
+ }
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for tbp1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF239AFZ/ and for more information on this tbp1 experiment, see https://www.encodeproject.org/experiments/ENCSR260AKX/.",
+ "trackId" : "c_elegans_PRJNA13758_tbp1-ENCFF239AFZ",
+ "name" : "tbp1",
"category" : [
"modERN",
"young adult"
],
- "trackId" : "c_elegans_PRJNA13758_tbp1-ENCFF239AFZ",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF239AFZ/@@download/ENCFF239AFZ.bigBed",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
- "displayId" : "tbp1-ENCFF239AFZ-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "color1" : "blue",
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
- }
- }
- ],
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF239AFZ/@@download/ENCFF239AFZ.bigBed",
- "locationType" : "UriLocation"
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "tbp1-ENCFF239AFZ-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- },
- "type" : "FeatureTrack",
- "name" : "tbp1",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for tbp1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF239AFZ/ and for more information on this tbp1 experiment, see https://www.encodeproject.org/experiments/ENCSR260AKX/."
+ ]
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modERN",
"late embryonic"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for lin-11 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF759MFC/ and for more information on this lin-11 experiment, see https://www.encodeproject.org/experiments/ENCSR656RPB/.",
+ "name" : "lin-11",
"trackId" : "c_elegans_PRJNA13758_lin-11-ENCFF759MFC",
"displays" : [
{
- "displayId" : "lin-11-ENCFF759MFC-LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
- "height" : 6
+ "height" : 6,
+ "color1" : "blue"
},
+ "displayId" : "lin-11-ENCFF759MFC-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF759MFC/@@download/ENCFF759MFC.bigBed",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "lin-11",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for lin-11 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF759MFC/ and for more information on this lin-11 experiment, see https://www.encodeproject.org/experiments/ENCSR656RPB/."
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF759MFC/@@download/ENCFF759MFC.bigBed"
+ },
+ "type" : "BigBedAdapter"
+ }
},
{
- "trackId" : "c_elegans_PRJNA13758_lin-54-ENCFF900QWR",
- "category" : [
- "modERN",
- "young adult"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "lin-54-ENCFF900QWR-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"color1" : "blue",
+ "height" : 6,
"type" : "SvgFeatureRenderer"
},
- "displayId" : "lin-54-ENCFF900QWR-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "name" : "lin-54",
"adapter" : {
"bigBedLocation" : {
"uri" : "https://www.encodeproject.org/files/ENCFF900QWR/@@download/ENCFF900QWR.bigBed",
@@ -38243,11 +37625,30 @@
},
"type" : "BigBedAdapter"
},
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
+ "category" : [
+ "modERN",
+ "young adult"
+ ],
+ "trackId" : "c_elegans_PRJNA13758_lin-54-ENCFF900QWR",
+ "name" : "lin-54",
"description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for lin-54 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF900QWR/ and for more information on this lin-54 experiment, see https://www.encodeproject.org/experiments/ENCSR117TRB/."
},
{
- "name" : "cebp-1",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "blue",
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "cebp-1-ENCFF119DMY-LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
@@ -38255,9 +37656,6 @@
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for cebp-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF119DMY/ and for more information on this cebp-1 experiment, see https://www.encodeproject.org/experiments/ENCSR993GFS/.",
- "trackId" : "c_elegans_PRJNA13758_cebp-1-ENCFF119DMY",
"category" : [
"modERN",
"young adult"
@@ -38265,29 +37663,13 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "displays" : [
- {
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "blue",
- "height" : 6
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "cebp-1-ENCFF119DMY-LinearBasicDisplay"
- }
- ]
+ "type" : "FeatureTrack",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for cebp-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF119DMY/ and for more information on this cebp-1 experiment, see https://www.encodeproject.org/experiments/ENCSR993GFS/.",
+ "trackId" : "c_elegans_PRJNA13758_cebp-1-ENCFF119DMY",
+ "name" : "cebp-1"
},
{
"type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF420MPO/@@download/ENCFF420MPO.bigBed",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "ceh-43",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-43 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF420MPO/ and for more information on this ceh-43 experiment, see https://www.encodeproject.org/experiments/ENCSR479XCM/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -38295,124 +37677,141 @@
"modERN",
"mixed stage (embryonic)"
],
+ "name" : "ceh-43",
"trackId" : "c_elegans_PRJNA13758_ceh-43-ENCFF420MPO",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-43 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF420MPO/ and for more information on this ceh-43 experiment, see https://www.encodeproject.org/experiments/ENCSR479XCM/.",
"displays" : [
{
- "displayId" : "ceh-43-ENCFF420MPO-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
+ "type" : "SvgFeatureRenderer",
"color1" : "blue",
- "type" : "SvgFeatureRenderer"
+ "height" : 6
},
+ "displayId" : "ceh-43-ENCFF420MPO-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF420MPO/@@download/ENCFF420MPO.bigBed",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
"displays" : [
{
"renderer" : {
- "height" : 6,
+ "type" : "SvgFeatureRenderer",
"color1" : "blue",
- "type" : "SvgFeatureRenderer"
+ "height" : 6
},
- "type" : "LinearBasicDisplay",
- "displayId" : "bed-3-ENCFF163VAD-LinearBasicDisplay"
+ "displayId" : "bed-3-ENCFF163VAD-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF163VAD/@@download/ENCFF163VAD.bigBed"
+ },
+ "type" : "BigBedAdapter"
+ },
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
"mixed stage (embryonic)"
],
"trackId" : "c_elegans_PRJNA13758_bed-3-ENCFF163VAD",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for bed-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF163VAD/ and for more information on this bed-3 experiment, see https://www.encodeproject.org/experiments/ENCSR239IAH/.",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF163VAD/@@download/ENCFF163VAD.bigBed",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "bed-3"
+ "name" : "bed-3",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for bed-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF163VAD/ and for more information on this bed-3 experiment, see https://www.encodeproject.org/experiments/ENCSR239IAH/."
},
{
- "name" : "M03D4.4",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF719VFM/@@download/ENCFF719VFM.bigBed"
- },
- "type" : "BigBedAdapter"
- },
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for M03D4.4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF719VFM/ and for more information on this M03D4.4 experiment, see https://www.encodeproject.org/experiments/ENCSR766ULH/.",
- "trackId" : "c_elegans_PRJNA13758_M03D4.4-ENCFF719VFM",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modERN",
"mixed stage (embryonic)"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for M03D4.4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF719VFM/ and for more information on this M03D4.4 experiment, see https://www.encodeproject.org/experiments/ENCSR766ULH/.",
+ "trackId" : "c_elegans_PRJNA13758_M03D4.4-ENCFF719VFM",
+ "name" : "M03D4.4",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "M03D4.4-ENCFF719VFM-LinearBasicDisplay",
"renderer" : {
+ "height" : 6,
"color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
- },
- "type" : "LinearBasicDisplay"
+ "type" : "SvgFeatureRenderer"
+ }
}
- ]
- },
- {
- "type" : "FeatureTrack",
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF674NWC/@@download/ENCFF674NWC.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF719VFM/@@download/ENCFF719VFM.bigBed",
+ "locationType" : "UriLocation"
}
- },
- "name" : "madf-2",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for madf-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF674NWC/ and for more information on this madf-2 experiment, see https://www.encodeproject.org/experiments/ENCSR442XYW/.",
+ }
+ },
+ {
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modERN",
"late embryonic"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "name" : "madf-2",
"trackId" : "c_elegans_PRJNA13758_madf-2-ENCFF674NWC",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for madf-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF674NWC/ and for more information on this madf-2 experiment, see https://www.encodeproject.org/experiments/ENCSR442XYW/.",
"displays" : [
{
"displayId" : "madf-2-ENCFF674NWC-LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
- "height" : 6
+ "height" : 6,
+ "color1" : "blue"
},
"type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF674NWC/@@download/ENCFF674NWC.bigBed",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ }
},
{
"displays" : [
{
- "displayId" : "sptf-2-ENCFF667MVT-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
+ "height" : 6,
"color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "sptf-2-ENCFF667MVT-LinearBasicDisplay"
}
],
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF667MVT/@@download/ENCFF667MVT.bigBed",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -38420,222 +37819,206 @@
"modERN",
"young adult"
],
+ "name" : "sptf-2",
"trackId" : "c_elegans_PRJNA13758_sptf-2-ENCFF667MVT",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for sptf-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF667MVT/ and for more information on this sptf-2 experiment, see https://www.encodeproject.org/experiments/ENCSR956TMJ/.",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF667MVT/@@download/ENCFF667MVT.bigBed",
- "locationType" : "UriLocation"
- }
- },
- "name" : "sptf-2"
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for sptf-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF667MVT/ and for more information on this sptf-2 experiment, see https://www.encodeproject.org/experiments/ENCSR956TMJ/."
},
{
- "displays" : [
- {
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "blue",
- "height" : 6
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "sptf-1-ENCFF528CSQ-LinearBasicDisplay"
- }
+ "trackId" : "c_elegans_PRJNA13758_sptf-1-ENCFF528CSQ",
+ "name" : "sptf-1",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for sptf-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF528CSQ/ and for more information on this sptf-1 experiment, see https://www.encodeproject.org/experiments/ENCSR823LPZ/.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
"mixed stage (embryonic)"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_sptf-1-ENCFF528CSQ",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for sptf-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF528CSQ/ and for more information on this sptf-1 experiment, see https://www.encodeproject.org/experiments/ENCSR823LPZ/.",
"adapter" : {
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF528CSQ/@@download/ENCFF528CSQ.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF528CSQ/@@download/ENCFF528CSQ.bigBed",
+ "locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "name" : "sptf-1"
- },
- {
"displays" : [
{
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
- "height" : 6
+ "height" : 6,
+ "color1" : "blue"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "drap-1-ENCFF847KEQ-LinearBasicDisplay"
+ "displayId" : "sptf-1-ENCFF528CSQ-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ],
+ ]
+ },
+ {
+ "name" : "drap-1",
"trackId" : "c_elegans_PRJNA13758_drap-1-ENCFF847KEQ",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for drap-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF847KEQ/ and for more information on this drap-1 experiment, see https://www.encodeproject.org/experiments/ENCSR617PLK/.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modERN",
"mixed stage (embryonic)"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for drap-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF847KEQ/ and for more information on this drap-1 experiment, see https://www.encodeproject.org/experiments/ENCSR617PLK/.",
- "name" : "drap-1",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF847KEQ/@@download/ENCFF847KEQ.bigBed"
- },
- "type" : "BigBedAdapter"
+ "uri" : "https://www.encodeproject.org/files/ENCFF847KEQ/@@download/ENCFF847KEQ.bigBed",
+ "locationType" : "UriLocation"
+ }
},
- "type" : "FeatureTrack"
+ "displays" : [
+ {
+ "displayId" : "drap-1-ENCFF847KEQ-LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "blue",
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
- "trackId" : "c_elegans_PRJNA13758_hlh-11-ENCFF047SMD",
- "category" : [
- "modERN",
- "L4 larva"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "hlh-11-ENCFF047SMD-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue"
- },
- "type" : "LinearBasicDisplay"
+ }
}
],
- "name" : "hlh-11",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF047SMD/@@download/ENCFF047SMD.bigBed",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF047SMD/@@download/ENCFF047SMD.bigBed"
}
},
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hlh-11 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF047SMD/ and for more information on this hlh-11 experiment, see https://www.encodeproject.org/experiments/ENCSR862DMN/."
+ "category" : [
+ "modERN",
+ "L4 larva"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hlh-11 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF047SMD/ and for more information on this hlh-11 experiment, see https://www.encodeproject.org/experiments/ENCSR862DMN/.",
+ "trackId" : "c_elegans_PRJNA13758_hlh-11-ENCFF047SMD",
+ "name" : "hlh-11"
},
{
"displays" : [
{
"displayId" : "T20F7.1-ENCFF155SFZ-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue",
- "height" : 6
+ "type" : "SvgFeatureRenderer"
},
"type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF155SFZ/@@download/ENCFF155SFZ.bigBed",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"category" : [
"modERN",
"L4 larva"
],
- "trackId" : "c_elegans_PRJNA13758_T20F7.1-ENCFF155SFZ",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for T20F7.1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF155SFZ/ and for more information on this T20F7.1 experiment, see https://www.encodeproject.org/experiments/ENCSR371ICA/.",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF155SFZ/@@download/ENCFF155SFZ.bigBed"
- }
- },
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for T20F7.1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF155SFZ/ and for more information on this T20F7.1 experiment, see https://www.encodeproject.org/experiments/ENCSR371ICA/.",
+ "trackId" : "c_elegans_PRJNA13758_T20F7.1-ENCFF155SFZ",
"name" : "T20F7.1"
},
{
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF221SHQ/@@download/ENCFF221SHQ.bigBed"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "ham-2",
"description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ham-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF221SHQ/ and for more information on this ham-2 experiment, see https://www.encodeproject.org/experiments/ENCSR575DJF/.",
+ "name" : "ham-2",
+ "trackId" : "c_elegans_PRJNA13758_ham-2-ENCFF221SHQ",
"category" : [
"modERN",
"mixed stage (embryonic)"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_ham-2-ENCFF221SHQ",
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF221SHQ/@@download/ENCFF221SHQ.bigBed"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
- "displayId" : "ham-2-ENCFF221SHQ-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "color1" : "blue",
- "height" : 6
- }
+ "height" : 6,
+ "color1" : "blue"
+ },
+ "displayId" : "ham-2-ENCFF221SHQ-LinearBasicDisplay"
}
]
},
{
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
"height" : 6,
"color1" : "blue",
"type" : "SvgFeatureRenderer"
},
- "displayId" : "ceh-63-ENCFF763IRW-LinearBasicDisplay"
+ "displayId" : "ceh-63-ENCFF763IRW-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "L1 larva"
- ],
- "trackId" : "c_elegans_PRJNA13758_ceh-63-ENCFF763IRW",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-63 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF763IRW/ and for more information on this ceh-63 experiment, see https://www.encodeproject.org/experiments/ENCSR182HOA/.",
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF763IRW/@@download/ENCFF763IRW.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF763IRW/@@download/ENCFF763IRW.bigBed",
+ "locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
- "name" : "ceh-63"
- },
- {
"category" : [
"modERN",
- "late embryonic"
+ "L1 larva"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_T23F11.4-ENCFF163FKK",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-63 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF763IRW/ and for more information on this ceh-63 experiment, see https://www.encodeproject.org/experiments/ENCSR182HOA/.",
+ "name" : "ceh-63",
+ "trackId" : "c_elegans_PRJNA13758_ceh-63-ENCFF763IRW"
+ },
+ {
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "T23F11.4-ENCFF163FKK-LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
+ "color1" : "blue",
"height" : 6
- },
- "type" : "LinearBasicDisplay"
+ }
}
],
"adapter" : {
@@ -38646,84 +38029,84 @@
}
},
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modERN",
+ "late embryonic"
+ ],
"name" : "T23F11.4",
+ "trackId" : "c_elegans_PRJNA13758_T23F11.4-ENCFF163FKK",
"description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for T23F11.4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF163FKK/ and for more information on this T23F11.4 experiment, see https://www.encodeproject.org/experiments/ENCSR434ALY/."
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for flh-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF177AWS/ and for more information on this flh-1 experiment, see https://www.encodeproject.org/experiments/ENCSR811ZML/.",
- "name" : "flh-1",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF177AWS/@@download/ENCFF177AWS.bigBed",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "flh-1-ENCFF177AWS-LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
+ "color1" : "blue",
"height" : 6
- },
- "displayId" : "flh-1-ENCFF177AWS-LinearBasicDisplay"
+ }
}
],
- "trackId" : "c_elegans_PRJNA13758_flh-1-ENCFF177AWS",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF177AWS/@@download/ENCFF177AWS.bigBed"
+ },
+ "type" : "BigBedAdapter"
+ },
"category" : [
"modERN",
"mixed stage (embryonic)"
- ]
- },
- {
- "trackId" : "c_elegans_PRJNA13758_ceh-27-ENCFF973XHS",
+ ],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for flh-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF177AWS/ and for more information on this flh-1 experiment, see https://www.encodeproject.org/experiments/ENCSR811ZML/.",
+ "trackId" : "c_elegans_PRJNA13758_flh-1-ENCFF177AWS",
+ "name" : "flh-1"
+ },
+ {
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-27 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF973XHS/ and for more information on this ceh-27 experiment, see https://www.encodeproject.org/experiments/ENCSR951SLK/.",
+ "name" : "ceh-27",
+ "trackId" : "c_elegans_PRJNA13758_ceh-27-ENCFF973XHS",
"category" : [
"modERN",
"young adult"
],
- "displays" : [
- {
- "displayId" : "ceh-27-ENCFF973XHS-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
- }
- }
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
- "name" : "ceh-27",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF973XHS/@@download/ENCFF973XHS.bigBed"
- }
+ "uri" : "https://www.encodeproject.org/files/ENCFF973XHS/@@download/ENCFF973XHS.bigBed",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-27 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF973XHS/ and for more information on this ceh-27 experiment, see https://www.encodeproject.org/experiments/ENCSR951SLK/."
- },
- {
"displays" : [
{
- "displayId" : "ztf-3-ENCFF647UFX-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "color1" : "blue",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "ceh-27-ENCFF973XHS-LinearBasicDisplay"
}
- ],
+ ]
+ },
+ {
+ "name" : "ztf-3",
"trackId" : "c_elegans_PRJNA13758_ztf-3-ENCFF647UFX",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ztf-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF647UFX/ and for more information on this ztf-3 experiment, see https://www.encodeproject.org/experiments/ENCSR565RZD/.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -38731,460 +38114,409 @@
"modERN",
"young adult"
],
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ztf-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF647UFX/ and for more information on this ztf-3 experiment, see https://www.encodeproject.org/experiments/ENCSR565RZD/.",
- "name" : "ztf-3",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF647UFX/@@download/ENCFF647UFX.bigBed"
- }
- }
- },
- {
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for pat-9 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF586TMB/ and for more information on this pat-9 experiment, see https://www.encodeproject.org/experiments/ENCSR572AWO/.",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF586TMB/@@download/ENCFF586TMB.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF647UFX/@@download/ENCFF647UFX.bigBed",
"locationType" : "UriLocation"
}
},
- "name" : "pat-9",
"displays" : [
{
- "displayId" : "pat-9-ENCFF586TMB-LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
- "height" : 6
+ "height" : 6,
+ "color1" : "blue"
},
+ "displayId" : "ztf-3-ENCFF647UFX-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ]
+ },
+ {
+ "displays" : [
+ {
+ "renderer" : {
+ "color1" : "blue",
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "pat-9-ENCFF586TMB-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF586TMB/@@download/ENCFF586TMB.bigBed"
+ }
+ },
"category" : [
"modERN",
"late embryonic"
],
- "trackId" : "c_elegans_PRJNA13758_pat-9-ENCFF586TMB"
- },
- {
- "name" : "attf-5",
"type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF649ZBL/@@download/ENCFF649ZBL.bigBed"
- },
- "type" : "BigBedAdapter"
- },
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for attf-5 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF649ZBL/ and for more information on this attf-5 experiment, see https://www.encodeproject.org/experiments/ENCSR677TRQ/.",
- "trackId" : "c_elegans_PRJNA13758_attf-5-ENCFF649ZBL",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for pat-9 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF586TMB/ and for more information on this pat-9 experiment, see https://www.encodeproject.org/experiments/ENCSR572AWO/.",
+ "name" : "pat-9",
+ "trackId" : "c_elegans_PRJNA13758_pat-9-ENCFF586TMB"
+ },
+ {
"category" : [
"modERN",
"young adult"
],
- "displays" : [
- {
- "renderer" : {
- "height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "attf-5-ENCFF649ZBL-LinearBasicDisplay"
- }
- ]
- },
- {
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for attf-5 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF649ZBL/ and for more information on this attf-5 experiment, see https://www.encodeproject.org/experiments/ENCSR677TRQ/.",
+ "trackId" : "c_elegans_PRJNA13758_attf-5-ENCFF649ZBL",
+ "name" : "attf-5",
"displays" : [
{
"renderer" : {
"color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "sem-2-ENCFF579FLI-LinearBasicDisplay"
+ "displayId" : "attf-5-ENCFF649ZBL-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "category" : [
- "modERN",
- "mixed stage (embryonic)"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_sem-2-ENCFF579FLI",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for sem-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF579FLI/ and for more information on this sem-2 experiment, see https://www.encodeproject.org/experiments/ENCSR641VZA/.",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF579FLI/@@download/ENCFF579FLI.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF649ZBL/@@download/ENCFF649ZBL.bigBed",
"locationType" : "UriLocation"
}
- },
- "name" : "sem-2"
+ }
},
{
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
- },
- "displayId" : "ztf-16-ENCFF319DZY-LinearBasicDisplay"
- }
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for sem-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF579FLI/ and for more information on this sem-2 experiment, see https://www.encodeproject.org/experiments/ENCSR641VZA/.",
+ "name" : "sem-2",
+ "trackId" : "c_elegans_PRJNA13758_sem-2-ENCFF579FLI",
"category" : [
"modERN",
- "late embryonic"
+ "mixed stage (embryonic)"
],
- "trackId" : "c_elegans_PRJNA13758_ztf-16-ENCFF319DZY",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ztf-16 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF319DZY/ and for more information on this ztf-16 experiment, see https://www.encodeproject.org/experiments/ENCSR647GMY/.",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF319DZY/@@download/ENCFF319DZY.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF579FLI/@@download/ENCFF579FLI.bigBed"
},
"type" : "BigBedAdapter"
},
- "name" : "ztf-16"
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "sem-2-ENCFF579FLI-LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "blue",
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ }
+ }
+ ]
},
{
"category" : [
"modERN",
- "young adult"
+ "late embryonic"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_F10E7.11-ENCFF124YBY",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ztf-16 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF319DZY/ and for more information on this ztf-16 experiment, see https://www.encodeproject.org/experiments/ENCSR647GMY/.",
+ "name" : "ztf-16",
+ "trackId" : "c_elegans_PRJNA13758_ztf-16-ENCFF319DZY",
"displays" : [
{
- "displayId" : "F10E7.11-ENCFF124YBY-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
- }
+ "color1" : "blue",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "ztf-16-ENCFF319DZY-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF124YBY/@@download/ENCFF124YBY.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF319DZY/@@download/ENCFF319DZY.bigBed",
"locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
- },
- "name" : "F10E7.11",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F10E7.11 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF124YBY/ and for more information on this F10E7.11 experiment, see https://www.encodeproject.org/experiments/ENCSR541RUY/."
+ }
},
{
"displays" : [
{
- "displayId" : "zim-3-ENCFF451OFD-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
+ "displayId" : "F10E7.11-ENCFF124YBY-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue",
- "height" : 6
- },
- "type" : "LinearBasicDisplay"
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "trackId" : "c_elegans_PRJNA13758_zim-3-ENCFF451OFD",
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF124YBY/@@download/ENCFF124YBY.bigBed"
+ },
+ "type" : "BigBedAdapter"
+ },
+ "category" : [
+ "modERN",
+ "young adult"
+ ],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F10E7.11 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF124YBY/ and for more information on this F10E7.11 experiment, see https://www.encodeproject.org/experiments/ENCSR541RUY/.",
+ "name" : "F10E7.11",
+ "trackId" : "c_elegans_PRJNA13758_F10E7.11-ENCFF124YBY"
+ },
+ {
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for zim-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF451OFD/ and for more information on this zim-3 experiment, see https://www.encodeproject.org/experiments/ENCSR406NQK/.",
+ "trackId" : "c_elegans_PRJNA13758_zim-3-ENCFF451OFD",
+ "name" : "zim-3",
"category" : [
"modERN",
"young adult"
],
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for zim-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF451OFD/ and for more information on this zim-3 experiment, see https://www.encodeproject.org/experiments/ENCSR406NQK/.",
- "name" : "zim-3",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF451OFD/@@download/ENCFF451OFD.bigBed",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF451OFD/@@download/ENCFF451OFD.bigBed"
}
- }
+ },
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "blue",
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "zim-3-ENCFF451OFD-LinearBasicDisplay"
+ }
+ ]
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modERN",
"mixed stage (embryonic)"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for cnd-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF507KJW/ and for more information on this cnd-1 experiment, see https://www.encodeproject.org/experiments/ENCSR296BKT/.",
"trackId" : "c_elegans_PRJNA13758_cnd-1-ENCFF507KJW",
+ "name" : "cnd-1",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "cnd-1-ENCFF507KJW-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "color1" : "blue",
+ "height" : 6
},
- "displayId" : "cnd-1-ENCFF507KJW-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
"uri" : "https://www.encodeproject.org/files/ENCFF507KJW/@@download/ENCFF507KJW.bigBed"
- }
- },
- "type" : "FeatureTrack",
- "name" : "cnd-1",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for cnd-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF507KJW/ and for more information on this cnd-1 experiment, see https://www.encodeproject.org/experiments/ENCSR296BKT/."
+ },
+ "type" : "BigBedAdapter"
+ }
},
{
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF679YEI/@@download/ENCFF679YEI.bigBed",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "pqm-1-ENCFF679YEI-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "blue",
+ "height" : 6
+ }
+ }
+ ],
"trackId" : "c_elegans_PRJNA13758_pqm-1-ENCFF679YEI",
+ "name" : "pqm-1",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for pqm-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF679YEI/ and for more information on this pqm-1 experiment, see https://www.encodeproject.org/experiments/ENCSR778ETM/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
"late embryonic"
- ],
+ ]
+ },
+ {
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "color1" : "blue",
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "pqm-1-ENCFF679YEI-LinearBasicDisplay"
+ "displayId" : "C38D4.7-ENCFF478POU-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "name" : "pqm-1",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF679YEI/@@download/ENCFF679YEI.bigBed",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for pqm-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF679YEI/ and for more information on this pqm-1 experiment, see https://www.encodeproject.org/experiments/ENCSR778ETM/."
- },
- {
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF478POU/@@download/ENCFF478POU.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF478POU/@@download/ENCFF478POU.bigBed",
+ "locationType" : "UriLocation"
}
},
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
- "name" : "C38D4.7",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for C38D4.7 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF478POU/ and for more information on this C38D4.7 experiment, see https://www.encodeproject.org/experiments/ENCSR626LGN/.",
"category" : [
"modERN",
"late embryonic"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"trackId" : "c_elegans_PRJNA13758_C38D4.7-ENCFF478POU",
- "displays" : [
- {
- "renderer" : {
- "height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "C38D4.7-ENCFF478POU-LinearBasicDisplay"
- }
- ]
+ "name" : "C38D4.7",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for C38D4.7 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF478POU/ and for more information on this C38D4.7 experiment, see https://www.encodeproject.org/experiments/ENCSR626LGN/."
},
{
- "displays" : [
- {
- "renderer" : {
- "height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "gei-8-ENCFF574OHJ-LinearBasicDisplay"
- }
- ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for gei-8 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF574OHJ/ and for more information on this gei-8 experiment, see https://www.encodeproject.org/experiments/ENCSR729RHJ/.",
+ "name" : "gei-8",
+ "trackId" : "c_elegans_PRJNA13758_gei-8-ENCFF574OHJ",
"category" : [
"modERN",
"L4 larva"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_gei-8-ENCFF574OHJ",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for gei-8 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF574OHJ/ and for more information on this gei-8 experiment, see https://www.encodeproject.org/experiments/ENCSR729RHJ/.",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF574OHJ/@@download/ENCFF574OHJ.bigBed"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "gei-8"
- },
- {
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-83 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF263UCR/ and for more information on this ceh-83 experiment, see https://www.encodeproject.org/experiments/ENCSR579XVH/.",
- "name" : "ceh-83",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF263UCR/@@download/ENCFF263UCR.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF574OHJ/@@download/ENCFF574OHJ.bigBed",
"locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "ceh-83-ENCFF263UCR-LinearBasicDisplay"
+ "displayId" : "gei-8-ENCFF574OHJ-LinearBasicDisplay"
}
- ],
- "trackId" : "c_elegans_PRJNA13758_ceh-83-ENCFF263UCR",
- "category" : [
- "modERN",
- "mixed stage (embryonic)"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
]
},
{
- "trackId" : "c_elegans_PRJNA13758_nhr-27-ENCFF325DWU",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"modERN",
- "young adult"
+ "mixed stage (embryonic)"
],
+ "name" : "ceh-83",
+ "trackId" : "c_elegans_PRJNA13758_ceh-83-ENCFF263UCR",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-83 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF263UCR/ and for more information on this ceh-83 experiment, see https://www.encodeproject.org/experiments/ENCSR579XVH/.",
"displays" : [
{
- "displayId" : "nhr-27-ENCFF325DWU-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue",
- "height" : 6
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "ceh-83-ENCFF263UCR-LinearBasicDisplay"
}
],
- "name" : "nhr-27",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF325DWU/@@download/ENCFF325DWU.bigBed",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF263UCR/@@download/ENCFF263UCR.bigBed"
},
"type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-27 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF325DWU/ and for more information on this nhr-27 experiment, see https://www.encodeproject.org/experiments/ENCSR542ICA/."
+ }
},
{
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF073WLL/@@download/ENCFF073WLL.bigBed",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "nhr-111",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-111 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF073WLL/ and for more information on this nhr-111 experiment, see https://www.encodeproject.org/experiments/ENCSR487OER/.",
- "category" : [
- "modERN",
- "L4 larva"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_nhr-111-ENCFF073WLL",
"displays" : [
{
- "displayId" : "nhr-111-ENCFF073WLL-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "nhr-27-ENCFF325DWU-LinearBasicDisplay"
}
- ]
- },
- {
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-6 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF038FYU/ and for more information on this ceh-6 experiment, see https://www.encodeproject.org/experiments/ENCSR994CUJ/.",
+ ],
"adapter" : {
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF038FYU/@@download/ENCFF038FYU.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF325DWU/@@download/ENCFF325DWU.bigBed",
+ "locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "name" : "ceh-6",
- "displays" : [
- {
- "displayId" : "ceh-6-ENCFF038FYU-LinearBasicDisplay",
- "renderer" : {
- "color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
- },
- "type" : "LinearBasicDisplay"
- }
- ],
"category" : [
"modERN",
- "late embryonic"
+ "young adult"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_ceh-6-ENCFF038FYU"
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-27 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF325DWU/ and for more information on this nhr-27 experiment, see https://www.encodeproject.org/experiments/ENCSR542ICA/.",
+ "name" : "nhr-27",
+ "trackId" : "c_elegans_PRJNA13758_nhr-27-ENCFF325DWU"
},
{
- "trackId" : "c_elegans_PRJNA13758_zip-4-ENCFF785UNB",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"modERN",
- "L1 larva"
+ "L4 larva"
],
+ "name" : "nhr-111",
+ "trackId" : "c_elegans_PRJNA13758_nhr-111-ENCFF073WLL",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-111 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF073WLL/ and for more information on this nhr-111 experiment, see https://www.encodeproject.org/experiments/ENCSR487OER/.",
"displays" : [
{
"type" : "LinearBasicDisplay",
@@ -39193,141 +38525,138 @@
"color1" : "blue",
"height" : 6
},
- "displayId" : "zip-4-ENCFF785UNB-LinearBasicDisplay"
+ "displayId" : "nhr-111-ENCFF073WLL-LinearBasicDisplay"
}
],
- "name" : "zip-4",
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF785UNB/@@download/ENCFF785UNB.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF073WLL/@@download/ENCFF073WLL.bigBed"
},
"type" : "BigBedAdapter"
- },
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for zip-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF785UNB/ and for more information on this zip-4 experiment, see https://www.encodeproject.org/experiments/ENCSR992JPS/."
+ }
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for akir-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF463LGJ/ and for more information on this akir-1 experiment, see https://www.encodeproject.org/experiments/ENCSR154LSU/.",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-6 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF038FYU/ and for more information on this ceh-6 experiment, see https://www.encodeproject.org/experiments/ENCSR994CUJ/.",
+ "trackId" : "c_elegans_PRJNA13758_ceh-6-ENCFF038FYU",
+ "name" : "ceh-6",
+ "category" : [
+ "modERN",
+ "late embryonic"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF463LGJ/@@download/ENCFF463LGJ.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF038FYU/@@download/ENCFF038FYU.bigBed",
"locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ }
},
- "type" : "FeatureTrack",
- "name" : "akir-1",
"displays" : [
{
- "displayId" : "akir-1-ENCFF463LGJ-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "ceh-6-ENCFF038FYU-LinearBasicDisplay",
"renderer" : {
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "color1" : "blue",
+ "type" : "SvgFeatureRenderer"
}
}
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "young adult"
- ],
- "trackId" : "c_elegans_PRJNA13758_akir-1-ENCFF463LGJ"
+ ]
},
{
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF785UNB/@@download/ENCFF785UNB.bigBed"
+ }
+ },
"displays" : [
{
- "displayId" : "Y5F2A.4-ENCFF478AHO-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"color1" : "blue",
+ "height" : 6,
"type" : "SvgFeatureRenderer"
- }
+ },
+ "displayId" : "zip-4-ENCFF785UNB-LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for zip-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF785UNB/ and for more information on this zip-4 experiment, see https://www.encodeproject.org/experiments/ENCSR992JPS/.",
+ "name" : "zip-4",
+ "trackId" : "c_elegans_PRJNA13758_zip-4-ENCFF785UNB",
"category" : [
"modERN",
- "L4 larva"
+ "L1 larva"
],
- "trackId" : "c_elegans_PRJNA13758_Y5F2A.4-ENCFF478AHO",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for Y5F2A.4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF478AHO/ and for more information on this Y5F2A.4 experiment, see https://www.encodeproject.org/experiments/ENCSR374WWP/.",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF478AHO/@@download/ENCFF478AHO.bigBed",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
"type" : "FeatureTrack",
- "name" : "Y5F2A.4"
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ]
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for gei-17 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF473GZW/ and for more information on this gei-17 experiment, see https://www.encodeproject.org/experiments/ENCSR041LFH/.",
- "name" : "gei-17",
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF473GZW/@@download/ENCFF473GZW.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF463LGJ/@@download/ENCFF463LGJ.bigBed"
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "gei-17-ENCFF473GZW-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
+ "color1" : "blue",
"height" : 6
- }
+ },
+ "displayId" : "akir-1-ENCFF463LGJ-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_gei-17-ENCFF473GZW",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for akir-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF463LGJ/ and for more information on this akir-1 experiment, see https://www.encodeproject.org/experiments/ENCSR154LSU/.",
+ "name" : "akir-1",
+ "trackId" : "c_elegans_PRJNA13758_akir-1-ENCFF463LGJ",
"category" : [
"modERN",
"young adult"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
]
},
{
- "name" : "sup-37",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for Y5F2A.4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF478AHO/ and for more information on this Y5F2A.4 experiment, see https://www.encodeproject.org/experiments/ENCSR374WWP/.",
+ "name" : "Y5F2A.4",
+ "trackId" : "c_elegans_PRJNA13758_Y5F2A.4-ENCFF478AHO",
+ "category" : [
+ "modERN",
+ "L4 larva"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF093DLG/@@download/ENCFF093DLG.bigBed",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF478AHO/@@download/ENCFF478AHO.bigBed"
}
},
- "type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for sup-37 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF093DLG/ and for more information on this sup-37 experiment, see https://www.encodeproject.org/experiments/ENCSR115ZDZ/.",
- "trackId" : "c_elegans_PRJNA13758_sup-37-ENCFF093DLG",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "L1 larva"
- ],
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue",
- "height" : 6
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "sup-37-ENCFF093DLG-LinearBasicDisplay"
+ "displayId" : "Y5F2A.4-ENCFF478AHO-LinearBasicDisplay"
}
]
},
@@ -39336,65 +38665,82 @@
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue"
},
- "displayId" : "ets-4-ENCFF507MBR-LinearBasicDisplay"
+ "displayId" : "gei-17-ENCFF473GZW-LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_ets-4-ENCFF507MBR",
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF473GZW/@@download/ENCFF473GZW.bigBed",
+ "locationType" : "UriLocation"
+ }
+ },
"category" : [
"modERN",
"young adult"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ets-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF507MBR/ and for more information on this ets-4 experiment, see https://www.encodeproject.org/experiments/ENCSR919QDM/.",
- "name" : "ets-4",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for gei-17 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF473GZW/ and for more information on this gei-17 experiment, see https://www.encodeproject.org/experiments/ENCSR041LFH/.",
+ "name" : "gei-17",
+ "trackId" : "c_elegans_PRJNA13758_gei-17-ENCFF473GZW"
+ },
+ {
+ "category" : [
+ "modERN",
+ "L1 larva"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for sup-37 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF093DLG/ and for more information on this sup-37 experiment, see https://www.encodeproject.org/experiments/ENCSR115ZDZ/.",
+ "name" : "sup-37",
+ "trackId" : "c_elegans_PRJNA13758_sup-37-ENCFF093DLG",
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "blue",
+ "height" : 6
+ },
+ "displayId" : "sup-37-ENCFF093DLG-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF507MBR/@@download/ENCFF507MBR.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF093DLG/@@download/ENCFF093DLG.bigBed",
"locationType" : "UriLocation"
}
- },
- "type" : "FeatureTrack"
+ }
},
{
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"color1" : "blue",
+ "height" : 6,
"type" : "SvgFeatureRenderer"
},
- "displayId" : "ets-7-ENCFF991KTZ-LinearBasicDisplay"
+ "displayId" : "ets-4-ENCFF507MBR-LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "early embryonic"
- ],
- "trackId" : "c_elegans_PRJNA13758_ets-7-ENCFF991KTZ",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ets-7 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF991KTZ/ and for more information on this ets-7 experiment, see https://www.encodeproject.org/experiments/ENCSR475ZYS/.",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF991KTZ/@@download/ENCFF991KTZ.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF507MBR/@@download/ENCFF507MBR.bigBed"
}
},
- "type" : "FeatureTrack",
- "name" : "ets-7"
- },
- {
- "trackId" : "c_elegans_PRJNA13758_snpc-3.4-ENCFF035KKA",
"category" : [
"modERN",
"young adult"
@@ -39402,316 +38748,240 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "displays" : [
- {
- "renderer" : {
- "color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "snpc-3.4-ENCFF035KKA-LinearBasicDisplay"
- }
- ],
- "name" : "snpc-3.4",
+ "type" : "FeatureTrack",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ets-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF507MBR/ and for more information on this ets-4 experiment, see https://www.encodeproject.org/experiments/ENCSR919QDM/.",
+ "trackId" : "c_elegans_PRJNA13758_ets-4-ENCFF507MBR",
+ "name" : "ets-4"
+ },
+ {
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF035KKA/@@download/ENCFF035KKA.bigBed"
- }
+ "uri" : "https://www.encodeproject.org/files/ENCFF991KTZ/@@download/ENCFF991KTZ.bigBed"
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for snpc-3.4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF035KKA/ and for more information on this snpc-3.4 experiment, see https://www.encodeproject.org/experiments/ENCSR726OQC/."
- },
- {
"displays" : [
{
- "displayId" : "rpc-1-ENCFF928HPS-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "color1" : "blue",
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "ets-7-ENCFF991KTZ-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
+ "trackId" : "c_elegans_PRJNA13758_ets-7-ENCFF991KTZ",
+ "name" : "ets-7",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ets-7 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF991KTZ/ and for more information on this ets-7 experiment, see https://www.encodeproject.org/experiments/ENCSR475ZYS/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
- "young adult"
- ],
- "trackId" : "c_elegans_PRJNA13758_rpc-1-ENCFF928HPS",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for rpc-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF928HPS/ and for more information on this rpc-1 experiment, see https://www.encodeproject.org/experiments/ENCSR668OMI/.",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF928HPS/@@download/ENCFF928HPS.bigBed",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "rpc-1"
+ "early embryonic"
+ ]
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for Y116A8C.19 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF009BRG/ and for more information on this Y116A8C.19 experiment, see https://www.encodeproject.org/experiments/ENCSR334YYP/.",
- "name" : "Y116A8C.19",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF009BRG/@@download/ENCFF009BRG.bigBed",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "snpc-3.4-ENCFF035KKA-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"color1" : "blue",
- "height" : 6
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "Y116A8C.19-ENCFF009BRG-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_Y116A8C.19-ENCFF009BRG",
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF035KKA/@@download/ENCFF035KKA.bigBed",
+ "locationType" : "UriLocation"
+ }
+ },
"category" : [
"modERN",
- "L1 larva"
+ "young adult"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
+ ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for snpc-3.4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF035KKA/ and for more information on this snpc-3.4 experiment, see https://www.encodeproject.org/experiments/ENCSR726OQC/.",
+ "name" : "snpc-3.4",
+ "trackId" : "c_elegans_PRJNA13758_snpc-3.4-ENCFF035KKA"
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modERN",
- "L4 larva"
+ "young adult"
],
- "trackId" : "c_elegans_PRJNA13758_zfp-2-ENCFF315LVT",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for rpc-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF928HPS/ and for more information on this rpc-1 experiment, see https://www.encodeproject.org/experiments/ENCSR668OMI/.",
+ "name" : "rpc-1",
+ "trackId" : "c_elegans_PRJNA13758_rpc-1-ENCFF928HPS",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"color1" : "blue",
"height" : 6
},
- "type" : "LinearBasicDisplay",
- "displayId" : "zfp-2-ENCFF315LVT-LinearBasicDisplay"
+ "displayId" : "rpc-1-ENCFF928HPS-LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF315LVT/@@download/ENCFF315LVT.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF928HPS/@@download/ENCFF928HPS.bigBed",
"locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "zfp-2",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for zfp-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF315LVT/ and for more information on this zfp-2 experiment, see https://www.encodeproject.org/experiments/ENCSR603SRL/."
+ }
+ }
},
{
- "trackId" : "c_elegans_PRJNA13758_unc-86-ENCFF772OWV",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
"L1 larva"
],
+ "trackId" : "c_elegans_PRJNA13758_Y116A8C.19-ENCFF009BRG",
+ "name" : "Y116A8C.19",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for Y116A8C.19 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF009BRG/ and for more information on this Y116A8C.19 experiment, see https://www.encodeproject.org/experiments/ENCSR334YYP/.",
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue"
},
- "displayId" : "unc-86-ENCFF772OWV-LinearBasicDisplay"
+ "displayId" : "Y116A8C.19-ENCFF009BRG-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "name" : "unc-86",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF772OWV/@@download/ENCFF772OWV.bigBed"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for unc-86 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF772OWV/ and for more information on this unc-86 experiment, see https://www.encodeproject.org/experiments/ENCSR807UTG/."
+ "uri" : "https://www.encodeproject.org/files/ENCFF009BRG/@@download/ENCFF009BRG.bigBed"
+ }
+ }
},
{
- "displays" : [
- {
- "displayId" : "hif-1-ENCFF555FAQ-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "height" : 6,
- "color1" : "blue",
- "type" : "SvgFeatureRenderer"
- }
- }
- ],
+ "trackId" : "c_elegans_PRJNA13758_zfp-2-ENCFF315LVT",
+ "name" : "zfp-2",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for zfp-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF315LVT/ and for more information on this zfp-2 experiment, see https://www.encodeproject.org/experiments/ENCSR603SRL/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
"L4 larva"
],
- "trackId" : "c_elegans_PRJNA13758_hif-1-ENCFF555FAQ",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hif-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF555FAQ/ and for more information on this hif-1 experiment, see https://www.encodeproject.org/experiments/ENCSR517OZM/.",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF555FAQ/@@download/ENCFF555FAQ.bigBed"
- }
+ "uri" : "https://www.encodeproject.org/files/ENCFF315LVT/@@download/ENCFF315LVT.bigBed"
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "name" : "hif-1"
- },
- {
"displays" : [
{
- "displayId" : "hlh-4-ENCFF868RBU-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "color1" : "blue",
- "height" : 6
- }
- }
- ],
- "trackId" : "c_elegans_PRJNA13758_hlh-4-ENCFF868RBU",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "L1 larva"
- ],
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hlh-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF868RBU/ and for more information on this hlh-4 experiment, see https://www.encodeproject.org/experiments/ENCSR498FBJ/.",
- "name" : "hlh-4",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF868RBU/@@download/ENCFF868RBU.bigBed",
- "locationType" : "UriLocation"
+ "height" : 6,
+ "color1" : "blue"
+ },
+ "displayId" : "zfp-2-ENCFF315LVT-LinearBasicDisplay"
}
- }
+ ]
},
{
- "trackId" : "c_elegans_PRJNA13758_hlh-8-ENCFF872QZC",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "late embryonic"
- ],
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "hlh-8-ENCFF872QZC-LinearBasicDisplay"
+ "displayId" : "unc-86-ENCFF772OWV-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "name" : "hlh-8",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF872QZC/@@download/ENCFF872QZC.bigBed"
- }
- },
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hlh-8 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF872QZC/ and for more information on this hlh-8 experiment, see https://www.encodeproject.org/experiments/ENCSR748QMA/."
- },
- {
- "name" : "F10B5.3",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF693NLH/@@download/ENCFF693NLH.bigBed",
- "locationType" : "UriLocation"
- }
+ "uri" : "https://www.encodeproject.org/files/ENCFF772OWV/@@download/ENCFF772OWV.bigBed"
+ },
+ "type" : "BigBedAdapter"
},
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F10B5.3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF693NLH/ and for more information on this F10B5.3 experiment, see https://www.encodeproject.org/experiments/ENCSR154XWT/.",
- "trackId" : "c_elegans_PRJNA13758_F10B5.3-ENCFF693NLH",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
- "L4 larva"
+ "L1 larva"
],
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "blue",
- "height" : 6
- },
- "displayId" : "F10B5.3-ENCFF693NLH-LinearBasicDisplay"
- }
- ]
+ "trackId" : "c_elegans_PRJNA13758_unc-86-ENCFF772OWV",
+ "name" : "unc-86",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for unc-86 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF772OWV/ and for more information on this unc-86 experiment, see https://www.encodeproject.org/experiments/ENCSR807UTG/."
},
{
"displays" : [
{
- "displayId" : "F22D6.2-ENCFF903FEW-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "color1" : "blue",
+ "height" : 6
},
+ "displayId" : "hif-1-ENCFF555FAQ-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF555FAQ/@@download/ENCFF555FAQ.bigBed"
+ },
+ "type" : "BigBedAdapter"
+ },
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
- "young adult"
+ "L4 larva"
],
- "trackId" : "c_elegans_PRJNA13758_F22D6.2-ENCFF903FEW",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F22D6.2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF903FEW/ and for more information on this F22D6.2 experiment, see https://www.encodeproject.org/experiments/ENCSR166DXK/.",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF903FEW/@@download/ENCFF903FEW.bigBed",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "F22D6.2"
+ "trackId" : "c_elegans_PRJNA13758_hif-1-ENCFF555FAQ",
+ "name" : "hif-1",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hif-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF555FAQ/ and for more information on this hif-1 experiment, see https://www.encodeproject.org/experiments/ENCSR517OZM/."
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modERN",
- "L4 larva"
+ "L1 larva"
],
- "trackId" : "c_elegans_PRJNA13758_nhr-48-ENCFF066GNC",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hlh-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF868RBU/ and for more information on this hlh-4 experiment, see https://www.encodeproject.org/experiments/ENCSR498FBJ/.",
+ "name" : "hlh-4",
+ "trackId" : "c_elegans_PRJNA13758_hlh-4-ENCFF868RBU",
"displays" : [
{
"renderer" : {
@@ -39719,127 +38989,96 @@
"color1" : "blue",
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "nhr-48-ENCFF066GNC-LinearBasicDisplay"
+ "displayId" : "hlh-4-ENCFF868RBU-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF066GNC/@@download/ENCFF066GNC.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF868RBU/@@download/ENCFF868RBU.bigBed",
+ "locationType" : "UriLocation"
}
- },
- "name" : "nhr-48",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-48 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF066GNC/ and for more information on this nhr-48 experiment, see https://www.encodeproject.org/experiments/ENCSR176TET/."
+ }
},
{
- "trackId" : "c_elegans_PRJNA13758_snpc-1.1-ENCFF381NRD",
+ "name" : "hlh-8",
+ "trackId" : "c_elegans_PRJNA13758_hlh-8-ENCFF872QZC",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hlh-8 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF872QZC/ and for more information on this hlh-8 experiment, see https://www.encodeproject.org/experiments/ENCSR748QMA/.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"modERN",
- "young adult"
- ],
- "displays" : [
- {
- "displayId" : "snpc-1.1-ENCFF381NRD-LinearBasicDisplay",
- "renderer" : {
- "height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
- },
- "type" : "LinearBasicDisplay"
- }
+ "late embryonic"
],
- "name" : "snpc-1.1",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF381NRD/@@download/ENCFF381NRD.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF872QZC/@@download/ENCFF872QZC.bigBed",
"locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for snpc-1.1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF381NRD/ and for more information on this snpc-1.1 experiment, see https://www.encodeproject.org/experiments/ENCSR032CWX/."
- },
- {
- "category" : [
- "modERN",
- "late embryonic"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_sdc-2-ENCFF005ETH",
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
- "height" : 6
+ "height" : 6,
+ "color1" : "blue"
},
- "displayId" : "sdc-2-ENCFF005ETH-LinearBasicDisplay"
+ "displayId" : "hlh-8-ENCFF872QZC-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ],
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF005ETH/@@download/ENCFF005ETH.bigBed",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "sdc-2",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for sdc-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF005ETH/ and for more information on this sdc-2 experiment, see https://www.encodeproject.org/experiments/ENCSR438PSB/."
+ ]
},
{
- "name" : "ref-2",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF320ZRR/@@download/ENCFF320ZRR.bigBed",
- "locationType" : "UriLocation"
- }
- },
+ "name" : "F10B5.3",
+ "trackId" : "c_elegans_PRJNA13758_F10B5.3-ENCFF693NLH",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F10B5.3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF693NLH/ and for more information on this F10B5.3 experiment, see https://www.encodeproject.org/experiments/ENCSR154XWT/.",
"type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ref-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF320ZRR/ and for more information on this ref-2 experiment, see https://www.encodeproject.org/experiments/ENCSR320EEP/.",
- "trackId" : "c_elegans_PRJNA13758_ref-2-ENCFF320ZRR",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"modERN",
- "late embryonic"
+ "L4 larva"
],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF693NLH/@@download/ENCFF693NLH.bigBed",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "displayId" : "ref-2-ENCFF320ZRR-LinearBasicDisplay",
"renderer" : {
"height" : 6,
"color1" : "blue",
"type" : "SvgFeatureRenderer"
},
+ "displayId" : "F10B5.3-ENCFF693NLH-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
]
},
{
- "trackId" : "c_elegans_PRJNA13758_nhr-179-ENCFF697CAP",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
"young adult"
],
+ "trackId" : "c_elegans_PRJNA13758_F22D6.2-ENCFF903FEW",
+ "name" : "F22D6.2",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F22D6.2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF903FEW/ and for more information on this F22D6.2 experiment, see https://www.encodeproject.org/experiments/ENCSR166DXK/.",
"displays" : [
{
- "displayId" : "nhr-179-ENCFF697CAP-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "F22D6.2-ENCFF903FEW-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"color1" : "blue",
@@ -39847,432 +39086,401 @@
}
}
],
- "name" : "nhr-179",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF697CAP/@@download/ENCFF697CAP.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF903FEW/@@download/ENCFF903FEW.bigBed",
"locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-179 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF697CAP/ and for more information on this nhr-179 experiment, see https://www.encodeproject.org/experiments/ENCSR710GXZ/."
+ }
+ }
},
{
+ "trackId" : "c_elegans_PRJNA13758_nhr-48-ENCFF066GNC",
+ "name" : "nhr-48",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-48 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF066GNC/ and for more information on this nhr-48 experiment, see https://www.encodeproject.org/experiments/ENCSR176TET/.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
+ "category" : [
+ "modERN",
+ "L4 larva"
+ ],
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF058IGA/@@download/ENCFF058IGA.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF066GNC/@@download/ENCFF066GNC.bigBed"
},
"type" : "BigBedAdapter"
},
- "name" : "syd-9",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for syd-9 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF058IGA/ and for more information on this syd-9 experiment, see https://www.encodeproject.org/experiments/ENCSR447EUI/.",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "late embryonic"
- ],
- "trackId" : "c_elegans_PRJNA13758_syd-9-ENCFF058IGA",
"displays" : [
{
+ "displayId" : "nhr-48-ENCFF066GNC-LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
+ "color1" : "blue",
"height" : 6
},
- "type" : "LinearBasicDisplay",
- "displayId" : "syd-9-ENCFF058IGA-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
]
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hrde-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF986COB/ and for more information on this hrde-1 experiment, see https://www.encodeproject.org/experiments/ENCSR548OPZ/.",
- "name" : "hrde-1",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF986COB/@@download/ENCFF986COB.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF381NRD/@@download/ENCFF381NRD.bigBed",
"locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
"displays" : [
{
+ "displayId" : "snpc-1.1-ENCFF381NRD-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue",
- "height" : 6
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "hrde-1-ENCFF986COB-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_hrde-1-ENCFF986COB",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for snpc-1.1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF381NRD/ and for more information on this snpc-1.1 experiment, see https://www.encodeproject.org/experiments/ENCSR032CWX/.",
+ "trackId" : "c_elegans_PRJNA13758_snpc-1.1-ENCFF381NRD",
+ "name" : "snpc-1.1",
"category" : [
"modERN",
"young adult"
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
+ ],
+ "type" : "FeatureTrack"
},
{
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modERN",
+ "late embryonic"
+ ],
+ "name" : "sdc-2",
+ "trackId" : "c_elegans_PRJNA13758_sdc-2-ENCFF005ETH",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for sdc-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF005ETH/ and for more information on this sdc-2 experiment, see https://www.encodeproject.org/experiments/ENCSR438PSB/.",
"displays" : [
{
- "displayId" : "aly-1-ENCFF092GJQ-LinearBasicDisplay",
+ "displayId" : "sdc-2-ENCFF005ETH-LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
- "height" : 6
+ "height" : 6,
+ "color1" : "blue"
},
"type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_aly-1-ENCFF092GJQ",
- "category" : [
- "modERN",
- "early embryonic"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for aly-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF092GJQ/ and for more information on this aly-1 experiment, see https://www.encodeproject.org/experiments/ENCSR836LVI/.",
- "name" : "aly-1",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF092GJQ/@@download/ENCFF092GJQ.bigBed"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack"
+ "uri" : "https://www.encodeproject.org/files/ENCFF005ETH/@@download/ENCFF005ETH.bigBed",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
- "category" : [
- "modERN",
- "late embryonic"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_elt-4-ENCFF118UUK",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "ref-2-ENCFF320ZRR-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue"
- },
- "displayId" : "elt-4-ENCFF118UUK-LinearBasicDisplay"
+ }
}
],
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF118UUK/@@download/ENCFF118UUK.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF320ZRR/@@download/ENCFF320ZRR.bigBed",
"locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
- "name" : "elt-4",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for elt-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF118UUK/ and for more information on this elt-4 experiment, see https://www.encodeproject.org/experiments/ENCSR714ZDK/."
+ "category" : [
+ "modERN",
+ "late embryonic"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ref-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF320ZRR/ and for more information on this ref-2 experiment, see https://www.encodeproject.org/experiments/ENCSR320EEP/.",
+ "name" : "ref-2",
+ "trackId" : "c_elegans_PRJNA13758_ref-2-ENCFF320ZRR"
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for fax-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF333ESJ/ and for more information on this fax-1 experiment, see https://www.encodeproject.org/experiments/ENCSR517JNQ/.",
- "name" : "fax-1",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF333ESJ/@@download/ENCFF333ESJ.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF697CAP/@@download/ENCFF697CAP.bigBed",
"locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ }
},
"displays" : [
{
- "displayId" : "fax-1-ENCFF333ESJ-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
+ "displayId" : "nhr-179-ENCFF697CAP-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"type" : "SvgFeatureRenderer",
- "color1" : "blue"
- },
- "type" : "LinearBasicDisplay"
+ "color1" : "blue",
+ "height" : 6
+ }
}
],
- "trackId" : "c_elegans_PRJNA13758_fax-1-ENCFF333ESJ",
+ "name" : "nhr-179",
+ "trackId" : "c_elegans_PRJNA13758_nhr-179-ENCFF697CAP",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-179 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF697CAP/ and for more information on this nhr-179 experiment, see https://www.encodeproject.org/experiments/ENCSR710GXZ/.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"modERN",
- "late embryonic"
+ "young adult"
]
},
{
- "trackId" : "c_elegans_PRJNA13758_xnd-1-ENCFF214IKK",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for syd-9 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF058IGA/ and for more information on this syd-9 experiment, see https://www.encodeproject.org/experiments/ENCSR447EUI/.",
+ "trackId" : "c_elegans_PRJNA13758_syd-9-ENCFF058IGA",
+ "name" : "syd-9",
"category" : [
"modERN",
- "young adult"
+ "late embryonic"
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF058IGA/@@download/ENCFF058IGA.bigBed",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "displayId" : "xnd-1-ENCFF214IKK-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "syd-9-ENCFF058IGA-LinearBasicDisplay",
"renderer" : {
+ "height" : 6,
"color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
+ "type" : "SvgFeatureRenderer"
}
}
- ],
- "name" : "xnd-1",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF214IKK/@@download/ENCFF214IKK.bigBed",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for xnd-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF214IKK/ and for more information on this xnd-1 experiment, see https://www.encodeproject.org/experiments/ENCSR327NRA/."
+ ]
},
{
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF829GJL/@@download/ENCFF829GJL.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF986COB/@@download/ENCFF986COB.bigBed",
+ "locationType" : "UriLocation"
}
},
- "name" : "B0035.1",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for B0035.1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF829GJL/ and for more information on this B0035.1 experiment, see https://www.encodeproject.org/experiments/ENCSR450GPA/.",
- "category" : [
- "modERN",
- "young adult"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_B0035.1-ENCFF829GJL",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
"height" : 6,
"color1" : "blue",
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "B0035.1-ENCFF829GJL-LinearBasicDisplay"
+ "displayId" : "hrde-1-ENCFF986COB-LinearBasicDisplay"
}
+ ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hrde-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF986COB/ and for more information on this hrde-1 experiment, see https://www.encodeproject.org/experiments/ENCSR548OPZ/.",
+ "name" : "hrde-1",
+ "trackId" : "c_elegans_PRJNA13758_hrde-1-ENCFF986COB",
+ "category" : [
+ "modERN",
+ "young adult"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
]
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modERN",
- "late embryonic"
+ "early embryonic"
],
- "trackId" : "c_elegans_PRJNA13758_nhr-232-ENCFF270KYW",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for aly-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF092GJQ/ and for more information on this aly-1 experiment, see https://www.encodeproject.org/experiments/ENCSR836LVI/.",
+ "name" : "aly-1",
+ "trackId" : "c_elegans_PRJNA13758_aly-1-ENCFF092GJQ",
"displays" : [
{
- "displayId" : "nhr-232-ENCFF270KYW-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "aly-1-ENCFF092GJQ-LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF270KYW/@@download/ENCFF270KYW.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF092GJQ/@@download/ENCFF092GJQ.bigBed",
"locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
- },
- "name" : "nhr-232",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-232 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF270KYW/ and for more information on this nhr-232 experiment, see https://www.encodeproject.org/experiments/ENCSR182IGG/."
+ }
},
{
- "category" : [
- "modERN",
- "late embryonic"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_ceh-2-ENCFF736OZW",
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF118UUK/@@download/ENCFF118UUK.bigBed"
+ }
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
+ "color1" : "blue",
"height" : 6
},
- "type" : "LinearBasicDisplay",
- "displayId" : "ceh-2-ENCFF736OZW-LinearBasicDisplay"
+ "displayId" : "elt-4-ENCFF118UUK-LinearBasicDisplay"
}
],
+ "trackId" : "c_elegans_PRJNA13758_elt-4-ENCFF118UUK",
+ "name" : "elt-4",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for elt-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF118UUK/ and for more information on this elt-4 experiment, see https://www.encodeproject.org/experiments/ENCSR714ZDK/.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "modERN",
+ "late embryonic"
+ ]
+ },
+ {
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF736OZW/@@download/ENCFF736OZW.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF333ESJ/@@download/ENCFF333ESJ.bigBed",
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "name" : "ceh-2",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF736OZW/ and for more information on this ceh-2 experiment, see https://www.encodeproject.org/experiments/ENCSR534TFA/."
- },
- {
"displays" : [
{
- "displayId" : "hlh-6-ENCFF266AXA-LinearBasicDisplay",
+ "displayId" : "fax-1-ENCFF333ESJ-LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
+ "color1" : "blue",
"height" : 6
},
"type" : "LinearBasicDisplay"
}
],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for fax-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF333ESJ/ and for more information on this fax-1 experiment, see https://www.encodeproject.org/experiments/ENCSR517JNQ/.",
+ "name" : "fax-1",
+ "trackId" : "c_elegans_PRJNA13758_fax-1-ENCFF333ESJ",
"category" : [
"modERN",
"late embryonic"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_hlh-6-ENCFF266AXA",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hlh-6 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF266AXA/ and for more information on this hlh-6 experiment, see https://www.encodeproject.org/experiments/ENCSR632XME/.",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF266AXA/@@download/ENCFF266AXA.bigBed"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "hlh-6"
+ ]
},
{
- "displays" : [
- {
- "renderer" : {
- "color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "mes-2-ENCFF085YJC-LinearBasicDisplay"
- }
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modERN",
- "L4 larva"
+ "young adult"
],
- "trackId" : "c_elegans_PRJNA13758_mes-2-ENCFF085YJC",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for mes-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF085YJC/ and for more information on this mes-2 experiment, see https://www.encodeproject.org/experiments/ENCSR977VOU/.",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF085YJC/@@download/ENCFF085YJC.bigBed"
- }
- },
"type" : "FeatureTrack",
- "name" : "mes-2"
- },
- {
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for xnd-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF214IKK/ and for more information on this xnd-1 experiment, see https://www.encodeproject.org/experiments/ENCSR327NRA/.",
+ "name" : "xnd-1",
+ "trackId" : "c_elegans_PRJNA13758_xnd-1-ENCFF214IKK",
"displays" : [
{
"renderer" : {
- "height" : 6,
"color1" : "blue",
+ "height" : 6,
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "unc-42-ENCFF733JRA-LinearBasicDisplay"
+ "displayId" : "xnd-1-ENCFF214IKK-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_unc-42-ENCFF733JRA",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "late embryonic"
- ],
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for unc-42 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF733JRA/ and for more information on this unc-42 experiment, see https://www.encodeproject.org/experiments/ENCSR124XUB/.",
- "name" : "unc-42",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF733JRA/@@download/ENCFF733JRA.bigBed",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF214IKK/@@download/ENCFF214IKK.bigBed"
},
"type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack"
+ }
},
{
+ "trackId" : "c_elegans_PRJNA13758_B0035.1-ENCFF829GJL",
+ "name" : "B0035.1",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for B0035.1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF829GJL/ and for more information on this B0035.1 experiment, see https://www.encodeproject.org/experiments/ENCSR450GPA/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
- "L4 larva"
+ "young adult"
],
- "trackId" : "c_elegans_PRJNA13758_F49E8.2-ENCFF059PKB",
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF829GJL/@@download/ENCFF829GJL.bigBed"
+ }
+ },
"displays" : [
{
- "displayId" : "F49E8.2-ENCFF059PKB-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "B0035.1-ENCFF829GJL-LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
+ "color1" : "blue",
"height" : 6
}
}
- ],
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF059PKB/@@download/ENCFF059PKB.bigBed"
- }
- },
- "type" : "FeatureTrack",
- "name" : "F49E8.2",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F49E8.2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF059PKB/ and for more information on this F49E8.2 experiment, see https://www.encodeproject.org/experiments/ENCSR013JXG/."
+ ]
},
{
- "trackId" : "c_elegans_PRJNA13758_die-1-ENCFF167BVE",
"category" : [
"modERN",
- "young adult"
+ "late embryonic"
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-232 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF270KYW/ and for more information on this nhr-232 experiment, see https://www.encodeproject.org/experiments/ENCSR182IGG/.",
+ "trackId" : "c_elegans_PRJNA13758_nhr-232-ENCFF270KYW",
+ "name" : "nhr-232",
"displays" : [
{
- "displayId" : "die-1-ENCFF167BVE-LinearBasicDisplay",
+ "displayId" : "nhr-232-ENCFF270KYW-LinearBasicDisplay",
"renderer" : {
"height" : 6,
"color1" : "blue",
@@ -40281,602 +39489,537 @@
"type" : "LinearBasicDisplay"
}
],
- "name" : "die-1",
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF167BVE/@@download/ENCFF167BVE.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF270KYW/@@download/ENCFF270KYW.bigBed",
+ "locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
- },
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for die-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF167BVE/ and for more information on this die-1 experiment, see https://www.encodeproject.org/experiments/ENCSR962KSG/."
+ }
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for sma-9 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF209LPE/ and for more information on this sma-9 experiment, see https://www.encodeproject.org/experiments/ENCSR639CLM/.",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF209LPE/@@download/ENCFF209LPE.bigBed",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "sma-9",
"displays" : [
{
- "displayId" : "sma-9-ENCFF209LPE-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"color1" : "blue",
+ "height" : 6,
"type" : "SvgFeatureRenderer"
- }
+ },
+ "displayId" : "ceh-2-ENCFF736OZW-LinearBasicDisplay"
}
],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF736OZW/@@download/ENCFF736OZW.bigBed",
+ "locationType" : "UriLocation"
+ }
+ },
"category" : [
"modERN",
- "L2 larva"
+ "late embryonic"
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_sma-9-ENCFF209LPE"
+ "type" : "FeatureTrack",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF736OZW/ and for more information on this ceh-2 experiment, see https://www.encodeproject.org/experiments/ENCSR534TFA/.",
+ "trackId" : "c_elegans_PRJNA13758_ceh-2-ENCFF736OZW",
+ "name" : "ceh-2"
},
{
- "trackId" : "c_elegans_PRJNA13758_efl-1-ENCFF127YXL",
- "category" : [
- "modERN",
- "young adult"
- ],
+ "name" : "hlh-6",
+ "trackId" : "c_elegans_PRJNA13758_hlh-6-ENCFF266AXA",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hlh-6 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF266AXA/ and for more information on this hlh-6 experiment, see https://www.encodeproject.org/experiments/ENCSR632XME/.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "displays" : [
- {
- "displayId" : "efl-1-ENCFF127YXL-LinearBasicDisplay",
- "renderer" : {
- "height" : 6,
- "color1" : "blue",
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay"
- }
+ "category" : [
+ "modERN",
+ "late embryonic"
],
- "name" : "efl-1",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF127YXL/@@download/ENCFF127YXL.bigBed"
- },
- "type" : "BigBedAdapter"
+ "uri" : "https://www.encodeproject.org/files/ENCFF266AXA/@@download/ENCFF266AXA.bigBed"
+ }
},
- "type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for efl-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF127YXL/ and for more information on this efl-1 experiment, see https://www.encodeproject.org/experiments/ENCSR130CZH/."
- },
- {
"displays" : [
{
- "displayId" : "rec-8-ENCFF523SUS-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"color1" : "blue",
- "height" : 6
- }
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "hlh-6-ENCFF266AXA-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
+ ]
+ },
+ {
+ "name" : "mes-2",
+ "trackId" : "c_elegans_PRJNA13758_mes-2-ENCFF085YJC",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for mes-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF085YJC/ and for more information on this mes-2 experiment, see https://www.encodeproject.org/experiments/ENCSR977VOU/.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
"category" : [
"modERN",
- "young adult"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
+ "L4 larva"
],
- "trackId" : "c_elegans_PRJNA13758_rec-8-ENCFF523SUS",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for rec-8 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF523SUS/ and for more information on this rec-8 experiment, see https://www.encodeproject.org/experiments/ENCSR689UBU/.",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF523SUS/@@download/ENCFF523SUS.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF085YJC/@@download/ENCFF085YJC.bigBed",
+ "locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "name" : "rec-8"
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "height" : 6,
+ "color1" : "blue"
+ },
+ "displayId" : "mes-2-ENCFF085YJC-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-31 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF473DVC/ and for more information on this ceh-31 experiment, see https://www.encodeproject.org/experiments/ENCSR420ATF/.",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF473DVC/@@download/ENCFF473DVC.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF733JRA/@@download/ENCFF733JRA.bigBed"
}
},
- "type" : "FeatureTrack",
- "name" : "ceh-31",
"displays" : [
{
- "displayId" : "ceh-31-ENCFF473DVC-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
- }
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "unc-42-ENCFF733JRA-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "category" : [
- "modERN",
- "late embryonic"
- ],
+ "trackId" : "c_elegans_PRJNA13758_unc-42-ENCFF733JRA",
+ "name" : "unc-42",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for unc-42 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF733JRA/ and for more information on this unc-42 experiment, see https://www.encodeproject.org/experiments/ENCSR124XUB/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_ceh-31-ENCFF473DVC"
+ "type" : "FeatureTrack",
+ "category" : [
+ "modERN",
+ "late embryonic"
+ ]
},
{
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF059PKB/@@download/ENCFF059PKB.bigBed",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
"renderer" : {
"color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "nhr-43-ENCFF792BGX-LinearBasicDisplay"
+ "displayId" : "F49E8.2-ENCFF059PKB-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_nhr-43-ENCFF792BGX",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F49E8.2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF059PKB/ and for more information on this F49E8.2 experiment, see https://www.encodeproject.org/experiments/ENCSR013JXG/.",
+ "name" : "F49E8.2",
+ "trackId" : "c_elegans_PRJNA13758_F49E8.2-ENCFF059PKB",
"category" : [
"modERN",
- "L3 larva"
+ "L4 larva"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-43 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF792BGX/ and for more information on this nhr-43 experiment, see https://www.encodeproject.org/experiments/ENCSR394KNZ/.",
- "name" : "nhr-43",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF792BGX/@@download/ENCFF792BGX.bigBed"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack"
+ ]
},
{
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for die-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF167BVE/ and for more information on this die-1 experiment, see https://www.encodeproject.org/experiments/ENCSR962KSG/.",
+ "name" : "die-1",
+ "trackId" : "c_elegans_PRJNA13758_die-1-ENCFF167BVE",
"category" : [
"modERN",
- "L1 larva"
+ "young adult"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_dsc-1-ENCFF639WNE",
- "displays" : [
- {
- "displayId" : "dsc-1-ENCFF639WNE-LinearBasicDisplay",
- "renderer" : {
- "height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
- },
- "type" : "LinearBasicDisplay"
- }
- ],
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF639WNE/@@download/ENCFF639WNE.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF167BVE/@@download/ENCFF167BVE.bigBed",
"locationType" : "UriLocation"
}
},
- "name" : "dsc-1",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for dsc-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF639WNE/ and for more information on this dsc-1 experiment, see https://www.encodeproject.org/experiments/ENCSR489SGT/."
- },
- {
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF823YFY/@@download/ENCFF823YFY.bigBed",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "rbr-2",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for rbr-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF823YFY/ and for more information on this rbr-2 experiment, see https://www.encodeproject.org/experiments/ENCSR274WQG/.",
- "category" : [
- "modERN",
- "L4 larva"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_rbr-2-ENCFF823YFY",
"displays" : [
{
- "displayId" : "rbr-2-ENCFF823YFY-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
+ "displayId" : "die-1-ENCFF167BVE-LinearBasicDisplay",
"renderer" : {
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
- },
- "type" : "LinearBasicDisplay"
+ "color1" : "blue",
+ "type" : "SvgFeatureRenderer"
+ }
}
]
},
{
- "name" : "snpc-4",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF867CXG/@@download/ENCFF867CXG.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF209LPE/@@download/ENCFF209LPE.bigBed",
"locationType" : "UriLocation"
}
},
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for snpc-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF867CXG/ and for more information on this snpc-4 experiment, see https://www.encodeproject.org/experiments/ENCSR032FII/.",
- "trackId" : "c_elegans_PRJNA13758_snpc-4-ENCFF867CXG",
- "category" : [
- "modERN",
- "young adult"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
- "displayId" : "snpc-4-ENCFF867CXG-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "color1" : "blue",
- "height" : 6
+ "height" : 6,
+ "color1" : "blue"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "sma-9-ENCFF209LPE-LinearBasicDisplay"
}
- ]
+ ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for sma-9 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF209LPE/ and for more information on this sma-9 experiment, see https://www.encodeproject.org/experiments/ENCSR639CLM/.",
+ "trackId" : "c_elegans_PRJNA13758_sma-9-ENCFF209LPE",
+ "name" : "sma-9",
+ "category" : [
+ "modERN",
+ "L2 larva"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack"
},
{
+ "name" : "efl-1",
+ "trackId" : "c_elegans_PRJNA13758_efl-1-ENCFF127YXL",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for efl-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF127YXL/ and for more information on this efl-1 experiment, see https://www.encodeproject.org/experiments/ENCSR130CZH/.",
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF806XPK/@@download/ENCFF806XPK.bigBed"
- }
- },
- "name" : "elt-1",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for elt-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF806XPK/ and for more information on this elt-1 experiment, see https://www.encodeproject.org/experiments/ENCSR715MIV/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"modERN",
- "mixed stage (embryonic)"
+ "young adult"
],
- "trackId" : "c_elegans_PRJNA13758_elt-1-ENCFF806XPK",
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF127YXL/@@download/ENCFF127YXL.bigBed"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
- "displayId" : "elt-1-ENCFF806XPK-LinearBasicDisplay",
+ "displayId" : "efl-1-ENCFF127YXL-LinearBasicDisplay",
"renderer" : {
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "color1" : "blue",
+ "type" : "SvgFeatureRenderer"
},
"type" : "LinearBasicDisplay"
}
]
},
{
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF178NLM/@@download/ENCFF178NLM.bigBed"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "lir-3",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for lir-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF178NLM/ and for more information on this lir-3 experiment, see https://www.encodeproject.org/experiments/ENCSR258OFT/.",
+ "trackId" : "c_elegans_PRJNA13758_rec-8-ENCFF523SUS",
+ "name" : "rec-8",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for rec-8 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF523SUS/ and for more information on this rec-8 experiment, see https://www.encodeproject.org/experiments/ENCSR689UBU/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
- "L1 larva"
+ "young adult"
],
- "trackId" : "c_elegans_PRJNA13758_lir-3-ENCFF178NLM",
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF523SUS/@@download/ENCFF523SUS.bigBed"
+ }
+ },
"displays" : [
{
- "displayId" : "lir-3-ENCFF178NLM-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"color1" : "blue",
"height" : 6
- }
+ },
+ "displayId" : "rec-8-ENCFF523SUS-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
]
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for let-607 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF588EOS/ and for more information on this let-607 experiment, see https://www.encodeproject.org/experiments/ENCSR701SBA/.",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF588EOS/@@download/ENCFF588EOS.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF473DVC/@@download/ENCFF473DVC.bigBed",
"locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "name" : "let-607",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "ceh-31-ENCFF473DVC-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue",
- "height" : 6
- },
- "displayId" : "let-607-ENCFF588EOS-LinearBasicDisplay"
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-31 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF473DVC/ and for more information on this ceh-31 experiment, see https://www.encodeproject.org/experiments/ENCSR420ATF/.",
+ "name" : "ceh-31",
+ "trackId" : "c_elegans_PRJNA13758_ceh-31-ENCFF473DVC",
"category" : [
"modERN",
- "young adult"
+ "late embryonic"
],
- "trackId" : "c_elegans_PRJNA13758_let-607-ENCFF588EOS"
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ]
},
{
- "displays" : [
- {
- "displayId" : "rnt-1-ENCFF354YVJ-LinearBasicDisplay",
- "renderer" : {
- "height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
- },
- "type" : "LinearBasicDisplay"
- }
- ],
- "trackId" : "c_elegans_PRJNA13758_rnt-1-ENCFF354YVJ",
"category" : [
"modERN",
- "late embryonic"
+ "L3 larva"
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for rnt-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF354YVJ/ and for more information on this rnt-1 experiment, see https://www.encodeproject.org/experiments/ENCSR427JJZ/.",
- "name" : "rnt-1",
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF354YVJ/@@download/ENCFF354YVJ.bigBed"
- }
- }
- },
- {
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-43 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF792BGX/ and for more information on this nhr-43 experiment, see https://www.encodeproject.org/experiments/ENCSR394KNZ/.",
+ "trackId" : "c_elegans_PRJNA13758_nhr-43-ENCFF792BGX",
+ "name" : "nhr-43",
"displays" : [
{
- "displayId" : "nhr-102-ENCFF790EIG-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
+ "color1" : "blue",
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "nhr-43-ENCFF792BGX-LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_nhr-102-ENCFF790EIG",
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF792BGX/@@download/ENCFF792BGX.bigBed",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ }
+ },
+ {
+ "trackId" : "c_elegans_PRJNA13758_dsc-1-ENCFF639WNE",
+ "name" : "dsc-1",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for dsc-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF639WNE/ and for more information on this dsc-1 experiment, see https://www.encodeproject.org/experiments/ENCSR489SGT/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
- "L4 larva"
+ "L1 larva"
],
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-102 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF790EIG/ and for more information on this nhr-102 experiment, see https://www.encodeproject.org/experiments/ENCSR735XWN/.",
- "name" : "nhr-102",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF790EIG/@@download/ENCFF790EIG.bigBed"
- },
- "type" : "BigBedAdapter"
+ "uri" : "https://www.encodeproject.org/files/ENCFF639WNE/@@download/ENCFF639WNE.bigBed"
+ }
},
- "type" : "FeatureTrack"
- },
- {
- "category" : [
- "modERN",
- "late embryonic"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_tbx-7-ENCFF137ZAX",
"displays" : [
{
- "displayId" : "tbx-7-ENCFF137ZAX-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"color1" : "blue",
"height" : 6
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "dsc-1-ENCFF639WNE-LinearBasicDisplay"
}
- ],
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF137ZAX/@@download/ENCFF137ZAX.bigBed",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "tbx-7",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for tbx-7 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF137ZAX/ and for more information on this tbx-7 experiment, see https://www.encodeproject.org/experiments/ENCSR536VXP/."
+ ]
},
{
- "trackId" : "c_elegans_PRJNA13758_nhr-47-ENCFF979GYO",
- "category" : [
- "modERN",
- "L1 larva"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
+ "displayId" : "rbr-2-ENCFF823YFY-LinearBasicDisplay",
"renderer" : {
+ "height" : 6,
"color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "nhr-47-ENCFF979GYO-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "name" : "nhr-47",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF979GYO/@@download/ENCFF979GYO.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF823YFY/@@download/ENCFF823YFY.bigBed"
}
},
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-47 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF979GYO/ and for more information on this nhr-47 experiment, see https://www.encodeproject.org/experiments/ENCSR321VWM/."
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "modERN",
+ "L4 larva"
+ ],
+ "trackId" : "c_elegans_PRJNA13758_rbr-2-ENCFF823YFY",
+ "name" : "rbr-2",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for rbr-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF823YFY/ and for more information on this rbr-2 experiment, see https://www.encodeproject.org/experiments/ENCSR274WQG/."
},
{
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF321GQG/@@download/ENCFF321GQG.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF867CXG/@@download/ENCFF867CXG.bigBed"
}
},
- "name" : "nhr-90",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-90 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF321GQG/ and for more information on this nhr-90 experiment, see https://www.encodeproject.org/experiments/ENCSR750IEF/.",
- "category" : [
- "modERN",
- "young adult"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_nhr-90-ENCFF321GQG",
"displays" : [
{
- "displayId" : "nhr-90-ENCFF321GQG-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "snpc-4-ENCFF867CXG-LinearBasicDisplay",
"renderer" : {
+ "height" : 6,
"color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
+ "type" : "SvgFeatureRenderer"
}
}
+ ],
+ "trackId" : "c_elegans_PRJNA13758_snpc-4-ENCFF867CXG",
+ "name" : "snpc-4",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for snpc-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF867CXG/ and for more information on this snpc-4 experiment, see https://www.encodeproject.org/experiments/ENCSR032FII/.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "modERN",
+ "young adult"
]
},
{
- "trackId" : "c_elegans_PRJNA13758_pag-3-ENCFF787ISK",
+ "name" : "elt-1",
+ "trackId" : "c_elegans_PRJNA13758_elt-1-ENCFF806XPK",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for elt-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF806XPK/ and for more information on this elt-1 experiment, see https://www.encodeproject.org/experiments/ENCSR715MIV/.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"modERN",
- "late embryonic"
+ "mixed stage (embryonic)"
],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF806XPK/@@download/ENCFF806XPK.bigBed",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "displayId" : "pag-3-ENCFF787ISK-LinearBasicDisplay",
"renderer" : {
+ "color1" : "blue",
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "type" : "SvgFeatureRenderer"
},
+ "displayId" : "elt-1-ENCFF806XPK-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
- ],
- "name" : "pag-3",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF787ISK/@@download/ENCFF787ISK.bigBed",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for pag-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF787ISK/ and for more information on this pag-3 experiment, see https://www.encodeproject.org/experiments/ENCSR813WNF/."
+ ]
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for C04F5.9 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF491BYF/ and for more information on this C04F5.9 experiment, see https://www.encodeproject.org/experiments/ENCSR917KLO/.",
- "name" : "C04F5.9",
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF491BYF/@@download/ENCFF491BYF.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF178NLM/@@download/ENCFF178NLM.bigBed"
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "C04F5.9-ENCFF491BYF-LinearBasicDisplay",
+ "displayId" : "lir-3-ENCFF178NLM-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
+ "type" : "SvgFeatureRenderer",
"color1" : "blue",
- "type" : "SvgFeatureRenderer"
+ "height" : 6
},
"type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_C04F5.9-ENCFF491BYF",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for lir-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF178NLM/ and for more information on this lir-3 experiment, see https://www.encodeproject.org/experiments/ENCSR258OFT/.",
+ "name" : "lir-3",
+ "trackId" : "c_elegans_PRJNA13758_lir-3-ENCFF178NLM",
"category" : [
"modERN",
"L1 larva"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
]
},
{
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF810EMI/@@download/ENCFF810EMI.bigBed"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "snpc-1.3",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for snpc-1.3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF810EMI/ and for more information on this snpc-1.3 experiment, see https://www.encodeproject.org/experiments/ENCSR192NDP/.",
+ "trackId" : "c_elegans_PRJNA13758_let-607-ENCFF588EOS",
+ "name" : "let-607",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for let-607 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF588EOS/ and for more information on this let-607 experiment, see https://www.encodeproject.org/experiments/ENCSR701SBA/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
"young adult"
],
- "trackId" : "c_elegans_PRJNA13758_snpc-1.3-ENCFF810EMI",
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF588EOS/@@download/ENCFF588EOS.bigBed",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
- "displayId" : "snpc-1.3-ENCFF810EMI-LinearBasicDisplay",
"renderer" : {
"height" : 6,
"color1" : "blue",
"type" : "SvgFeatureRenderer"
},
+ "displayId" : "let-607-ENCFF588EOS-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
]
@@ -40884,1053 +40027,898 @@
{
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "rnt-1-ENCFF354YVJ-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"color1" : "blue",
- "height" : 6
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "ceh-18-ENCFF733HIQ-LinearBasicDisplay"
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF354YVJ/@@download/ENCFF354YVJ.bigBed",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"category" : [
"modERN",
"late embryonic"
],
- "trackId" : "c_elegans_PRJNA13758_ceh-18-ENCFF733HIQ",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-18 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF733HIQ/ and for more information on this ceh-18 experiment, see https://www.encodeproject.org/experiments/ENCSR252OVI/.",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF733HIQ/@@download/ENCFF733HIQ.bigBed"
- }
- },
"type" : "FeatureTrack",
- "name" : "ceh-18"
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for rnt-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF354YVJ/ and for more information on this rnt-1 experiment, see https://www.encodeproject.org/experiments/ENCSR427JJZ/.",
+ "name" : "rnt-1",
+ "trackId" : "c_elegans_PRJNA13758_rnt-1-ENCFF354YVJ"
},
{
- "name" : "ceh-14",
+ "name" : "nhr-102",
+ "trackId" : "c_elegans_PRJNA13758_nhr-102-ENCFF790EIG",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-102 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF790EIG/ and for more information on this nhr-102 experiment, see https://www.encodeproject.org/experiments/ENCSR735XWN/.",
"type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF440MQK/@@download/ENCFF440MQK.bigBed"
- },
- "type" : "BigBedAdapter"
- },
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-14 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF440MQK/ and for more information on this ceh-14 experiment, see https://www.encodeproject.org/experiments/ENCSR673WIC/.",
- "trackId" : "c_elegans_PRJNA13758_ceh-14-ENCFF440MQK",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"modERN",
- "late embryonic"
+ "L4 larva"
],
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF790EIG/@@download/ENCFF790EIG.bigBed",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
- "displayId" : "ceh-14-ENCFF440MQK-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
+ "color1" : "blue",
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "nhr-102-ENCFF790EIG-LinearBasicDisplay"
}
]
},
{
- "name" : "ceh-34",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF154WQK/@@download/ENCFF154WQK.bigBed"
- },
- "type" : "BigBedAdapter"
- },
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-34 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF154WQK/ and for more information on this ceh-34 experiment, see https://www.encodeproject.org/experiments/ENCSR507XRY/.",
- "trackId" : "c_elegans_PRJNA13758_ceh-34-ENCFF154WQK",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
"late embryonic"
],
+ "trackId" : "c_elegans_PRJNA13758_tbx-7-ENCFF137ZAX",
+ "name" : "tbx-7",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for tbx-7 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF137ZAX/ and for more information on this tbx-7 experiment, see https://www.encodeproject.org/experiments/ENCSR536VXP/.",
"displays" : [
{
- "displayId" : "ceh-34-ENCFF154WQK-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
"height" : 6,
"color1" : "blue",
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "tbx-7-ENCFF137ZAX-LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF137ZAX/@@download/ENCFF137ZAX.bigBed",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
- "late embryonic"
+ "L1 larva"
],
- "trackId" : "c_elegans_PRJNA13758_dve-1-ENCFF986MWK",
+ "trackId" : "c_elegans_PRJNA13758_nhr-47-ENCFF979GYO",
+ "name" : "nhr-47",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-47 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF979GYO/ and for more information on this nhr-47 experiment, see https://www.encodeproject.org/experiments/ENCSR321VWM/.",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"color1" : "blue",
+ "height" : 6,
"type" : "SvgFeatureRenderer"
},
- "displayId" : "dve-1-ENCFF986MWK-LinearBasicDisplay"
+ "displayId" : "nhr-47-ENCFF979GYO-LinearBasicDisplay"
}
],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF986MWK/@@download/ENCFF986MWK.bigBed",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF979GYO/@@download/ENCFF979GYO.bigBed"
}
- },
- "type" : "FeatureTrack",
- "name" : "dve-1",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for dve-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF986MWK/ and for more information on this dve-1 experiment, see https://www.encodeproject.org/experiments/ENCSR774DUH/."
+ }
},
{
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "height" : 6,
+ "color1" : "blue",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "nhr-90-ENCFF321GQG-LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF452EXF/@@download/ENCFF452EXF.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF321GQG/@@download/ENCFF321GQG.bigBed",
+ "locationType" : "UriLocation"
}
},
- "name" : "spr-1",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for spr-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF452EXF/ and for more information on this spr-1 experiment, see https://www.encodeproject.org/experiments/ENCSR256CRR/.",
"category" : [
"modERN",
- "L4 larva"
+ "young adult"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_spr-1-ENCFF452EXF",
- "displays" : [
- {
- "renderer" : {
- "height" : 6,
- "color1" : "blue",
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "spr-1-ENCFF452EXF-LinearBasicDisplay"
- }
- ]
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-90 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF321GQG/ and for more information on this nhr-90 experiment, see https://www.encodeproject.org/experiments/ENCSR750IEF/.",
+ "name" : "nhr-90",
+ "trackId" : "c_elegans_PRJNA13758_nhr-90-ENCFF321GQG"
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ztf-18 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF394SEY/ and for more information on this ztf-18 experiment, see https://www.encodeproject.org/experiments/ENCSR943FFC/.",
- "name" : "ztf-18",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF394SEY/@@download/ENCFF394SEY.bigBed"
- },
- "type" : "BigBedAdapter"
+ "uri" : "https://www.encodeproject.org/files/ENCFF787ISK/@@download/ENCFF787ISK.bigBed",
+ "locationType" : "UriLocation"
+ }
},
- "type" : "FeatureTrack",
"displays" : [
{
+ "displayId" : "pag-3-ENCFF787ISK-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"color1" : "blue",
- "height" : 6
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "ztf-18-ENCFF394SEY-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_ztf-18-ENCFF394SEY",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for pag-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF787ISK/ and for more information on this pag-3 experiment, see https://www.encodeproject.org/experiments/ENCSR813WNF/.",
+ "name" : "pag-3",
+ "trackId" : "c_elegans_PRJNA13758_pag-3-ENCFF787ISK",
"category" : [
"modERN",
- "young adult"
+ "late embryonic"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
]
},
{
- "name" : "mec-3",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF727NQQ/@@download/ENCFF727NQQ.bigBed"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for mec-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF727NQQ/ and for more information on this mec-3 experiment, see https://www.encodeproject.org/experiments/ENCSR957OLT/.",
- "trackId" : "c_elegans_PRJNA13758_mec-3-ENCFF727NQQ",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for C04F5.9 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF491BYF/ and for more information on this C04F5.9 experiment, see https://www.encodeproject.org/experiments/ENCSR917KLO/.",
+ "trackId" : "c_elegans_PRJNA13758_C04F5.9-ENCFF491BYF",
+ "name" : "C04F5.9",
"category" : [
"modERN",
- "late embryonic"
+ "L1 larva"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF491BYF/@@download/ENCFF491BYF.bigBed",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "displayId" : "mec-3-ENCFF727NQQ-LinearBasicDisplay",
+ "displayId" : "C04F5.9-ENCFF491BYF-LinearBasicDisplay",
"renderer" : {
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "color1" : "blue",
+ "type" : "SvgFeatureRenderer"
},
"type" : "LinearBasicDisplay"
}
]
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for lim-6 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF940KUE/ and for more information on this lim-6 experiment, see https://www.encodeproject.org/experiments/ENCSR753PGF/.",
- "name" : "lim-6",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF940KUE/@@download/ENCFF940KUE.bigBed",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue",
- "height" : 6
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "lim-6-ENCFF940KUE-LinearBasicDisplay"
+ "displayId" : "snpc-1.3-ENCFF810EMI-LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_lim-6-ENCFF940KUE",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "late embryonic"
- ]
- },
- {
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for cey-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF971JYG/ and for more information on this cey-2 experiment, see https://www.encodeproject.org/experiments/ENCSR456YDF/.",
- "name" : "cey-2",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF971JYG/@@download/ENCFF971JYG.bigBed"
- },
- "type" : "BigBedAdapter"
- },
- "displays" : [
- {
- "displayId" : "cey-2-ENCFF971JYG-LinearBasicDisplay",
- "renderer" : {
- "height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
- },
- "type" : "LinearBasicDisplay"
+ "uri" : "https://www.encodeproject.org/files/ENCFF810EMI/@@download/ENCFF810EMI.bigBed",
+ "locationType" : "UriLocation"
}
- ],
- "trackId" : "c_elegans_PRJNA13758_cey-2-ENCFF971JYG",
+ },
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"modERN",
- "L4 larva"
- ]
+ "young adult"
+ ],
+ "name" : "snpc-1.3",
+ "trackId" : "c_elegans_PRJNA13758_snpc-1.3-ENCFF810EMI",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for snpc-1.3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF810EMI/ and for more information on this snpc-1.3 experiment, see https://www.encodeproject.org/experiments/ENCSR192NDP/."
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for madf-10 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF363QUH/ and for more information on this madf-10 experiment, see https://www.encodeproject.org/experiments/ENCSR133RTP/.",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF363QUH/@@download/ENCFF363QUH.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF733HIQ/@@download/ENCFF733HIQ.bigBed",
"locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "name" : "madf-10",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
- "height" : 6
+ "height" : 6,
+ "color1" : "blue"
},
- "displayId" : "madf-10-ENCFF363QUH-LinearBasicDisplay"
+ "displayId" : "ceh-18-ENCFF733HIQ-LinearBasicDisplay"
}
],
+ "name" : "ceh-18",
+ "trackId" : "c_elegans_PRJNA13758_ceh-18-ENCFF733HIQ",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-18 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF733HIQ/ and for more information on this ceh-18 experiment, see https://www.encodeproject.org/experiments/ENCSR252OVI/.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"modERN",
- "young adult"
- ],
- "trackId" : "c_elegans_PRJNA13758_madf-10-ENCFF363QUH"
+ "late embryonic"
+ ]
},
{
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
- "midembryonic"
+ "late embryonic"
],
- "trackId" : "c_elegans_PRJNA13758_med-1-ENCFF487CDH",
+ "trackId" : "c_elegans_PRJNA13758_ceh-14-ENCFF440MQK",
+ "name" : "ceh-14",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-14 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF440MQK/ and for more information on this ceh-14 experiment, see https://www.encodeproject.org/experiments/ENCSR673WIC/.",
"displays" : [
{
- "displayId" : "med-1-ENCFF487CDH-LinearBasicDisplay",
+ "displayId" : "ceh-14-ENCFF440MQK-LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
+ "color1" : "blue",
"height" : 6
},
"type" : "LinearBasicDisplay"
}
],
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF487CDH/@@download/ENCFF487CDH.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF440MQK/@@download/ENCFF440MQK.bigBed",
"locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "med-1",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for med-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF487CDH/ and for more information on this med-1 experiment, see https://www.encodeproject.org/experiments/ENCSR397XGG/."
+ },
+ "type" : "BigBedAdapter"
+ }
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for fkh-6 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF530CJD/ and for more information on this fkh-6 experiment, see https://www.encodeproject.org/experiments/ENCSR695HLU/.",
- "name" : "fkh-6",
+ "trackId" : "c_elegans_PRJNA13758_ceh-34-ENCFF154WQK",
+ "name" : "ceh-34",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-34 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF154WQK/ and for more information on this ceh-34 experiment, see https://www.encodeproject.org/experiments/ENCSR507XRY/.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "modERN",
+ "late embryonic"
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF530CJD/@@download/ENCFF530CJD.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF154WQK/@@download/ENCFF154WQK.bigBed"
}
},
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "fkh-6-ENCFF530CJD-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
+ "displayId" : "ceh-34-ENCFF154WQK-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
+ "type" : "SvgFeatureRenderer",
"color1" : "blue",
- "type" : "SvgFeatureRenderer"
- }
+ "height" : 6
+ },
+ "type" : "LinearBasicDisplay"
}
- ],
- "trackId" : "c_elegans_PRJNA13758_fkh-6-ENCFF530CJD",
- "category" : [
- "modERN",
- "late embryonic"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
]
},
{
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "height" : 6,
- "color1" : "blue",
- "type" : "SvgFeatureRenderer"
- },
- "displayId" : "F13H6.1-ENCFF575RXU-LinearBasicDisplay"
- }
- ],
- "category" : [
- "modERN",
- "late embryonic"
- ],
+ "trackId" : "c_elegans_PRJNA13758_dve-1-ENCFF986MWK",
+ "name" : "dve-1",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for dve-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF986MWK/ and for more information on this dve-1 experiment, see https://www.encodeproject.org/experiments/ENCSR774DUH/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_F13H6.1-ENCFF575RXU",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F13H6.1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF575RXU/ and for more information on this F13H6.1 experiment, see https://www.encodeproject.org/experiments/ENCSR111LGE/.",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF575RXU/@@download/ENCFF575RXU.bigBed"
- }
- },
- "name" : "F13H6.1"
- },
- {
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-25 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF650GUI/ and for more information on this nhr-25 experiment, see https://www.encodeproject.org/experiments/ENCSR338HCL/.",
- "name" : "nhr-25",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF650GUI/@@download/ENCFF650GUI.bigBed"
- },
- "type" : "BigBedAdapter"
- },
"type" : "FeatureTrack",
- "displays" : [
- {
- "displayId" : "nhr-25-ENCFF650GUI-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "blue",
- "height" : 6
- }
- }
- ],
- "trackId" : "c_elegans_PRJNA13758_nhr-25-ENCFF650GUI",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "L4 larva"
- ]
- },
- {
- "displays" : [
- {
- "renderer" : {
- "height" : 6,
- "color1" : "blue",
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "T07F8.4-ENCFF204OYH-LinearBasicDisplay"
- }
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modERN",
- "young adult"
+ "late embryonic"
],
- "trackId" : "c_elegans_PRJNA13758_T07F8.4-ENCFF204OYH",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for T07F8.4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF204OYH/ and for more information on this T07F8.4 experiment, see https://www.encodeproject.org/experiments/ENCSR955ZWH/.",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF204OYH/@@download/ENCFF204OYH.bigBed",
- "locationType" : "UriLocation"
- }
- },
- "name" : "T07F8.4"
- },
- {
- "name" : "nhr-71",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF832PRA/@@download/ENCFF832PRA.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF986MWK/@@download/ENCFF986MWK.bigBed",
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-71 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF832PRA/ and for more information on this nhr-71 experiment, see https://www.encodeproject.org/experiments/ENCSR266SPL/.",
- "trackId" : "c_elegans_PRJNA13758_nhr-71-ENCFF832PRA",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "L1 larva"
- ],
"displays" : [
{
- "displayId" : "nhr-71-ENCFF832PRA-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
"height" : 6,
"color1" : "blue",
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "dve-1-ENCFF986MWK-LinearBasicDisplay"
}
]
},
{
- "trackId" : "c_elegans_PRJNA13758_K09A11.1-ENCFF833CMT",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "late embryonic"
- ],
"displays" : [
{
- "displayId" : "K09A11.1-ENCFF833CMT-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "color1" : "blue",
- "height" : 6
- }
+ "height" : 6,
+ "color1" : "blue"
+ },
+ "displayId" : "spr-1-ENCFF452EXF-LinearBasicDisplay"
}
],
- "name" : "K09A11.1",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF833CMT/@@download/ENCFF833CMT.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF452EXF/@@download/ENCFF452EXF.bigBed",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigBedAdapter"
},
+ "category" : [
+ "modERN",
+ "L4 larva"
+ ],
"type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for K09A11.1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF833CMT/ and for more information on this K09A11.1 experiment, see https://www.encodeproject.org/experiments/ENCSR898ATP/."
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for spr-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF452EXF/ and for more information on this spr-1 experiment, see https://www.encodeproject.org/experiments/ENCSR256CRR/.",
+ "name" : "spr-1",
+ "trackId" : "c_elegans_PRJNA13758_spr-1-ENCFF452EXF"
},
{
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "ztf-18-ENCFF394SEY-LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 6,
- "color1" : "blue",
- "type" : "SvgFeatureRenderer"
+ "color1" : "blue"
},
- "displayId" : "lir-3-ENCFF147OSA-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "category" : [
- "modERN",
- "L4 larva"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_lir-3-ENCFF147OSA",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for lir-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF147OSA/ and for more information on this lir-3 experiment, see https://www.encodeproject.org/experiments/ENCSR408FDZ/.",
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF147OSA/@@download/ENCFF147OSA.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF394SEY/@@download/ENCFF394SEY.bigBed"
},
"type" : "BigBedAdapter"
},
+ "category" : [
+ "modERN",
+ "young adult"
+ ],
"type" : "FeatureTrack",
- "name" : "lir-3"
- },
- {
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "category" : [
- "modERN",
- "L1 larva"
- ],
- "trackId" : "c_elegans_PRJNA13758_nhr-20-ENCFF528QQP",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ztf-18 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF394SEY/ and for more information on this ztf-18 experiment, see https://www.encodeproject.org/experiments/ENCSR943FFC/.",
+ "name" : "ztf-18",
+ "trackId" : "c_elegans_PRJNA13758_ztf-18-ENCFF394SEY"
+ },
+ {
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "mec-3-ENCFF727NQQ-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
+ "type" : "SvgFeatureRenderer",
"color1" : "blue",
- "type" : "SvgFeatureRenderer"
+ "height" : 6
},
- "displayId" : "nhr-20-ENCFF528QQP-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF528QQP/@@download/ENCFF528QQP.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF727NQQ/@@download/ENCFF727NQQ.bigBed",
"locationType" : "UriLocation"
}
},
- "name" : "nhr-20",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-20 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF528QQP/ and for more information on this nhr-20 experiment, see https://www.encodeproject.org/experiments/ENCSR620JQF/."
- },
- {
- "name" : "nfya-1",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF567OHA/@@download/ENCFF567OHA.bigBed"
- }
- },
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nfya-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF567OHA/ and for more information on this nfya-1 experiment, see https://www.encodeproject.org/experiments/ENCSR653IDD/.",
- "trackId" : "c_elegans_PRJNA13758_nfya-1-ENCFF567OHA",
"category" : [
"modERN",
- "L3 larva"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
+ "late embryonic"
],
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
- },
- "displayId" : "nfya-1-ENCFF567OHA-LinearBasicDisplay"
- }
- ]
+ "trackId" : "c_elegans_PRJNA13758_mec-3-ENCFF727NQQ",
+ "name" : "mec-3",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for mec-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF727NQQ/ and for more information on this mec-3 experiment, see https://www.encodeproject.org/experiments/ENCSR957OLT/."
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F49E8.2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF333QZX/ and for more information on this F49E8.2 experiment, see https://www.encodeproject.org/experiments/ENCSR529PIJ/.",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF333QZX/@@download/ENCFF333QZX.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF940KUE/@@download/ENCFF940KUE.bigBed",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "name" : "F49E8.2",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "lim-6-ENCFF940KUE-LinearBasicDisplay",
"renderer" : {
"color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "F49E8.2-ENCFF333QZX-LinearBasicDisplay"
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ }
}
],
+ "trackId" : "c_elegans_PRJNA13758_lim-6-ENCFF940KUE",
+ "name" : "lim-6",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for lim-6 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF940KUE/ and for more information on this lim-6 experiment, see https://www.encodeproject.org/experiments/ENCSR753PGF/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
- "young adult"
- ],
- "trackId" : "c_elegans_PRJNA13758_F49E8.2-ENCFF333QZX"
+ "late embryonic"
+ ]
},
{
+ "category" : [
+ "modERN",
+ "L4 larva"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for cey-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF971JYG/ and for more information on this cey-2 experiment, see https://www.encodeproject.org/experiments/ENCSR456YDF/.",
+ "name" : "cey-2",
+ "trackId" : "c_elegans_PRJNA13758_cey-2-ENCFF971JYG",
"displays" : [
{
- "displayId" : "dpl-1-ENCFF404BSG-LinearBasicDisplay",
+ "displayId" : "cey-2-ENCFF971JYG-LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
- "height" : 6
+ "height" : 6,
+ "color1" : "blue"
},
"type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_dpl-1-ENCFF404BSG",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "young adult"
- ],
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for dpl-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF404BSG/ and for more information on this dpl-1 experiment, see https://www.encodeproject.org/experiments/ENCSR768FFN/.",
- "name" : "dpl-1",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF404BSG/@@download/ENCFF404BSG.bigBed",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF971JYG/@@download/ENCFF971JYG.bigBed"
}
}
},
{
- "trackId" : "c_elegans_PRJNA13758_xbp-1-ENCFF827YCQ",
"category" : [
"modERN",
- "L1 larva"
+ "young adult"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for madf-10 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF363QUH/ and for more information on this madf-10 experiment, see https://www.encodeproject.org/experiments/ENCSR133RTP/.",
+ "name" : "madf-10",
+ "trackId" : "c_elegans_PRJNA13758_madf-10-ENCFF363QUH",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "madf-10-ENCFF363QUH-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"color1" : "blue",
+ "height" : 6,
"type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "xbp-1-ENCFF827YCQ-LinearBasicDisplay"
+ }
}
],
- "name" : "xbp-1",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF827YCQ/@@download/ENCFF827YCQ.bigBed"
- }
- },
- "type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for xbp-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF827YCQ/ and for more information on this xbp-1 experiment, see https://www.encodeproject.org/experiments/ENCSR470XFF/."
+ "uri" : "https://www.encodeproject.org/files/ENCFF363QUH/@@download/ENCFF363QUH.bigBed"
+ },
+ "type" : "BigBedAdapter"
+ }
},
{
- "displays" : [
- {
- "renderer" : {
- "height" : 6,
- "color1" : "blue",
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "dmd-4-ENCFF449UDD-LinearBasicDisplay"
- }
- ],
- "trackId" : "c_elegans_PRJNA13758_dmd-4-ENCFF449UDD",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
- "late embryonic"
+ "midembryonic"
+ ],
+ "trackId" : "c_elegans_PRJNA13758_med-1-ENCFF487CDH",
+ "name" : "med-1",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for med-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF487CDH/ and for more information on this med-1 experiment, see https://www.encodeproject.org/experiments/ENCSR397XGG/.",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "med-1-ENCFF487CDH-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "blue",
+ "height" : 6
+ }
+ }
],
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for dmd-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF449UDD/ and for more information on this dmd-4 experiment, see https://www.encodeproject.org/experiments/ENCSR379UPR/.",
- "name" : "dmd-4",
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF449UDD/@@download/ENCFF449UDD.bigBed",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF487CDH/@@download/ENCFF487CDH.bigBed"
},
"type" : "BigBedAdapter"
}
},
{
- "trackId" : "c_elegans_PRJNA13758_swsn-7-ENCFF153GRE",
"category" : [
"modERN",
- "L1 larva"
+ "late embryonic"
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for fkh-6 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF530CJD/ and for more information on this fkh-6 experiment, see https://www.encodeproject.org/experiments/ENCSR695HLU/.",
+ "trackId" : "c_elegans_PRJNA13758_fkh-6-ENCFF530CJD",
+ "name" : "fkh-6",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "fkh-6-ENCFF530CJD-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"color1" : "blue",
+ "height" : 6,
"type" : "SvgFeatureRenderer"
- },
- "displayId" : "swsn-7-ENCFF153GRE-LinearBasicDisplay"
+ }
}
],
- "name" : "swsn-7",
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF530CJD/@@download/ENCFF530CJD.bigBed",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ }
+ },
+ {
+ "trackId" : "c_elegans_PRJNA13758_F13H6.1-ENCFF575RXU",
+ "name" : "F13H6.1",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F13H6.1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF575RXU/ and for more information on this F13H6.1 experiment, see https://www.encodeproject.org/experiments/ENCSR111LGE/.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
+ "category" : [
+ "modERN",
+ "late embryonic"
+ ],
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF153GRE/@@download/ENCFF153GRE.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF575RXU/@@download/ENCFF575RXU.bigBed"
},
"type" : "BigBedAdapter"
},
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for swsn-7 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF153GRE/ and for more information on this swsn-7 experiment, see https://www.encodeproject.org/experiments/ENCSR406IHG/."
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "height" : 6,
+ "color1" : "blue"
+ },
+ "displayId" : "F13H6.1-ENCFF575RXU-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for snpc-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF786HUM/ and for more information on this snpc-4 experiment, see https://www.encodeproject.org/experiments/ENCSR623HHL/.",
- "name" : "snpc-4",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-25 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF650GUI/ and for more information on this nhr-25 experiment, see https://www.encodeproject.org/experiments/ENCSR338HCL/.",
+ "name" : "nhr-25",
+ "trackId" : "c_elegans_PRJNA13758_nhr-25-ENCFF650GUI",
+ "category" : [
+ "modERN",
+ "L4 larva"
+ ],
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF786HUM/@@download/ENCFF786HUM.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF650GUI/@@download/ENCFF650GUI.bigBed",
"locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
"displays" : [
{
- "displayId" : "snpc-4-ENCFF786HUM-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
+ "displayId" : "nhr-25-ENCFF650GUI-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"color1" : "blue",
"height" : 6
- },
- "type" : "LinearBasicDisplay"
+ }
}
- ],
- "trackId" : "c_elegans_PRJNA13758_snpc-4-ENCFF786HUM",
+ ]
+ },
+ {
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for T07F8.4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF204OYH/ and for more information on this T07F8.4 experiment, see https://www.encodeproject.org/experiments/ENCSR955ZWH/.",
+ "name" : "T07F8.4",
+ "trackId" : "c_elegans_PRJNA13758_T07F8.4-ENCFF204OYH",
"category" : [
"modERN",
"young adult"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
- },
- {
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for sox-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF185TQQ/ and for more information on this sox-4 experiment, see https://www.encodeproject.org/experiments/ENCSR345JIR/.",
- "type" : "FeatureTrack",
+ ],
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF185TQQ/@@download/ENCFF185TQQ.bigBed"
- },
- "type" : "BigBedAdapter"
+ "uri" : "https://www.encodeproject.org/files/ENCFF204OYH/@@download/ENCFF204OYH.bigBed"
+ }
},
- "name" : "sox-4",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "sox-4-ENCFF185TQQ-LinearBasicDisplay"
+ "displayId" : "T07F8.4-ENCFF204OYH-LinearBasicDisplay"
}
- ],
+ ]
+ },
+ {
+ "trackId" : "c_elegans_PRJNA13758_nhr-71-ENCFF832PRA",
+ "name" : "nhr-71",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-71 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF832PRA/ and for more information on this nhr-71 experiment, see https://www.encodeproject.org/experiments/ENCSR266SPL/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
"L1 larva"
],
- "trackId" : "c_elegans_PRJNA13758_sox-4-ENCFF185TQQ"
- },
- {
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F37D6.2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF916IJO/ and for more information on this F37D6.2 experiment, see https://www.encodeproject.org/experiments/ENCSR905YIL/.",
- "name" : "F37D6.2",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF916IJO/@@download/ENCFF916IJO.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF832PRA/@@download/ENCFF832PRA.bigBed",
"locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ }
},
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "F37D6.2-ENCFF916IJO-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"color1" : "blue",
"height" : 6
- }
+ },
+ "displayId" : "nhr-71-ENCFF832PRA-LinearBasicDisplay"
}
- ],
- "trackId" : "c_elegans_PRJNA13758_F37D6.2-ENCFF916IJO",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "L4 larva"
]
},
{
- "name" : "ZK185.1",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF526KTZ/@@download/ENCFF526KTZ.bigBed"
- }
- },
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ZK185.1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF526KTZ/ and for more information on this ZK185.1 experiment, see https://www.encodeproject.org/experiments/ENCSR543FLP/.",
- "trackId" : "c_elegans_PRJNA13758_ZK185.1-ENCFF526KTZ",
"category" : [
"modERN",
- "young adult"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
+ "late embryonic"
],
+ "trackId" : "c_elegans_PRJNA13758_K09A11.1-ENCFF833CMT",
+ "name" : "K09A11.1",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for K09A11.1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF833CMT/ and for more information on this K09A11.1 experiment, see https://www.encodeproject.org/experiments/ENCSR898ATP/.",
"displays" : [
{
- "displayId" : "ZK185.1-ENCFF526KTZ-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "color1" : "blue",
- "height" : 6
+ "height" : 6,
+ "color1" : "blue"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "K09A11.1-ENCFF833CMT-LinearBasicDisplay"
}
- ]
- },
- {
- "name" : "hlh-30",
+ ],
"adapter" : {
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF283COC/@@download/ENCFF283COC.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF833CMT/@@download/ENCFF833CMT.bigBed",
+ "locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hlh-30 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF283COC/ and for more information on this hlh-30 experiment, see https://www.encodeproject.org/experiments/ENCSR246PQU/.",
- "trackId" : "c_elegans_PRJNA13758_hlh-30-ENCFF283COC",
+ }
+ },
+ {
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
"L4 larva"
],
+ "trackId" : "c_elegans_PRJNA13758_lir-3-ENCFF147OSA",
+ "name" : "lir-3",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for lir-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF147OSA/ and for more information on this lir-3 experiment, see https://www.encodeproject.org/experiments/ENCSR408FDZ/.",
"displays" : [
{
- "displayId" : "hlh-30-ENCFF283COC-LinearBasicDisplay",
+ "displayId" : "lir-3-ENCFF147OSA-LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
- "height" : 6
+ "height" : 6,
+ "color1" : "blue"
},
"type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF147OSA/@@download/ENCFF147OSA.bigBed",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for daf-16 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF738DCR/ and for more information on this daf-16 experiment, see https://www.encodeproject.org/experiments/ENCSR946AUI/.",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF738DCR/@@download/ENCFF738DCR.bigBed"
- }
+ "uri" : "https://www.encodeproject.org/files/ENCFF528QQP/@@download/ENCFF528QQP.bigBed"
+ },
+ "type" : "BigBedAdapter"
},
- "name" : "daf-16",
"displays" : [
{
"renderer" : {
- "type" : "SvgFeatureRenderer",
"color1" : "blue",
- "height" : 6
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "daf-16-ENCFF738DCR-LinearBasicDisplay"
+ "displayId" : "nhr-20-ENCFF528QQP-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-20 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF528QQP/ and for more information on this nhr-20 experiment, see https://www.encodeproject.org/experiments/ENCSR620JQF/.",
+ "name" : "nhr-20",
+ "trackId" : "c_elegans_PRJNA13758_nhr-20-ENCFF528QQP",
"category" : [
"modERN",
- "L4 larva"
+ "L1 larva"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_daf-16-ENCFF738DCR"
+ ]
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for efl-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF814OEZ/ and for more information on this efl-1 experiment, see https://www.encodeproject.org/experiments/ENCSR622QSS/.",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nfya-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF567OHA/ and for more information on this nfya-1 experiment, see https://www.encodeproject.org/experiments/ENCSR653IDD/.",
+ "name" : "nfya-1",
+ "trackId" : "c_elegans_PRJNA13758_nfya-1-ENCFF567OHA",
+ "category" : [
+ "modERN",
+ "L3 larva"
+ ],
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF814OEZ/@@download/ENCFF814OEZ.bigBed"
- }
- },
- "name" : "efl-1",
- "displays" : [
- {
- "displayId" : "efl-1-ENCFF814OEZ-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "blue",
- "height" : 6
- }
- }
- ],
- "category" : [
- "modERN",
- "young adult"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_efl-1-ENCFF814OEZ"
- },
- {
- "trackId" : "c_elegans_PRJNA13758_egl-13-ENCFF171PAS",
- "category" : [
- "modERN",
- "L1 larva"
- ],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF567OHA/@@download/ENCFF567OHA.bigBed",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
- "displayId" : "egl-13-ENCFF171PAS-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
+ "displayId" : "nfya-1-ENCFF567OHA-LinearBasicDisplay",
"renderer" : {
"height" : 6,
"color1" : "blue",
"type" : "SvgFeatureRenderer"
- }
- }
- ],
- "name" : "egl-13",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF171PAS/@@download/ENCFF171PAS.bigBed"
+ },
+ "type" : "LinearBasicDisplay"
}
- },
- "type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for egl-13 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF171PAS/ and for more information on this egl-13 experiment, see https://www.encodeproject.org/experiments/ENCSR522TSE/."
+ ]
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for dve-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF808FTE/ and for more information on this dve-1 experiment, see https://www.encodeproject.org/experiments/ENCSR694VLW/.",
- "name" : "dve-1",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF808FTE/@@download/ENCFF808FTE.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF333QZX/@@download/ENCFF333QZX.bigBed"
}
},
- "type" : "FeatureTrack",
"displays" : [
{
"renderer" : {
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "color1" : "blue",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "dve-1-ENCFF808FTE-LinearBasicDisplay"
+ "displayId" : "F49E8.2-ENCFF333QZX-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_dve-1-ENCFF808FTE",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F49E8.2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF333QZX/ and for more information on this F49E8.2 experiment, see https://www.encodeproject.org/experiments/ENCSR529PIJ/.",
+ "name" : "F49E8.2",
+ "trackId" : "c_elegans_PRJNA13758_F49E8.2-ENCFF333QZX",
"category" : [
"modERN",
- "L4 larva"
+ "young adult"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
]
@@ -41938,449 +40926,421 @@
{
"displays" : [
{
- "displayId" : "daf-16-ENCFF626HBN-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "color1" : "blue",
- "height" : 6
- }
+ "height" : 6,
+ "color1" : "blue"
+ },
+ "displayId" : "dpl-1-ENCFF404BSG-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "L4 larva"
- ],
- "trackId" : "c_elegans_PRJNA13758_daf-16-ENCFF626HBN",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for daf-16 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF626HBN/ and for more information on this daf-16 experiment, see https://www.encodeproject.org/experiments/ENCSR081BBL/.",
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF626HBN/@@download/ENCFF626HBN.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF404BSG/@@download/ENCFF404BSG.bigBed"
},
"type" : "BigBedAdapter"
},
- "name" : "daf-16"
+ "category" : [
+ "modERN",
+ "young adult"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for dpl-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF404BSG/ and for more information on this dpl-1 experiment, see https://www.encodeproject.org/experiments/ENCSR768FFN/.",
+ "name" : "dpl-1",
+ "trackId" : "c_elegans_PRJNA13758_dpl-1-ENCFF404BSG"
},
{
- "trackId" : "c_elegans_PRJNA13758_unc-130-ENCFF026EGR",
+ "trackId" : "c_elegans_PRJNA13758_xbp-1-ENCFF827YCQ",
+ "name" : "xbp-1",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for xbp-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF827YCQ/ and for more information on this xbp-1 experiment, see https://www.encodeproject.org/experiments/ENCSR470XFF/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
- "L4 larva"
- ],
- "displays" : [
- {
- "displayId" : "unc-130-ENCFF026EGR-LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "blue",
- "height" : 6
- },
- "type" : "LinearBasicDisplay"
- }
+ "L1 larva"
],
- "name" : "unc-130",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF026EGR/@@download/ENCFF026EGR.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF827YCQ/@@download/ENCFF827YCQ.bigBed"
}
},
- "type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for unc-130 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF026EGR/ and for more information on this unc-130 experiment, see https://www.encodeproject.org/experiments/ENCSR968HCJ/."
- },
- {
"displays" : [
{
- "displayId" : "ceh-32-ENCFF712XFS-LinearBasicDisplay",
+ "displayId" : "xbp-1-ENCFF827YCQ-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue",
- "height" : 6
+ "type" : "SvgFeatureRenderer"
},
"type" : "LinearBasicDisplay"
}
- ],
+ ]
+ },
+ {
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for dmd-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF449UDD/ and for more information on this dmd-4 experiment, see https://www.encodeproject.org/experiments/ENCSR379UPR/.",
+ "trackId" : "c_elegans_PRJNA13758_dmd-4-ENCFF449UDD",
+ "name" : "dmd-4",
"category" : [
"modERN",
- "L4 larva"
+ "late embryonic"
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_ceh-32-ENCFF712XFS",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-32 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF712XFS/ and for more information on this ceh-32 experiment, see https://www.encodeproject.org/experiments/ENCSR329YGE/.",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF712XFS/@@download/ENCFF712XFS.bigBed",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "ceh-32"
- },
- {
- "name" : "ets-4",
"type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF453AMX/@@download/ENCFF453AMX.bigBed",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF449UDD/@@download/ENCFF449UDD.bigBed"
},
"type" : "BigBedAdapter"
},
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ets-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF453AMX/ and for more information on this ets-4 experiment, see https://www.encodeproject.org/experiments/ENCSR260GEE/.",
- "trackId" : "c_elegans_PRJNA13758_ets-4-ENCFF453AMX",
- "category" : [
- "modERN",
- "late embryonic"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
- "displayId" : "ets-4-ENCFF453AMX-LinearBasicDisplay",
+ "displayId" : "dmd-4-ENCFF449UDD-LinearBasicDisplay",
"renderer" : {
+ "color1" : "blue",
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "type" : "SvgFeatureRenderer"
},
"type" : "LinearBasicDisplay"
}
]
},
{
- "name" : "unc-130",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF800ALO/@@download/ENCFF800ALO.bigBed"
- }
- },
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for unc-130 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF800ALO/ and for more information on this unc-130 experiment, see https://www.encodeproject.org/experiments/ENCSR435FDM/.",
- "trackId" : "c_elegans_PRJNA13758_unc-130-ENCFF800ALO",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for swsn-7 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF153GRE/ and for more information on this swsn-7 experiment, see https://www.encodeproject.org/experiments/ENCSR406IHG/.",
+ "trackId" : "c_elegans_PRJNA13758_swsn-7-ENCFF153GRE",
+ "name" : "swsn-7",
"category" : [
"modERN",
- "young adult"
+ "L1 larva"
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF153GRE/@@download/ENCFF153GRE.bigBed",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
- "displayId" : "unc-130-ENCFF800ALO-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
+ "displayId" : "swsn-7-ENCFF153GRE-LinearBasicDisplay",
"renderer" : {
"height" : 6,
"color1" : "blue",
"type" : "SvgFeatureRenderer"
- }
+ },
+ "type" : "LinearBasicDisplay"
}
]
},
{
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
- },
- "displayId" : "hlh-30-ENCFF206SEQ-LinearBasicDisplay"
- }
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "late embryonic"
- ],
- "trackId" : "c_elegans_PRJNA13758_hlh-30-ENCFF206SEQ",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hlh-30 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF206SEQ/ and for more information on this hlh-30 experiment, see https://www.encodeproject.org/experiments/ENCSR091KQX/.",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF206SEQ/@@download/ENCFF206SEQ.bigBed"
- }
- },
"type" : "FeatureTrack",
- "name" : "hlh-30"
- },
- {
- "trackId" : "c_elegans_PRJNA13758_rnt-1-ENCFF184OQV",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"modERN",
- "L1 larva"
+ "young adult"
],
+ "name" : "snpc-4",
+ "trackId" : "c_elegans_PRJNA13758_snpc-4-ENCFF786HUM",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for snpc-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF786HUM/ and for more information on this snpc-4 experiment, see https://www.encodeproject.org/experiments/ENCSR623HHL/.",
"displays" : [
{
- "displayId" : "rnt-1-ENCFF184OQV-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "color1" : "blue",
+ "height" : 6
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "snpc-4-ENCFF786HUM-LinearBasicDisplay"
}
],
- "name" : "rnt-1",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF184OQV/@@download/ENCFF184OQV.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF786HUM/@@download/ENCFF786HUM.bigBed",
"locationType" : "UriLocation"
}
- },
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for rnt-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF184OQV/ and for more information on this rnt-1 experiment, see https://www.encodeproject.org/experiments/ENCSR597WQR/."
+ }
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for duxl-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF165NJP/ and for more information on this duxl-1 experiment, see https://www.encodeproject.org/experiments/ENCSR674PDL/.",
- "name" : "duxl-1",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF165NJP/@@download/ENCFF165NJP.bigBed"
- },
- "type" : "BigBedAdapter"
+ "uri" : "https://www.encodeproject.org/files/ENCFF185TQQ/@@download/ENCFF185TQQ.bigBed"
+ }
},
- "type" : "FeatureTrack",
"displays" : [
{
+ "displayId" : "sox-4-ENCFF185TQQ-LinearBasicDisplay",
"renderer" : {
"color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "duxl-1-ENCFF165NJP-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_duxl-1-ENCFF165NJP",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for sox-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF185TQQ/ and for more information on this sox-4 experiment, see https://www.encodeproject.org/experiments/ENCSR345JIR/.",
+ "trackId" : "c_elegans_PRJNA13758_sox-4-ENCFF185TQQ",
+ "name" : "sox-4",
"category" : [
"modERN",
- "L4 larva"
+ "L1 larva"
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
+ ],
+ "type" : "FeatureTrack"
},
{
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF916IJO/@@download/ENCFF916IJO.bigBed",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 6,
- "color1" : "blue",
- "type" : "SvgFeatureRenderer"
+ "color1" : "blue"
},
- "displayId" : "odd-2-ENCFF388KLR-LinearBasicDisplay"
+ "displayId" : "F37D6.2-ENCFF916IJO-LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_odd-2-ENCFF388KLR",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F37D6.2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF916IJO/ and for more information on this F37D6.2 experiment, see https://www.encodeproject.org/experiments/ENCSR905YIL/.",
+ "trackId" : "c_elegans_PRJNA13758_F37D6.2-ENCFF916IJO",
+ "name" : "F37D6.2",
+ "category" : [
+ "modERN",
+ "L4 larva"
+ ],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack"
+ },
+ {
"category" : [
"modERN",
- "late embryonic"
+ "young adult"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for odd-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF388KLR/ and for more information on this odd-2 experiment, see https://www.encodeproject.org/experiments/ENCSR426MPH/.",
- "name" : "odd-2",
"type" : "FeatureTrack",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ZK185.1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF526KTZ/ and for more information on this ZK185.1 experiment, see https://www.encodeproject.org/experiments/ENCSR543FLP/.",
+ "trackId" : "c_elegans_PRJNA13758_ZK185.1-ENCFF526KTZ",
+ "name" : "ZK185.1",
+ "displays" : [
+ {
+ "displayId" : "ZK185.1-ENCFF526KTZ-LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "blue",
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF388KLR/@@download/ENCFF388KLR.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF526KTZ/@@download/ENCFF526KTZ.bigBed",
"locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
}
},
{
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF283COC/@@download/ENCFF283COC.bigBed"
+ }
+ },
"displays" : [
{
+ "displayId" : "hlh-30-ENCFF283COC-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"color1" : "blue",
"height" : 6
},
- "type" : "LinearBasicDisplay",
- "displayId" : "nhr-90-ENCFF222AUT-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "category" : [
- "modERN",
- "L1 larva"
- ],
+ "trackId" : "c_elegans_PRJNA13758_hlh-30-ENCFF283COC",
+ "name" : "hlh-30",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hlh-30 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF283COC/ and for more information on this hlh-30 experiment, see https://www.encodeproject.org/experiments/ENCSR246PQU/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_nhr-90-ENCFF222AUT",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-90 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF222AUT/ and for more information on this nhr-90 experiment, see https://www.encodeproject.org/experiments/ENCSR311NAQ/.",
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF222AUT/@@download/ENCFF222AUT.bigBed",
- "locationType" : "UriLocation"
- }
- },
- "name" : "nhr-90"
+ "category" : [
+ "modERN",
+ "L4 larva"
+ ]
},
{
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "daf-16-ENCFF738DCR-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "blue",
+ "height" : 6
+ }
+ }
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF005QGG/@@download/ENCFF005QGG.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF738DCR/@@download/ENCFF738DCR.bigBed",
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "name" : "lsy-27",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for lsy-27 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF005QGG/ and for more information on this lsy-27 experiment, see https://www.encodeproject.org/experiments/ENCSR158PGO/.",
"category" : [
"modERN",
- "young adult"
+ "L4 larva"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_lsy-27-ENCFF005QGG",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for daf-16 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF738DCR/ and for more information on this daf-16 experiment, see https://www.encodeproject.org/experiments/ENCSR946AUI/.",
+ "name" : "daf-16",
+ "trackId" : "c_elegans_PRJNA13758_daf-16-ENCFF738DCR"
+ },
+ {
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF814OEZ/@@download/ENCFF814OEZ.bigBed"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
- "displayId" : "lsy-27-ENCFF005QGG-LinearBasicDisplay",
+ "displayId" : "efl-1-ENCFF814OEZ-LinearBasicDisplay",
"renderer" : {
+ "color1" : "blue",
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "type" : "SvgFeatureRenderer"
},
"type" : "LinearBasicDisplay"
}
+ ],
+ "trackId" : "c_elegans_PRJNA13758_efl-1-ENCFF814OEZ",
+ "name" : "efl-1",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for efl-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF814OEZ/ and for more information on this efl-1 experiment, see https://www.encodeproject.org/experiments/ENCSR622QSS/.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "modERN",
+ "young adult"
]
},
{
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for egl-13 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF171PAS/ and for more information on this egl-13 experiment, see https://www.encodeproject.org/experiments/ENCSR522TSE/.",
+ "trackId" : "c_elegans_PRJNA13758_egl-13-ENCFF171PAS",
+ "name" : "egl-13",
"category" : [
"modERN",
- "late embryonic"
+ "L1 larva"
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_nfya-1-ENCFF173AEU",
- "displays" : [
- {
- "displayId" : "nfya-1-ENCFF173AEU-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "blue",
- "height" : 6
- }
- }
- ],
+ "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF173AEU/@@download/ENCFF173AEU.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF171PAS/@@download/ENCFF171PAS.bigBed"
}
},
- "type" : "FeatureTrack",
- "name" : "nfya-1",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nfya-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF173AEU/ and for more information on this nfya-1 experiment, see https://www.encodeproject.org/experiments/ENCSR859SHA/."
- },
- {
- "category" : [
- "modERN",
- "young adult"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_F23B12.7-ENCFF154LUL",
"displays" : [
{
- "displayId" : "F23B12.7-ENCFF154LUL-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
+ "displayId" : "egl-13-ENCFF171PAS-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"color1" : "blue",
"height" : 6
- },
- "type" : "LinearBasicDisplay"
+ }
}
- ],
- "type" : "FeatureTrack",
+ ]
+ },
+ {
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF154LUL/@@download/ENCFF154LUL.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF808FTE/@@download/ENCFF808FTE.bigBed"
},
"type" : "BigBedAdapter"
},
- "name" : "F23B12.7",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F23B12.7 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF154LUL/ and for more information on this F23B12.7 experiment, see https://www.encodeproject.org/experiments/ENCSR076LYI/."
- },
- {
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for sma-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF055GQP/ and for more information on this sma-3 experiment, see https://www.encodeproject.org/experiments/ENCSR992FVB/.",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF055GQP/@@download/ENCFF055GQP.bigBed",
- "locationType" : "UriLocation"
- }
- },
- "name" : "sma-3",
"displays" : [
{
- "displayId" : "sma-3-ENCFF055GQP-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
+ "type" : "SvgFeatureRenderer",
"color1" : "blue",
- "type" : "SvgFeatureRenderer"
- }
+ "height" : 6
+ },
+ "displayId" : "dve-1-ENCFF808FTE-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for dve-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF808FTE/ and for more information on this dve-1 experiment, see https://www.encodeproject.org/experiments/ENCSR694VLW/.",
+ "trackId" : "c_elegans_PRJNA13758_dve-1-ENCFF808FTE",
+ "name" : "dve-1",
"category" : [
"modERN",
- "L2 larva"
+ "L4 larva"
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_sma-3-ENCFF055GQP"
+ "type" : "FeatureTrack"
},
{
- "trackId" : "c_elegans_PRJNA13758_nhr-80-ENCFF737MUB",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
- "young adult"
+ "L4 larva"
],
+ "trackId" : "c_elegans_PRJNA13758_daf-16-ENCFF626HBN",
+ "name" : "daf-16",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for daf-16 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF626HBN/ and for more information on this daf-16 experiment, see https://www.encodeproject.org/experiments/ENCSR081BBL/.",
"displays" : [
{
- "displayId" : "nhr-80-ENCFF737MUB-LinearBasicDisplay",
+ "displayId" : "daf-16-ENCFF626HBN-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"color1" : "blue",
@@ -42389,115 +41349,143 @@
"type" : "LinearBasicDisplay"
}
],
- "name" : "nhr-80",
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF737MUB/@@download/ENCFF737MUB.bigBed",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF626HBN/@@download/ENCFF626HBN.bigBed"
},
"type" : "BigBedAdapter"
- },
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-80 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF737MUB/ and for more information on this nhr-80 experiment, see https://www.encodeproject.org/experiments/ENCSR557ZYT/."
+ }
},
{
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF026EGR/@@download/ENCFF026EGR.bigBed"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "color1" : "blue",
- "height" : 6
+ "height" : 6,
+ "color1" : "blue"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "lin-40-ENCFF470MYD-LinearBasicDisplay"
+ "displayId" : "unc-130-ENCFF026EGR-LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_lin-40-ENCFF470MYD",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for unc-130 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF026EGR/ and for more information on this unc-130 experiment, see https://www.encodeproject.org/experiments/ENCSR968HCJ/.",
+ "name" : "unc-130",
+ "trackId" : "c_elegans_PRJNA13758_unc-130-ENCFF026EGR",
"category" : [
"modERN",
- "young adult"
+ "L4 larva"
],
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for lin-40 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF470MYD/ and for more information on this lin-40 experiment, see https://www.encodeproject.org/experiments/ENCSR133PLZ/.",
- "name" : "lin-40",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF470MYD/@@download/ENCFF470MYD.bigBed",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack"
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ]
},
{
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF903HOE/@@download/ENCFF903HOE.bigBed",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF712XFS/@@download/ENCFF712XFS.bigBed"
+ }
},
- "name" : "tbx-2",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for tbx-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF903HOE/ and for more information on this tbx-2 experiment, see https://www.encodeproject.org/experiments/ENCSR344UEX/.",
- "category" : [
- "modERN",
- "L3 larva"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_tbx-2-ENCFF903HOE",
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue",
- "height" : 6
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "tbx-2-ENCFF903HOE-LinearBasicDisplay"
+ "displayId" : "ceh-32-ENCFF712XFS-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-32 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF712XFS/ and for more information on this ceh-32 experiment, see https://www.encodeproject.org/experiments/ENCSR329YGE/.",
+ "trackId" : "c_elegans_PRJNA13758_ceh-32-ENCFF712XFS",
+ "name" : "ceh-32",
+ "category" : [
+ "modERN",
+ "L4 larva"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack"
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ztf-11 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF524NZN/ and for more information on this ztf-11 experiment, see https://www.encodeproject.org/experiments/ENCSR185SVY/.",
- "name" : "ztf-11",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF524NZN/@@download/ENCFF524NZN.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF453AMX/@@download/ENCFF453AMX.bigBed"
}
},
- "type" : "FeatureTrack",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "ets-4-ENCFF453AMX-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue",
- "height" : 6
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "ztf-11-ENCFF524NZN-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_ztf-11-ENCFF524NZN",
+ "name" : "ets-4",
+ "trackId" : "c_elegans_PRJNA13758_ets-4-ENCFF453AMX",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ets-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF453AMX/ and for more information on this ets-4 experiment, see https://www.encodeproject.org/experiments/ENCSR260GEE/.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modERN",
- "L1 larva"
- ],
+ "late embryonic"
+ ]
+ },
+ {
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "modERN",
+ "young adult"
+ ],
+ "trackId" : "c_elegans_PRJNA13758_unc-130-ENCFF800ALO",
+ "name" : "unc-130",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for unc-130 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF800ALO/ and for more information on this unc-130 experiment, see https://www.encodeproject.org/experiments/ENCSR435FDM/.",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "unc-130-ENCFF800ALO-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "blue",
+ "height" : 6
+ }
+ }
+ ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF800ALO/@@download/ENCFF800ALO.bigBed",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
"displays" : [
{
- "displayId" : "tbx-2-ENCFF811JTQ-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "hlh-30-ENCFF206SEQ-LinearBasicDisplay",
"renderer" : {
"height" : 6,
"color1" : "blue",
@@ -42505,6 +41493,14 @@
}
}
],
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF206SEQ/@@download/ENCFF206SEQ.bigBed",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -42512,220 +41508,235 @@
"modERN",
"late embryonic"
],
- "trackId" : "c_elegans_PRJNA13758_tbx-2-ENCFF811JTQ",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for tbx-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF811JTQ/ and for more information on this tbx-2 experiment, see https://www.encodeproject.org/experiments/ENCSR162MNX/.",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF811JTQ/@@download/ENCFF811JTQ.bigBed"
- }
- },
- "name" : "tbx-2"
+ "name" : "hlh-30",
+ "trackId" : "c_elegans_PRJNA13758_hlh-30-ENCFF206SEQ",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hlh-30 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF206SEQ/ and for more information on this hlh-30 experiment, see https://www.encodeproject.org/experiments/ENCSR091KQX/."
},
{
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF494PRR/@@download/ENCFF494PRR.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF184OQV/@@download/ENCFF184OQV.bigBed"
},
"type" : "BigBedAdapter"
},
- "name" : "blmp-1",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for blmp-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF494PRR/ and for more information on this blmp-1 experiment, see https://www.encodeproject.org/experiments/ENCSR744BON/.",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "L2 larva"
- ],
- "trackId" : "c_elegans_PRJNA13758_blmp-1-ENCFF494PRR",
"displays" : [
{
- "displayId" : "blmp-1-ENCFF494PRR-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue",
- "height" : 6
+ "type" : "SvgFeatureRenderer"
},
+ "displayId" : "rnt-1-ENCFF184OQV-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
+ ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for rnt-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF184OQV/ and for more information on this rnt-1 experiment, see https://www.encodeproject.org/experiments/ENCSR597WQR/.",
+ "name" : "rnt-1",
+ "trackId" : "c_elegans_PRJNA13758_rnt-1-ENCFF184OQV",
+ "category" : [
+ "modERN",
+ "L1 larva"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
]
},
{
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "modERN",
+ "L4 larva"
+ ],
+ "trackId" : "c_elegans_PRJNA13758_duxl-1-ENCFF165NJP",
+ "name" : "duxl-1",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for duxl-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF165NJP/ and for more information on this duxl-1 experiment, see https://www.encodeproject.org/experiments/ENCSR674PDL/.",
"displays" : [
{
- "displayId" : "hmg-11-ENCFF170SNE-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "duxl-1-ENCFF165NJP-LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "L3 larva"
- ],
- "trackId" : "c_elegans_PRJNA13758_hmg-11-ENCFF170SNE",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hmg-11 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF170SNE/ and for more information on this hmg-11 experiment, see https://www.encodeproject.org/experiments/ENCSR376OYD/.",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF170SNE/@@download/ENCFF170SNE.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF165NJP/@@download/ENCFF165NJP.bigBed",
+ "locationType" : "UriLocation"
}
- },
- "type" : "FeatureTrack",
- "name" : "hmg-11"
+ }
},
{
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF724VTZ/@@download/ENCFF724VTZ.bigBed"
- },
- "type" : "BigBedAdapter"
- },
- "name" : "F13H6.1",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F13H6.1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF724VTZ/ and for more information on this F13H6.1 experiment, see https://www.encodeproject.org/experiments/ENCSR359GJP/.",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"category" : [
"modERN",
- "L2 larva"
+ "late embryonic"
],
- "trackId" : "c_elegans_PRJNA13758_F13H6.1-ENCFF724VTZ",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for odd-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF388KLR/ and for more information on this odd-2 experiment, see https://www.encodeproject.org/experiments/ENCSR426MPH/.",
+ "trackId" : "c_elegans_PRJNA13758_odd-2-ENCFF388KLR",
+ "name" : "odd-2",
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "color1" : "blue",
+ "height" : 6
},
- "displayId" : "F13H6.1-ENCFF724VTZ-LinearBasicDisplay"
+ "displayId" : "odd-2-ENCFF388KLR-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF388KLR/@@download/ENCFF388KLR.bigBed",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for tbx-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF852JBM/ and for more information on this tbx-2 experiment, see https://www.encodeproject.org/experiments/ENCSR238YNR/.",
- "name" : "tbx-2",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF852JBM/@@download/ENCFF852JBM.bigBed"
- }
+ "uri" : "https://www.encodeproject.org/files/ENCFF222AUT/@@download/ENCFF222AUT.bigBed"
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
"displays" : [
{
"renderer" : {
- "height" : 6,
"color1" : "blue",
+ "height" : 6,
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "tbx-2-ENCFF852JBM-LinearBasicDisplay"
+ "displayId" : "nhr-90-ENCFF222AUT-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_tbx-2-ENCFF852JBM",
+ "trackId" : "c_elegans_PRJNA13758_nhr-90-ENCFF222AUT",
+ "name" : "nhr-90",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-90 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF222AUT/ and for more information on this nhr-90 experiment, see https://www.encodeproject.org/experiments/ENCSR311NAQ/.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
"L1 larva"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
]
},
{
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF005QGG/@@download/ENCFF005QGG.bigBed",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "lsy-27-ENCFF005QGG-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"color1" : "blue",
"height" : 6
- },
- "displayId" : "rec-8-ENCFF836TTN-LinearBasicDisplay"
+ }
}
],
- "trackId" : "c_elegans_PRJNA13758_rec-8-ENCFF836TTN",
+ "trackId" : "c_elegans_PRJNA13758_lsy-27-ENCFF005QGG",
+ "name" : "lsy-27",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for lsy-27 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF005QGG/ and for more information on this lsy-27 experiment, see https://www.encodeproject.org/experiments/ENCSR158PGO/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
"young adult"
- ],
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for rec-8 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF836TTN/ and for more information on this rec-8 experiment, see https://www.encodeproject.org/experiments/ENCSR806QUX/.",
- "name" : "rec-8",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF836TTN/@@download/ENCFF836TTN.bigBed"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack"
+ ]
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-90 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF655GFG/ and for more information on this ceh-90 experiment, see https://www.encodeproject.org/experiments/ENCSR891WMQ/.",
+ "name" : "nfya-1",
+ "trackId" : "c_elegans_PRJNA13758_nfya-1-ENCFF173AEU",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nfya-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF173AEU/ and for more information on this nfya-1 experiment, see https://www.encodeproject.org/experiments/ENCSR859SHA/.",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modERN",
+ "late embryonic"
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF655GFG/@@download/ENCFF655GFG.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF173AEU/@@download/ENCFF173AEU.bigBed",
+ "locationType" : "UriLocation"
}
},
- "name" : "ceh-90",
"displays" : [
{
+ "displayId" : "nfya-1-ENCFF173AEU-LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
- "height" : 6
+ "height" : 6,
+ "color1" : "blue"
},
+ "type" : "LinearBasicDisplay"
+ }
+ ]
+ },
+ {
+ "displays" : [
+ {
"type" : "LinearBasicDisplay",
- "displayId" : "ceh-90-ENCFF655GFG-LinearBasicDisplay"
+ "displayId" : "F23B12.7-ENCFF154LUL-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "height" : 6,
+ "color1" : "blue"
+ }
}
],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF154LUL/@@download/ENCFF154LUL.bigBed"
+ },
+ "type" : "BigBedAdapter"
+ },
"category" : [
"modERN",
- "L1 larva"
+ "young adult"
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_ceh-90-ENCFF655GFG"
+ "type" : "FeatureTrack",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F23B12.7 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF154LUL/ and for more information on this F23B12.7 experiment, see https://www.encodeproject.org/experiments/ENCSR076LYI/.",
+ "trackId" : "c_elegans_PRJNA13758_F23B12.7-ENCFF154LUL",
+ "name" : "F23B12.7"
},
{
- "category" : [
- "modERN",
- "L1 larva"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_fkh-4-ENCFF104JOE",
"displays" : [
{
- "displayId" : "fkh-4-ENCFF104JOE-LinearBasicDisplay",
+ "displayId" : "sma-3-ENCFF055GQP-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"color1" : "blue",
- "height" : 6
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
},
"type" : "LinearBasicDisplay"
}
@@ -42733,1303 +41744,1686 @@
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF104JOE/@@download/ENCFF104JOE.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF055GQP/@@download/ENCFF055GQP.bigBed"
},
"type" : "BigBedAdapter"
},
+ "category" : [
+ "modERN",
+ "L2 larva"
+ ],
"type" : "FeatureTrack",
- "name" : "fkh-4",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for fkh-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF104JOE/ and for more information on this fkh-4 experiment, see https://www.encodeproject.org/experiments/ENCSR371DPT/."
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for sma-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF055GQP/ and for more information on this sma-3 experiment, see https://www.encodeproject.org/experiments/ENCSR992FVB/.",
+ "name" : "sma-3",
+ "trackId" : "c_elegans_PRJNA13758_sma-3-ENCFF055GQP"
},
{
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF737MUB/@@download/ENCFF737MUB.bigBed",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "displayId" : "mxl-1-ENCFF078KCE-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "color1" : "blue",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "nhr-80-ENCFF737MUB-LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_mxl-1-ENCFF078KCE",
- "category" : [
- "modERN",
- "young adult"
- ],
+ "trackId" : "c_elegans_PRJNA13758_nhr-80-ENCFF737MUB",
+ "name" : "nhr-80",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-80 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF737MUB/ and for more information on this nhr-80 experiment, see https://www.encodeproject.org/experiments/ENCSR557ZYT/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for mxl-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF078KCE/ and for more information on this mxl-1 experiment, see https://www.encodeproject.org/experiments/ENCSR264JKE/.",
- "name" : "mxl-1",
"type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF078KCE/@@download/ENCFF078KCE.bigBed"
- },
- "type" : "BigBedAdapter"
- }
+ "category" : [
+ "modERN",
+ "young adult"
+ ]
},
{
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF038IUP/@@download/ENCFF038IUP.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF470MYD/@@download/ENCFF470MYD.bigBed",
"locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
- "name" : "pag-3",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for pag-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF038IUP/ and for more information on this pag-3 experiment, see https://www.encodeproject.org/experiments/ENCSR680ZDH/.",
+ "displays" : [
+ {
+ "renderer" : {
+ "color1" : "blue",
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "lin-40-ENCFF470MYD-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
+ "trackId" : "c_elegans_PRJNA13758_lin-40-ENCFF470MYD",
+ "name" : "lin-40",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for lin-40 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF470MYD/ and for more information on this lin-40 experiment, see https://www.encodeproject.org/experiments/ENCSR133PLZ/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
- "L1 larva"
+ "young adult"
+ ]
+ },
+ {
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for tbx-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF903HOE/ and for more information on this tbx-2 experiment, see https://www.encodeproject.org/experiments/ENCSR344UEX/.",
+ "trackId" : "c_elegans_PRJNA13758_tbx-2-ENCFF903HOE",
+ "name" : "tbx-2",
+ "category" : [
+ "modERN",
+ "L3 larva"
],
- "trackId" : "c_elegans_PRJNA13758_pag-3-ENCFF038IUP",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF903HOE/@@download/ENCFF903HOE.bigBed"
+ }
+ },
"displays" : [
{
- "displayId" : "pag-3-ENCFF038IUP-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"color1" : "blue",
"height" : 6
},
+ "displayId" : "tbx-2-ENCFF903HOE-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
]
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for irx-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF545QMO/ and for more information on this irx-1 experiment, see https://www.encodeproject.org/experiments/ENCSR938NRX/.",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF545QMO/@@download/ENCFF545QMO.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF524NZN/@@download/ENCFF524NZN.bigBed",
+ "locationType" : "UriLocation"
}
},
- "name" : "irx-1",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
- "height" : 6
+ "height" : 6,
+ "color1" : "blue"
},
- "displayId" : "irx-1-ENCFF545QMO-LinearBasicDisplay"
+ "displayId" : "ztf-11-ENCFF524NZN-LinearBasicDisplay"
}
],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ztf-11 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF524NZN/ and for more information on this ztf-11 experiment, see https://www.encodeproject.org/experiments/ENCSR185SVY/.",
+ "name" : "ztf-11",
+ "trackId" : "c_elegans_PRJNA13758_ztf-11-ENCFF524NZN",
"category" : [
"modERN",
"L1 larva"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_irx-1-ENCFF545QMO"
+ ]
},
{
- "trackId" : "c_elegans_PRJNA13758_nfya-1-ENCFF174GXE",
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF811JTQ/@@download/ENCFF811JTQ.bigBed",
+ "locationType" : "UriLocation"
+ }
+ },
+ "displays" : [
+ {
+ "renderer" : {
+ "height" : 6,
+ "color1" : "blue",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "tbx-2-ENCFF811JTQ-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
+ "trackId" : "c_elegans_PRJNA13758_tbx-2-ENCFF811JTQ",
+ "name" : "tbx-2",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for tbx-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF811JTQ/ and for more information on this tbx-2 experiment, see https://www.encodeproject.org/experiments/ENCSR162MNX/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
- "young adult"
- ],
+ "late embryonic"
+ ]
+ },
+ {
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
"height" : 6,
"color1" : "blue",
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "nfya-1-ENCFF174GXE-LinearBasicDisplay"
+ "displayId" : "blmp-1-ENCFF494PRR-LinearBasicDisplay"
}
],
- "name" : "nfya-1",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF174GXE/@@download/ENCFF174GXE.bigBed",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF494PRR/@@download/ENCFF494PRR.bigBed"
}
},
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nfya-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF174GXE/ and for more information on this nfya-1 experiment, see https://www.encodeproject.org/experiments/ENCSR581THE/."
+ "category" : [
+ "modERN",
+ "L2 larva"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for blmp-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF494PRR/ and for more information on this blmp-1 experiment, see https://www.encodeproject.org/experiments/ENCSR744BON/.",
+ "name" : "blmp-1",
+ "trackId" : "c_elegans_PRJNA13758_blmp-1-ENCFF494PRR"
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F55B11.4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF506QZK/ and for more information on this F55B11.4 experiment, see https://www.encodeproject.org/experiments/ENCSR698RXJ/.",
- "name" : "F55B11.4",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hmg-11 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF170SNE/ and for more information on this hmg-11 experiment, see https://www.encodeproject.org/experiments/ENCSR376OYD/.",
+ "name" : "hmg-11",
+ "trackId" : "c_elegans_PRJNA13758_hmg-11-ENCFF170SNE",
+ "category" : [
+ "modERN",
+ "L3 larva"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF506QZK/@@download/ENCFF506QZK.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF170SNE/@@download/ENCFF170SNE.bigBed",
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "F55B11.4-ENCFF506QZK-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
+ "type" : "SvgFeatureRenderer",
"color1" : "blue",
- "type" : "SvgFeatureRenderer"
+ "height" : 6
+ },
+ "displayId" : "hmg-11-ENCFF170SNE-LinearBasicDisplay"
+ }
+ ]
+ },
+ {
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF724VTZ/@@download/ENCFF724VTZ.bigBed"
+ },
+ "type" : "BigBedAdapter"
+ },
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "height" : 6,
+ "color1" : "blue"
},
+ "displayId" : "F13H6.1-ENCFF724VTZ-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_F55B11.4-ENCFF506QZK",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F13H6.1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF724VTZ/ and for more information on this F13H6.1 experiment, see https://www.encodeproject.org/experiments/ENCSR359GJP/.",
+ "trackId" : "c_elegans_PRJNA13758_F13H6.1-ENCFF724VTZ",
+ "name" : "F13H6.1",
"category" : [
"modERN",
- "young adult"
+ "L2 larva"
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
+ ],
+ "type" : "FeatureTrack"
},
{
- "trackId" : "c_elegans_PRJNA13758_fkh-8-ENCFF538UTT",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
"L1 larva"
],
+ "trackId" : "c_elegans_PRJNA13758_tbx-2-ENCFF852JBM",
+ "name" : "tbx-2",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for tbx-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF852JBM/ and for more information on this tbx-2 experiment, see https://www.encodeproject.org/experiments/ENCSR238YNR/.",
"displays" : [
{
"renderer" : {
+ "color1" : "blue",
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "fkh-8-ENCFF538UTT-LinearBasicDisplay"
+ "displayId" : "tbx-2-ENCFF852JBM-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "name" : "fkh-8",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF538UTT/@@download/ENCFF538UTT.bigBed"
- }
- },
- "type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for fkh-8 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF538UTT/ and for more information on this fkh-8 experiment, see https://www.encodeproject.org/experiments/ENCSR435RXY/."
+ "uri" : "https://www.encodeproject.org/files/ENCFF852JBM/@@download/ENCFF852JBM.bigBed"
+ },
+ "type" : "BigBedAdapter"
+ }
},
{
"displays" : [
{
- "displayId" : "fkh-3-ENCFF139YOY-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"color1" : "blue",
+ "height" : 6,
"type" : "SvgFeatureRenderer"
},
+ "displayId" : "rec-8-ENCFF836TTN-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF836TTN/@@download/ENCFF836TTN.bigBed",
+ "locationType" : "UriLocation"
+ }
+ },
"category" : [
"modERN",
"young adult"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_fkh-3-ENCFF139YOY",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for fkh-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF139YOY/ and for more information on this fkh-3 experiment, see https://www.encodeproject.org/experiments/ENCSR717JMX/.",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF139YOY/@@download/ENCFF139YOY.bigBed",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "fkh-3"
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for rec-8 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF836TTN/ and for more information on this rec-8 experiment, see https://www.encodeproject.org/experiments/ENCSR806QUX/.",
+ "name" : "rec-8",
+ "trackId" : "c_elegans_PRJNA13758_rec-8-ENCFF836TTN"
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for lsy-12 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF238OZR/ and for more information on this lsy-12 experiment, see https://www.encodeproject.org/experiments/ENCSR272KZJ/.",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF238OZR/@@download/ENCFF238OZR.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF655GFG/@@download/ENCFF655GFG.bigBed",
"locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ }
},
- "type" : "FeatureTrack",
- "name" : "lsy-12",
"displays" : [
{
- "displayId" : "lsy-12-ENCFF238OZR-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "color1" : "blue",
- "height" : 6
+ "height" : 6,
+ "color1" : "blue"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "ceh-90-ENCFF655GFG-LinearBasicDisplay"
}
],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-90 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF655GFG/ and for more information on this ceh-90 experiment, see https://www.encodeproject.org/experiments/ENCSR891WMQ/.",
+ "trackId" : "c_elegans_PRJNA13758_ceh-90-ENCFF655GFG",
+ "name" : "ceh-90",
"category" : [
"modERN",
- "L3 larva"
+ "L1 larva"
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_lsy-12-ENCFF238OZR"
+ "type" : "FeatureTrack"
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for cog-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF859IPZ/ and for more information on this cog-1 experiment, see https://www.encodeproject.org/experiments/ENCSR422XRE/.",
- "name" : "cog-1",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF859IPZ/@@download/ENCFF859IPZ.bigBed"
- },
- "type" : "BigBedAdapter"
- },
- "displays" : [
- {
- "displayId" : "cog-1-ENCFF859IPZ-LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "blue",
- "height" : 6
- },
- "type" : "LinearBasicDisplay"
- }
- ],
- "trackId" : "c_elegans_PRJNA13758_cog-1-ENCFF859IPZ",
- "category" : [
- "modERN",
- "midembryonic"
- ],
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ]
- },
- {
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for mls-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF573LMJ/ and for more information on this mls-2 experiment, see https://www.encodeproject.org/experiments/ENCSR668BTV/.",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF573LMJ/@@download/ENCFF573LMJ.bigBed",
- "locationType" : "UriLocation"
- }
- },
- "name" : "mls-2",
- "displays" : [
- {
- "displayId" : "mls-2-ENCFF573LMJ-LinearBasicDisplay",
- "renderer" : {
- "color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
- },
- "type" : "LinearBasicDisplay"
- }
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
- "mixed stage (embryonic)"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
+ "L1 larva"
],
- "trackId" : "c_elegans_PRJNA13758_mls-2-ENCFF573LMJ"
- },
- {
+ "trackId" : "c_elegans_PRJNA13758_fkh-4-ENCFF104JOE",
+ "name" : "fkh-4",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for fkh-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF104JOE/ and for more information on this fkh-4 experiment, see https://www.encodeproject.org/experiments/ENCSR371DPT/.",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue"
},
- "displayId" : "tbx-9-ENCFF755JFG-LinearBasicDisplay"
+ "displayId" : "fkh-4-ENCFF104JOE-LinearBasicDisplay"
}
],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF104JOE/@@download/ENCFF104JOE.bigBed"
+ },
+ "type" : "BigBedAdapter"
+ }
+ },
+ {
+ "trackId" : "c_elegans_PRJNA13758_mxl-1-ENCFF078KCE",
+ "name" : "mxl-1",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for mxl-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF078KCE/ and for more information on this mxl-1 experiment, see https://www.encodeproject.org/experiments/ENCSR264JKE/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
"young adult"
],
- "trackId" : "c_elegans_PRJNA13758_tbx-9-ENCFF755JFG",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for tbx-9 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF755JFG/ and for more information on this tbx-9 experiment, see https://www.encodeproject.org/experiments/ENCSR819NBT/.",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF755JFG/@@download/ENCFF755JFG.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF078KCE/@@download/ENCFF078KCE.bigBed"
}
},
- "name" : "tbx-9"
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "mxl-1-ENCFF078KCE-LinearBasicDisplay",
+ "renderer" : {
+ "height" : 6,
+ "color1" : "blue",
+ "type" : "SvgFeatureRenderer"
+ }
+ }
+ ]
},
{
- "name" : "Y22D7AL.16",
+ "name" : "pag-3",
+ "trackId" : "c_elegans_PRJNA13758_pag-3-ENCFF038IUP",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for pag-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF038IUP/ and for more information on this pag-3 experiment, see https://www.encodeproject.org/experiments/ENCSR680ZDH/.",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modERN",
+ "L1 larva"
+ ],
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF329QXX/@@download/ENCFF329QXX.bigBed"
- }
+ "uri" : "https://www.encodeproject.org/files/ENCFF038IUP/@@download/ENCFF038IUP.bigBed"
+ },
+ "type" : "BigBedAdapter"
},
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for Y22D7AL.16 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF329QXX/ and for more information on this Y22D7AL.16 experiment, see https://www.encodeproject.org/experiments/ENCSR643BKM/.",
- "trackId" : "c_elegans_PRJNA13758_Y22D7AL.16-ENCFF329QXX",
- "category" : [
- "modERN",
- "late embryonic"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"color1" : "blue",
"height" : 6
},
- "displayId" : "Y22D7AL.16-ENCFF329QXX-LinearBasicDisplay"
+ "displayId" : "pag-3-ENCFF038IUP-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
]
},
{
+ "name" : "irx-1",
+ "trackId" : "c_elegans_PRJNA13758_irx-1-ENCFF545QMO",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for irx-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF545QMO/ and for more information on this irx-1 experiment, see https://www.encodeproject.org/experiments/ENCSR938NRX/.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"modERN",
- "early embryonic"
+ "L1 larva"
],
- "trackId" : "c_elegans_PRJNA13758_B0310.2-ENCFF945LXL",
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF545QMO/@@download/ENCFF545QMO.bigBed"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 6,
- "color1" : "blue",
- "type" : "SvgFeatureRenderer"
+ "color1" : "blue"
},
- "displayId" : "B0310.2-ENCFF945LXL-LinearBasicDisplay"
- }
- ],
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF945LXL/@@download/ENCFF945LXL.bigBed",
- "locationType" : "UriLocation"
+ "displayId" : "irx-1-ENCFF545QMO-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- },
- "type" : "FeatureTrack",
- "name" : "B0310.2",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for B0310.2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF945LXL/ and for more information on this B0310.2 experiment, see https://www.encodeproject.org/experiments/ENCSR806JUF/."
+ ]
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-85 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF976HPP/ and for more information on this nhr-85 experiment, see https://www.encodeproject.org/experiments/ENCSR107BQR/.",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF976HPP/@@download/ENCFF976HPP.bigBed",
- "locationType" : "UriLocation"
- }
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF174GXE/@@download/ENCFF174GXE.bigBed"
+ },
+ "type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "name" : "nhr-85",
"displays" : [
{
"renderer" : {
"color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "nhr-85-ENCFF976HPP-LinearBasicDisplay"
+ "displayId" : "nfya-1-ENCFF174GXE-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nfya-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF174GXE/ and for more information on this nfya-1 experiment, see https://www.encodeproject.org/experiments/ENCSR581THE/.",
+ "trackId" : "c_elegans_PRJNA13758_nfya-1-ENCFF174GXE",
+ "name" : "nfya-1",
"category" : [
"modERN",
- "L1 larva"
+ "young adult"
],
- "trackId" : "c_elegans_PRJNA13758_nhr-85-ENCFF976HPP"
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack"
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for gmeb-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF824NMH/ and for more information on this gmeb-2 experiment, see https://www.encodeproject.org/experiments/ENCSR057TFD/.",
- "name" : "gmeb-2",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF824NMH/@@download/ENCFF824NMH.bigBed"
- },
- "type" : "BigBedAdapter"
+ "uri" : "https://www.encodeproject.org/files/ENCFF506QZK/@@download/ENCFF506QZK.bigBed",
+ "locationType" : "UriLocation"
+ }
},
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"color1" : "blue",
+ "height" : 6,
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "gmeb-2-ENCFF824NMH-LinearBasicDisplay"
+ "displayId" : "F55B11.4-ENCFF506QZK-LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_gmeb-2-ENCFF824NMH",
+ "name" : "F55B11.4",
+ "trackId" : "c_elegans_PRJNA13758_F55B11.4-ENCFF506QZK",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F55B11.4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF506QZK/ and for more information on this F55B11.4 experiment, see https://www.encodeproject.org/experiments/ENCSR698RXJ/.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"modERN",
- "late embryonic"
+ "young adult"
]
},
{
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF786EDH/@@download/ENCFF786EDH.bigBed"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "zip-5",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for zip-5 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF786EDH/ and for more information on this zip-5 experiment, see https://www.encodeproject.org/experiments/ENCSR686FKU/.",
"category" : [
"modERN",
- "late embryonic"
+ "L1 larva"
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_zip-5-ENCFF786EDH",
+ "type" : "FeatureTrack",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for fkh-8 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF538UTT/ and for more information on this fkh-8 experiment, see https://www.encodeproject.org/experiments/ENCSR435RXY/.",
+ "trackId" : "c_elegans_PRJNA13758_fkh-8-ENCFF538UTT",
+ "name" : "fkh-8",
"displays" : [
{
+ "displayId" : "fkh-8-ENCFF538UTT-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "zip-5-ENCFF786EDH-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
- ]
- },
- {
- "type" : "FeatureTrack",
+ ],
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF725IHQ/@@download/ENCFF725IHQ.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF538UTT/@@download/ENCFF538UTT.bigBed",
"locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
- },
- "name" : "npax-4",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for npax-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF725IHQ/ and for more information on this npax-4 experiment, see https://www.encodeproject.org/experiments/ENCSR980XNE/.",
+ }
+ },
+ {
+ "trackId" : "c_elegans_PRJNA13758_fkh-3-ENCFF139YOY",
+ "name" : "fkh-3",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for fkh-3 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF139YOY/ and for more information on this fkh-3 experiment, see https://www.encodeproject.org/experiments/ENCSR717JMX/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
- "late embryonic"
+ "young adult"
],
- "trackId" : "c_elegans_PRJNA13758_npax-4-ENCFF725IHQ",
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF139YOY/@@download/ENCFF139YOY.bigBed",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "fkh-3-ENCFF139YOY-LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 6,
- "color1" : "blue",
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "npax-4-ENCFF725IHQ-LinearBasicDisplay"
+ "color1" : "blue"
+ }
}
]
},
{
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "modERN",
+ "L3 larva"
+ ],
+ "trackId" : "c_elegans_PRJNA13758_lsy-12-ENCFF238OZR",
+ "name" : "lsy-12",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for lsy-12 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF238OZR/ and for more information on this lsy-12 experiment, see https://www.encodeproject.org/experiments/ENCSR272KZJ/.",
"displays" : [
{
- "displayId" : "B0261.1-ENCFF158IBD-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
- "height" : 6
+ "height" : 6,
+ "color1" : "blue"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "lsy-12-ENCFF238OZR-LinearBasicDisplay"
}
],
- "category" : [
- "modERN",
- "young adult"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_B0261.1-ENCFF158IBD",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for B0261.1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF158IBD/ and for more information on this B0261.1 experiment, see https://www.encodeproject.org/experiments/ENCSR316ASH/.",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF158IBD/@@download/ENCFF158IBD.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF238OZR/@@download/ENCFF238OZR.bigBed"
}
- },
- "type" : "FeatureTrack",
- "name" : "B0261.1"
+ }
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for che-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF482GOQ/ and for more information on this che-1 experiment, see https://www.encodeproject.org/experiments/ENCSR598GFQ/.",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "cog-1-ENCFF859IPZ-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "blue",
+ "height" : 6
+ }
+ }
+ ],
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF482GOQ/@@download/ENCFF482GOQ.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF859IPZ/@@download/ENCFF859IPZ.bigBed",
"locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ }
},
"type" : "FeatureTrack",
- "name" : "che-1",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modERN",
+ "midembryonic"
+ ],
+ "name" : "cog-1",
+ "trackId" : "c_elegans_PRJNA13758_cog-1-ENCFF859IPZ",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for cog-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF859IPZ/ and for more information on this cog-1 experiment, see https://www.encodeproject.org/experiments/ENCSR422XRE/."
+ },
+ {
"displays" : [
{
"renderer" : {
- "height" : 6,
"type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "che-1-ENCFF482GOQ-LinearBasicDisplay"
+ "displayId" : "mls-2-ENCFF573LMJ-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF573LMJ/@@download/ENCFF573LMJ.bigBed"
+ },
+ "type" : "BigBedAdapter"
+ },
+ "category" : [
+ "modERN",
+ "mixed stage (embryonic)"
+ ],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for mls-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF573LMJ/ and for more information on this mls-2 experiment, see https://www.encodeproject.org/experiments/ENCSR668BTV/.",
+ "trackId" : "c_elegans_PRJNA13758_mls-2-ENCFF573LMJ",
+ "name" : "mls-2"
+ },
+ {
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for tbx-9 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF755JFG/ and for more information on this tbx-9 experiment, see https://www.encodeproject.org/experiments/ENCSR819NBT/.",
+ "name" : "tbx-9",
+ "trackId" : "c_elegans_PRJNA13758_tbx-9-ENCFF755JFG",
"category" : [
"modERN",
- "late embryonic"
+ "young adult"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_che-1-ENCFF482GOQ"
- },
- {
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for sdz-38 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF052YIV/ and for more information on this sdz-38 experiment, see https://www.encodeproject.org/experiments/ENCSR505TSF/.",
- "name" : "sdz-38",
"adapter" : {
+ "type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF052YIV/@@download/ENCFF052YIV.bigBed",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF755JFG/@@download/ENCFF755JFG.bigBed"
+ }
},
- "type" : "FeatureTrack",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "tbx-9-ENCFF755JFG-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"color1" : "blue",
+ "height" : 6,
"type" : "SvgFeatureRenderer"
},
- "displayId" : "sdz-38-ENCFF052YIV-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
- ],
- "trackId" : "c_elegans_PRJNA13758_sdz-38-ENCFF052YIV",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "young adult"
]
},
{
- "name" : "hnd-1",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "height" : 6,
+ "color1" : "blue"
+ },
+ "displayId" : "Y22D7AL.16-ENCFF329QXX-LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF967ZEP/@@download/ENCFF967ZEP.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF329QXX/@@download/ENCFF329QXX.bigBed",
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hnd-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF967ZEP/ and for more information on this hnd-1 experiment, see https://www.encodeproject.org/experiments/ENCSR374HBD/.",
- "trackId" : "c_elegans_PRJNA13758_hnd-1-ENCFF967ZEP",
+ "category" : [
+ "modERN",
+ "late embryonic"
+ ],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for Y22D7AL.16 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF329QXX/ and for more information on this Y22D7AL.16 experiment, see https://www.encodeproject.org/experiments/ENCSR643BKM/.",
+ "trackId" : "c_elegans_PRJNA13758_Y22D7AL.16-ENCFF329QXX",
+ "name" : "Y22D7AL.16"
+ },
+ {
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for B0310.2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF945LXL/ and for more information on this B0310.2 experiment, see https://www.encodeproject.org/experiments/ENCSR806JUF/.",
+ "trackId" : "c_elegans_PRJNA13758_B0310.2-ENCFF945LXL",
+ "name" : "B0310.2",
"category" : [
"modERN",
"early embryonic"
],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF945LXL/@@download/ENCFF945LXL.bigBed"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "blue",
- "type" : "SvgFeatureRenderer",
- "height" : 6
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "hnd-1-ENCFF967ZEP-LinearBasicDisplay"
+ "displayId" : "B0310.2-ENCFF945LXL-LinearBasicDisplay"
}
]
},
{
- "type" : "FeatureTrack",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF226OII/@@download/ENCFF226OII.bigBed",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF976HPP/@@download/ENCFF976HPP.bigBed"
}
},
- "name" : "mel-28",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for mel-28 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF226OII/ and for more information on this mel-28 experiment, see https://www.encodeproject.org/experiments/ENCSR518VJU/.",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "young adult"
- ],
- "trackId" : "c_elegans_PRJNA13758_mel-28-ENCFF226OII",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "color1" : "blue",
- "height" : 6
+ "height" : 6,
+ "color1" : "blue"
},
- "displayId" : "mel-28-ENCFF226OII-LinearBasicDisplay"
+ "displayId" : "nhr-85-ENCFF976HPP-LinearBasicDisplay"
}
+ ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for nhr-85 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF976HPP/ and for more information on this nhr-85 experiment, see https://www.encodeproject.org/experiments/ENCSR107BQR/.",
+ "name" : "nhr-85",
+ "trackId" : "c_elegans_PRJNA13758_nhr-85-ENCFF976HPP",
+ "category" : [
+ "modERN",
+ "L1 larva"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
]
},
{
+ "name" : "gmeb-2",
+ "trackId" : "c_elegans_PRJNA13758_gmeb-2-ENCFF824NMH",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for gmeb-2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF824NMH/ and for more information on this gmeb-2 experiment, see https://www.encodeproject.org/experiments/ENCSR057TFD/.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"modERN",
- "L4_young adult"
+ "late embryonic"
],
- "trackId" : "c_elegans_PRJNA13758_him-1-ENCFF253FRD",
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF824NMH/@@download/ENCFF824NMH.bigBed",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
+ "displayId" : "gmeb-2-ENCFF824NMH-LinearBasicDisplay",
"renderer" : {
+ "color1" : "blue",
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "him-1-ENCFF253FRD-LinearBasicDisplay"
- }
- ],
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF253FRD/@@download/ENCFF253FRD.bigBed"
+ "type" : "LinearBasicDisplay"
}
- },
- "name" : "him-1",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for him-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF253FRD/ and for more information on this him-1 experiment, see https://www.encodeproject.org/experiments/ENCSR607BSL/."
+ ]
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for snu-23 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF877FHQ/ and for more information on this snu-23 experiment, see https://www.encodeproject.org/experiments/ENCSR320MVY/.",
+ "name" : "zip-5",
+ "trackId" : "c_elegans_PRJNA13758_zip-5-ENCFF786EDH",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for zip-5 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF786EDH/ and for more information on this zip-5 experiment, see https://www.encodeproject.org/experiments/ENCSR686FKU/.",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modERN",
+ "late embryonic"
+ ],
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF877FHQ/@@download/ENCFF877FHQ.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF786EDH/@@download/ENCFF786EDH.bigBed",
"locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
- "name" : "snu-23",
"displays" : [
{
"renderer" : {
- "height" : 6,
"color1" : "blue",
+ "height" : 6,
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "snu-23-ENCFF877FHQ-LinearBasicDisplay"
+ "displayId" : "zip-5-ENCFF786EDH-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "L1 larva"
- ],
- "trackId" : "c_elegans_PRJNA13758_snu-23-ENCFF877FHQ"
+ ]
},
{
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for npax-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF725IHQ/ and for more information on this npax-4 experiment, see https://www.encodeproject.org/experiments/ENCSR980XNE/.",
+ "trackId" : "c_elegans_PRJNA13758_npax-4-ENCFF725IHQ",
+ "name" : "npax-4",
+ "category" : [
+ "modERN",
+ "late embryonic"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF725IHQ/@@download/ENCFF725IHQ.bigBed"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
- "displayId" : "dao-5-ENCFF034WER-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "npax-4-ENCFF725IHQ-LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
+ "color1" : "blue",
"height" : 6
}
}
+ ]
+ },
+ {
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "blue",
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "B0261.1-ENCFF158IBD-LinearBasicDisplay"
+ }
],
- "trackId" : "c_elegans_PRJNA13758_dao-5-ENCFF034WER",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "L4_young adult"
- ],
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for dao-5 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF034WER/ and for more information on this dao-5 experiment, see https://www.encodeproject.org/experiments/ENCSR213XFQ/.",
- "name" : "dao-5",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF034WER/@@download/ENCFF034WER.bigBed",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF158IBD/@@download/ENCFF158IBD.bigBed"
}
},
- "type" : "FeatureTrack"
+ "category" : [
+ "modERN",
+ "young adult"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for B0261.1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF158IBD/ and for more information on this B0261.1 experiment, see https://www.encodeproject.org/experiments/ENCSR316ASH/.",
+ "name" : "B0261.1",
+ "trackId" : "c_elegans_PRJNA13758_B0261.1-ENCFF158IBD"
},
{
+ "category" : [
+ "modERN",
+ "late embryonic"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for che-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF482GOQ/ and for more information on this che-1 experiment, see https://www.encodeproject.org/experiments/ENCSR598GFQ/.",
+ "trackId" : "c_elegans_PRJNA13758_che-1-ENCFF482GOQ",
+ "name" : "che-1",
"displays" : [
{
+ "displayId" : "che-1-ENCFF482GOQ-LinearBasicDisplay",
"renderer" : {
"height" : 6,
"color1" : "blue",
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "ceh-24-ENCFF773RLK-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_ceh-24-ENCFF773RLK",
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF482GOQ/@@download/ENCFF482GOQ.bigBed"
+ },
+ "type" : "BigBedAdapter"
+ }
+ },
+ {
"category" : [
"modERN",
- "late embryonic"
+ "young adult"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-24 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF773RLK/ and for more information on this ceh-24 experiment, see https://www.encodeproject.org/experiments/ENCSR282OTW/.",
- "name" : "ceh-24",
- "type" : "FeatureTrack",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for sdz-38 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF052YIV/ and for more information on this sdz-38 experiment, see https://www.encodeproject.org/experiments/ENCSR505TSF/.",
+ "name" : "sdz-38",
+ "trackId" : "c_elegans_PRJNA13758_sdz-38-ENCFF052YIV",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "sdz-38-ENCFF052YIV-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "height" : 6,
+ "color1" : "blue"
+ }
+ }
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF773RLK/@@download/ENCFF773RLK.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF052YIV/@@download/ENCFF052YIV.bigBed"
}
}
},
{
"category" : [
"modERN",
- "young adult"
+ "early embryonic"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_chd-7-ENCFF814XNV",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hnd-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF967ZEP/ and for more information on this hnd-1 experiment, see https://www.encodeproject.org/experiments/ENCSR374HBD/.",
+ "name" : "hnd-1",
+ "trackId" : "c_elegans_PRJNA13758_hnd-1-ENCFF967ZEP",
"displays" : [
{
- "displayId" : "chd-7-ENCFF814XNV-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue"
},
+ "displayId" : "hnd-1-ENCFF967ZEP-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF814XNV/@@download/ENCFF814XNV.bigBed",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF967ZEP/@@download/ENCFF967ZEP.bigBed"
},
"type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "chd-7",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for chd-7 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF814XNV/ and for more information on this chd-7 experiment, see https://www.encodeproject.org/experiments/ENCSR010MNU/."
+ }
},
{
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF226OII/@@download/ENCFF226OII.bigBed"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
- "displayId" : "mes-4-ENCFF048AAE-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
+ "displayId" : "mel-28-ENCFF226OII-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue"
- },
- "type" : "LinearBasicDisplay"
+ }
}
],
- "trackId" : "c_elegans_PRJNA13758_mes-4-ENCFF048AAE",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for mel-28 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF226OII/ and for more information on this mel-28 experiment, see https://www.encodeproject.org/experiments/ENCSR518VJU/.",
+ "name" : "mel-28",
+ "trackId" : "c_elegans_PRJNA13758_mel-28-ENCFF226OII",
"category" : [
"modERN",
"young adult"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
- ],
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for mes-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF048AAE/ and for more information on this mes-4 experiment, see https://www.encodeproject.org/experiments/ENCSR665UXV/.",
- "name" : "mes-4",
- "adapter" : {
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF048AAE/@@download/ENCFF048AAE.bigBed"
- },
- "type" : "BigBedAdapter"
- },
- "type" : "FeatureTrack"
+ ]
},
{
- "name" : "C08G9.2",
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF215SBJ/@@download/ENCFF215SBJ.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF253FRD/@@download/ENCFF253FRD.bigBed",
+ "locationType" : "UriLocation"
}
},
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "blue",
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "him-1-ENCFF253FRD-LinearBasicDisplay"
+ }
+ ],
+ "name" : "him-1",
+ "trackId" : "c_elegans_PRJNA13758_him-1-ENCFF253FRD",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for him-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF253FRD/ and for more information on this him-1 experiment, see https://www.encodeproject.org/experiments/ENCSR607BSL/.",
"type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for C08G9.2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF215SBJ/ and for more information on this C08G9.2 experiment, see https://www.encodeproject.org/experiments/ENCSR101QFW/.",
- "trackId" : "c_elegans_PRJNA13758_C08G9.2-ENCFF215SBJ",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"modERN",
- "late embryonic"
+ "L4_young adult"
+ ]
+ },
+ {
+ "category" : [
+ "modERN",
+ "L1 larva"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for snu-23 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF877FHQ/ and for more information on this snu-23 experiment, see https://www.encodeproject.org/experiments/ENCSR320MVY/.",
+ "name" : "snu-23",
+ "trackId" : "c_elegans_PRJNA13758_snu-23-ENCFF877FHQ",
"displays" : [
{
- "displayId" : "C08G9.2-ENCFF215SBJ-LinearBasicDisplay",
+ "displayId" : "snu-23-ENCFF877FHQ-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue"
},
"type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF877FHQ/@@download/ENCFF877FHQ.bigBed",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ }
},
{
- "trackId" : "c_elegans_PRJNA13758_ceh-36-ENCFF524NXN",
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF034WER/@@download/ENCFF034WER.bigBed"
+ },
+ "type" : "BigBedAdapter"
+ },
+ "displays" : [
+ {
+ "renderer" : {
+ "color1" : "blue",
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "dao-5-ENCFF034WER-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
+ "trackId" : "c_elegans_PRJNA13758_dao-5-ENCFF034WER",
+ "name" : "dao-5",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for dao-5 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF034WER/ and for more information on this dao-5 experiment, see https://www.encodeproject.org/experiments/ENCSR213XFQ/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
- "early embryonic"
- ],
+ "L4_young adult"
+ ]
+ },
+ {
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "ceh-24-ENCFF773RLK-LinearBasicDisplay",
"renderer" : {
- "color1" : "blue",
"type" : "SvgFeatureRenderer",
+ "color1" : "blue",
"height" : 6
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "ceh-36-ENCFF524NXN-LinearBasicDisplay"
+ }
}
],
- "name" : "ceh-36",
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF524NXN/@@download/ENCFF524NXN.bigBed"
- }
+ "uri" : "https://www.encodeproject.org/files/ENCFF773RLK/@@download/ENCFF773RLK.bigBed"
+ },
+ "type" : "BigBedAdapter"
},
"type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-36 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF524NXN/ and for more information on this ceh-36 experiment, see https://www.encodeproject.org/experiments/ENCSR002FCO/."
- },
- {
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "category" : [
+ "modERN",
+ "late embryonic"
+ ],
+ "name" : "ceh-24",
+ "trackId" : "c_elegans_PRJNA13758_ceh-24-ENCFF773RLK",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-24 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF773RLK/ and for more information on this ceh-24 experiment, see https://www.encodeproject.org/experiments/ENCSR282OTW/."
+ },
+ {
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for chd-7 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF814XNV/ and for more information on this chd-7 experiment, see https://www.encodeproject.org/experiments/ENCSR010MNU/.",
+ "name" : "chd-7",
+ "trackId" : "c_elegans_PRJNA13758_chd-7-ENCFF814XNV",
"category" : [
"modERN",
"young adult"
],
- "trackId" : "c_elegans_PRJNA13758_hlh-12-ENCFF845OMA",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF814XNV/@@download/ENCFF814XNV.bigBed",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"color1" : "blue",
"height" : 6
},
- "displayId" : "hlh-12-ENCFF845OMA-LinearBasicDisplay"
- }
- ],
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF845OMA/@@download/ENCFF845OMA.bigBed"
+ "displayId" : "chd-7-ENCFF814XNV-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- },
- "name" : "hlh-12",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hlh-12 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF845OMA/ and for more information on this hlh-12 experiment, see https://www.encodeproject.org/experiments/ENCSR292NVQ/."
+ ]
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "mixed stage (embryonic)"
- ],
- "trackId" : "c_elegans_PRJNA13758_unc-120-ENCFF370PQI",
"displays" : [
{
- "displayId" : "unc-120-ENCFF370PQI-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"color1" : "blue",
+ "height" : 6,
"type" : "SvgFeatureRenderer"
- }
+ },
+ "displayId" : "mes-4-ENCFF048AAE-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF370PQI/@@download/ENCFF370PQI.bigBed"
- }
+ "uri" : "https://www.encodeproject.org/files/ENCFF048AAE/@@download/ENCFF048AAE.bigBed",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
},
+ "category" : [
+ "modERN",
+ "young adult"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
- "name" : "unc-120",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for unc-120 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF370PQI/ and for more information on this unc-120 experiment, see https://www.encodeproject.org/experiments/ENCSR456GSL/."
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for mes-4 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF048AAE/ and for more information on this mes-4 experiment, see https://www.encodeproject.org/experiments/ENCSR665UXV/.",
+ "trackId" : "c_elegans_PRJNA13758_mes-4-ENCFF048AAE",
+ "name" : "mes-4"
},
{
+ "name" : "C08G9.2",
+ "trackId" : "c_elegans_PRJNA13758_C08G9.2-ENCFF215SBJ",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for C08G9.2 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF215SBJ/ and for more information on this C08G9.2 experiment, see https://www.encodeproject.org/experiments/ENCSR101QFW/.",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "modERN",
+ "late embryonic"
+ ],
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF558HLP/@@download/ENCFF558HLP.bigBed"
- }
+ "uri" : "https://www.encodeproject.org/files/ENCFF215SBJ/@@download/ENCFF215SBJ.bigBed"
+ },
+ "type" : "BigBedAdapter"
},
- "name" : "hmbx-1",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hmbx-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF558HLP/ and for more information on this hmbx-1 experiment, see https://www.encodeproject.org/experiments/ENCSR889PUP/.",
- "category" : [
- "modERN",
- "early embryonic"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_hmbx-1-ENCFF558HLP",
"displays" : [
{
- "displayId" : "hmbx-1-ENCFF558HLP-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
+ "displayId" : "C08G9.2-ENCFF215SBJ-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
+ "type" : "SvgFeatureRenderer",
"color1" : "blue",
- "type" : "SvgFeatureRenderer"
- }
+ "height" : 6
+ },
+ "type" : "LinearBasicDisplay"
}
]
},
{
- "name" : "pop-1",
+ "trackId" : "c_elegans_PRJNA13758_ceh-36-ENCFF524NXN",
+ "name" : "ceh-36",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-36 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF524NXN/ and for more information on this ceh-36 experiment, see https://www.encodeproject.org/experiments/ENCSR002FCO/.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "modERN",
+ "early embryonic"
+ ],
"adapter" : {
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF939TKO/@@download/ENCFF939TKO.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF524NXN/@@download/ENCFF524NXN.bigBed"
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for pop-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF939TKO/ and for more information on this pop-1 experiment, see https://www.encodeproject.org/experiments/ENCSR880RBB/.",
- "trackId" : "c_elegans_PRJNA13758_pop-1-ENCFF939TKO",
- "category" : [
- "modERN",
- "early embryonic"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
- "displayId" : "pop-1-ENCFF939TKO-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
+ "displayId" : "ceh-36-ENCFF524NXN-LinearBasicDisplay",
"renderer" : {
+ "color1" : "blue",
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
}
]
},
{
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-48 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF784CKU/ and for more information on this ceh-48 experiment, see https://www.encodeproject.org/experiments/ENCSR844VCY/.",
- "name" : "ceh-48",
"adapter" : {
"bigBedLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF784CKU/@@download/ENCFF784CKU.bigBed"
+ "uri" : "https://www.encodeproject.org/files/ENCFF845OMA/@@download/ENCFF845OMA.bigBed",
+ "locationType" : "UriLocation"
},
"type" : "BigBedAdapter"
},
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "ceh-48-ENCFF784CKU-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "hlh-12-ENCFF845OMA-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue"
}
}
],
- "trackId" : "c_elegans_PRJNA13758_ceh-48-ENCFF784CKU",
+ "trackId" : "c_elegans_PRJNA13758_hlh-12-ENCFF845OMA",
+ "name" : "hlh-12",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hlh-12 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF845OMA/ and for more information on this hlh-12 experiment, see https://www.encodeproject.org/experiments/ENCSR292NVQ/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"modERN",
- "late embryonic"
+ "young adult"
]
},
{
- "name" : "ceh-9",
- "type" : "FeatureTrack",
- "adapter" : {
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF590HHF/@@download/ENCFF590HHF.bigBed",
- "locationType" : "UriLocation"
- },
- "type" : "BigBedAdapter"
- },
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-9 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF590HHF/ and for more information on this ceh-9 experiment, see https://www.encodeproject.org/experiments/ENCSR432MSI/.",
- "trackId" : "c_elegans_PRJNA13758_ceh-9-ENCFF590HHF",
"category" : [
"modERN",
- "late embryonic"
+ "mixed stage (embryonic)"
],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for unc-120 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF370PQI/ and for more information on this unc-120 experiment, see https://www.encodeproject.org/experiments/ENCSR456GSL/.",
+ "trackId" : "c_elegans_PRJNA13758_unc-120-ENCFF370PQI",
+ "name" : "unc-120",
"displays" : [
{
- "displayId" : "ceh-9-ENCFF590HHF-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
+ "height" : 6,
"color1" : "blue",
- "height" : 6
+ "type" : "SvgFeatureRenderer"
},
+ "displayId" : "unc-120-ENCFF370PQI-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
- ]
- },
- {
+ ],
"adapter" : {
- "type" : "BigBedAdapter",
"bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://www.encodeproject.org/files/ENCFF928KWT/@@download/ENCFF928KWT.bigBed"
- }
- },
+ "uri" : "https://www.encodeproject.org/files/ENCFF370PQI/@@download/ENCFF370PQI.bigBed"
+ },
+ "type" : "BigBedAdapter"
+ }
+ },
+ {
+ "name" : "hmbx-1",
+ "trackId" : "c_elegans_PRJNA13758_hmbx-1-ENCFF558HLP",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for hmbx-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF558HLP/ and for more information on this hmbx-1 experiment, see https://www.encodeproject.org/experiments/ENCSR889PUP/.",
"type" : "FeatureTrack",
- "name" : "T26A5.8",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for T26A5.8 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF928KWT/ and for more information on this T26A5.8 experiment, see https://www.encodeproject.org/experiments/ENCSR537QPX/.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
"modERN",
- "young adult"
+ "early embryonic"
],
- "trackId" : "c_elegans_PRJNA13758_T26A5.8-ENCFF928KWT",
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF558HLP/@@download/ENCFF558HLP.bigBed",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 6,
- "color1" : "blue",
- "type" : "SvgFeatureRenderer"
+ "color1" : "blue"
},
- "displayId" : "T26A5.8-ENCFF928KWT-LinearBasicDisplay"
+ "displayId" : "hmbx-1-ENCFF558HLP-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
]
},
{
- "trackId" : "c_elegans_PRJNA13758_him-1-ENCFF007GWU",
- "category" : [
- "modERN",
- "young adult"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF939TKO/@@download/ENCFF939TKO.bigBed",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigBedAdapter"
+ },
"displays" : [
{
- "displayId" : "him-1-ENCFF007GWU-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
+ "color1" : "blue",
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "blue"
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "pop-1-ENCFF939TKO-LinearBasicDisplay"
}
],
- "name" : "him-1",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF007GWU/@@download/ENCFF007GWU.bigBed",
- "locationType" : "UriLocation"
- }
- },
+ "trackId" : "c_elegans_PRJNA13758_pop-1-ENCFF939TKO",
+ "name" : "pop-1",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for pop-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF939TKO/ and for more information on this pop-1 experiment, see https://www.encodeproject.org/experiments/ENCSR880RBB/.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for him-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF007GWU/ and for more information on this him-1 experiment, see https://www.encodeproject.org/experiments/ENCSR110CKX/."
+ "category" : [
+ "modERN",
+ "early embryonic"
+ ]
},
{
- "name" : "F52B5.7",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-48 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF784CKU/ and for more information on this ceh-48 experiment, see https://www.encodeproject.org/experiments/ENCSR844VCY/.",
+ "name" : "ceh-48",
+ "trackId" : "c_elegans_PRJNA13758_ceh-48-ENCFF784CKU",
+ "category" : [
+ "modERN",
+ "late embryonic"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
"type" : "BigBedAdapter",
"bigBedLocation" : {
- "uri" : "https://www.encodeproject.org/files/ENCFF613YIZ/@@download/ENCFF613YIZ.bigBed",
+ "uri" : "https://www.encodeproject.org/files/ENCFF784CKU/@@download/ENCFF784CKU.bigBed",
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F52B5.7 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF613YIZ/ and for more information on this F52B5.7 experiment, see https://www.encodeproject.org/experiments/ENCSR323LIQ/.",
- "trackId" : "c_elegans_PRJNA13758_F52B5.7-ENCFF613YIZ",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "modERN",
- "young adult"
- ],
"displays" : [
{
"renderer" : {
- "type" : "SvgFeatureRenderer",
"color1" : "blue",
- "height" : 6
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "F52B5.7-ENCFF613YIZ-LinearBasicDisplay"
+ "displayId" : "ceh-48-ENCFF784CKU-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
]
},
{
- "description" : "These are operons published by Blumenthal et al, Nature 417: 851-854 (2002).",
- "name" : "Operons",
+ "category" : [
+ "modERN",
+ "late embryonic"
+ ],
"type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Operons/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for ceh-9 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF590HHF/ and for more information on this ceh-9 experiment, see https://www.encodeproject.org/experiments/ENCSR432MSI/.",
+ "name" : "ceh-9",
+ "trackId" : "c_elegans_PRJNA13758_ceh-9-ENCFF590HHF",
+ "displays" : [
+ {
+ "displayId" : "ceh-9-ENCFF590HHF-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "height" : 6,
+ "color1" : "blue"
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ],
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF590HHF/@@download/ENCFF590HHF.bigBed"
+ },
+ "type" : "BigBedAdapter"
+ }
+ },
+ {
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for T26A5.8 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF928KWT/ and for more information on this T26A5.8 experiment, see https://www.encodeproject.org/experiments/ENCSR537QPX/.",
+ "trackId" : "c_elegans_PRJNA13758_T26A5.8-ENCFF928KWT",
+ "name" : "T26A5.8",
+ "category" : [
+ "modERN",
+ "young adult"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF928KWT/@@download/ENCFF928KWT.bigBed"
+ }
+ },
"displays" : [
{
- "displayId" : "operons-c_elegans_PRJNA13758-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "T26A5.8-ENCFF928KWT-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "color1" : "green"
+ "height" : 6,
+ "color1" : "blue"
}
}
- ],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ ]
+ },
+ {
+ "adapter" : {
+ "bigBedLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://www.encodeproject.org/files/ENCFF007GWU/@@download/ENCFF007GWU.bigBed"
+ },
+ "type" : "BigBedAdapter"
},
- "trackId" : "c_elegans_PRJNA13758_operons",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "him-1-ENCFF007GWU-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "height" : 6,
+ "color1" : "blue"
+ }
+ }
+ ],
+ "name" : "him-1",
+ "trackId" : "c_elegans_PRJNA13758_him-1-ENCFF007GWU",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for him-1 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF007GWU/ and for more information on this him-1 experiment, see https://www.encodeproject.org/experiments/ENCSR110CKX/.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
- "Genes",
- "Curated Genes"
+ "modERN",
+ "young adult"
]
},
{
+ "trackId" : "c_elegans_PRJNA13758_F52B5.7-ENCFF613YIZ",
+ "name" : "F52B5.7",
+ "description" : "Data from the modERN project hosted at the https://www.encodeproject.org/. Data for F52B5.7 was generated at the Kevin White, UChicago lab. For more information on the data specifically for this track, see https://www.encodeproject.org/files/ENCFF613YIZ/ and for more information on this F52B5.7 experiment, see https://www.encodeproject.org/experiments/ENCSR323LIQ/.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "modERN",
+ "young adult"
+ ],
+ "adapter" : {
+ "type" : "BigBedAdapter",
+ "bigBedLocation" : {
+ "uri" : "https://www.encodeproject.org/files/ENCFF613YIZ/@@download/ENCFF613YIZ.bigBed",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "displayId" : "TTCN_sequence_search_c_elegans_PRJNA13758-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
+ "displayId" : "F52B5.7-ENCFF613YIZ-LinearBasicDisplay",
"renderer" : {
- "color1" : "SlateBlue",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "height" : 4,
- "showDescriptions" : false
- }
+ "color1" : "blue",
+ "height" : 6
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ]
+ },
+ {
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
+ "displays" : [
+ {
+ "renderer" : {
+ "color1" : "green",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "operons-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/Operons/{refseq}/trackData.jsonz"
+ }
+ },
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
+ "trackId" : "c_elegans_PRJNA13758_operons",
+ "name" : "Operons",
+ "description" : "These are operons published by Blumenthal et al, Nature 417: 851-854 (2002)."
+ },
+ {
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
+ "trackId" : "c_elegans_PRJNA13758_TTCN_sequence_search",
+ "name" : "Cas12e TTCN PAM sites",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "trackId" : "c_elegans_PRJNA13758_TTCN_sequence_search",
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "FeatureTrack",
"adapter" : {
"type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
"type" : "BgzipFastaAdapter",
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA13758.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
- },
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA13758.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
- },
"gziLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA13758.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
+ },
+ "faiLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA13758.WS284.genomic.fa.gz.fai"
+ },
+ "fastaLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA13758.WS284.genomic.fa.gz"
}
},
"search" : "TTC."
},
- "type" : "FeatureTrack",
- "name" : "Cas12e TTCN PAM sites"
+ "displays" : [
+ {
+ "displayId" : "TTCN_sequence_search_c_elegans_PRJNA13758-LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "SlateBlue",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
+ "name" : "Cas12a TTN PAM sites",
"trackId" : "c_elegans_PRJNA13758_TTN_sequence_search",
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
@@ -44037,73 +43431,71 @@
"Externally Sourced Resources",
"CRISPR predictions"
],
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "Indigo",
- "showDescriptions" : false,
- "height" : 4
- },
- "displayId" : "TTN_sequence_search_c_elegans_PRJNA13758-LinearBasicDisplay"
- }
- ],
- "name" : "Cas12a TTN PAM sites",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
"gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA13758.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA13758.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
},
+ "type" : "BgzipFastaAdapter",
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA13758.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
"fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA13758.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA13758.WS284.genomic.fa.gz"
}
},
+ "type" : "SequenceSearchAdapter",
"search" : "TT."
},
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time."
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
+ "height" : 4,
+ "showLabels" : false,
+ "color1" : "Indigo"
+ },
+ "displayId" : "TTN_sequence_search_c_elegans_PRJNA13758-LinearBasicDisplay"
+ }
+ ]
},
{
- "trackId" : "c_elegans_PRJNA13758_NNGRRT_sequence_search",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "FeatureTrack",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
+ "trackId" : "c_elegans_PRJNA13758_NNGRRT_sequence_search",
+ "name" : "SaCas9 NNGRRT PAM sites",
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "NNGRRT_sequence_search_c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "DarkViolet",
"showDescriptions" : false,
"height" : 4,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "DarkViolet"
+ "showLabels" : false
},
- "displayId" : "NNGRRT_sequence_search_c_elegans_PRJNA13758-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "name" : "SaCas9 NNGRRT PAM sites",
"adapter" : {
- "type" : "SequenceSearchAdapter",
- "search" : "..G[AG][AG]T",
"sequenceAdapter" : {
"gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA13758.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA13758.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
},
+ "type" : "BgzipFastaAdapter",
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA13758.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
@@ -44111,450 +43503,346 @@
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA13758.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
- },
- "type" : "BgzipFastaAdapter"
- }
- },
- "type" : "FeatureTrack",
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time."
+ }
+ },
+ "type" : "SequenceSearchAdapter",
+ "search" : "..G[AG][AG]T"
+ }
},
{
"description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
+ "name" : "SpCas9 NGG PAM sites",
+ "trackId" : "c_elegans_PRJNA13758_NGG_sequence_search",
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"adapter" : {
+ "search" : ".GG",
"type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
"fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA13758.WS284.genomic.fa.gz"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA13758.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
},
"faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA13758.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA13758.WS284.genomic.fa.gz.fai"
},
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA13758.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
}
- },
- "search" : ".GG"
+ }
},
- "type" : "FeatureTrack",
- "name" : "SpCas9 NGG PAM sites",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "NGG_sequence_search_c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
+ "color1" : "RebeccaPurple",
+ "showLabels" : false,
"showDescriptions" : false,
"height" : 4,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "RebeccaPurple"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "NGG_sequence_search_c_elegans_PRJNA13758-LinearBasicDisplay"
+ "type" : "SvgFeatureRenderer"
+ }
}
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "trackId" : "c_elegans_PRJNA13758_NGG_sequence_search"
+ ]
},
{
- "trackId" : "c_elegans_PRJNA13758_polya_clusters_plus_strand",
- "category" : [
- "Externally Sourced Resources",
- "Atlas"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"displays" : [
{
- "displayId" : "polya_clusters_plus_strand-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"color1" : "purple"
},
+ "displayId" : "polya_clusters_plus_strand-c_elegans_PRJNA13758-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
- "name" : "polyA clusters plus strand",
- "type" : "FeatureTrack",
"adapter" : {
"bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/jbrowse/data/c_elegans/tracks/atlas_plus.2.0.ce11.bb",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/jbrowse/data/c_elegans/tracks/atlas_plus.2.0.ce11.bb"
},
"type" : "BigBedAdapter"
},
- "description" : "https://polyasite.unibas.ch/atlas - Clusters of polyA sites using a bespoke clustering procedure which groups together closely-spaced poly(A) sites, that most likely are due to imprecision in cleavage or processing. Construction of the clusters was broadened to include sites with lower read support that were located from -12 to +12 nucleotides around sites with strong support. In another pass, sites that were located within 25 nucleotides of each other were clustered together, and finally, for clusters with no annotated poly(A) signals a more permissive distance of 50 nucleotides was used in clustering."
- },
- {
- "trackId" : "c_elegans_PRJNA13758_polya_clusters_minus_strand",
- "category" : [
- "Externally Sourced Resources",
- "Atlas"
- ],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "displays" : [
- {
- "renderer" : {
- "color1" : "purple",
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "polya_clusters_minus_strand-c_elegans_PRJNA13758-LinearBasicDisplay"
- }
+ "category" : [
+ "Externally Sourced Resources",
+ "Atlas"
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
- "name" : "polyA clusters minus strand",
- "adapter" : {
- "type" : "BigBedAdapter",
- "bigBedLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/jbrowse/data/c_elegans/tracks/atlas_minus.2.0.ce11.bb",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
+ "name" : "polyA clusters plus strand",
+ "trackId" : "c_elegans_PRJNA13758_polya_clusters_plus_strand",
"description" : "https://polyasite.unibas.ch/atlas - Clusters of polyA sites using a bespoke clustering procedure which groups together closely-spaced poly(A) sites, that most likely are due to imprecision in cleavage or processing. Construction of the clusters was broadened to include sites with lower read support that were located from -12 to +12 nucleotides around sites with strong support. In another pass, sites that were located within 25 nucleotides of each other were clustered together, and finally, for clusters with no annotated poly(A) signals a more permissive distance of 50 nucleotides was used in clustering."
},
{
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display.",
- "type" : "FeatureTrack",
"adapter" : {
- "rootUrlTemplate" : {
+ "bigBedLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/RNASeq introns/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/jbrowse/data/c_elegans/tracks/atlas_minus.2.0.ce11.bb"
},
- "type" : "NCListAdapter"
+ "type" : "BigBedAdapter"
+ },
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "name" : "RNASeq introns",
"displays" : [
{
- "displayId" : "rnaseq_introns-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
+ "displayId" : "polya_clusters_minus_strand-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "green"
- },
- "mouseover" : "jexl:get(feature,'score')+' reads'",
- "type" : "LinearBasicDisplay"
+ "color1" : "purple",
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "category" : [
- "Expression"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_rnaseq_introns"
- },
- {
+ "name" : "polyA clusters minus strand",
+ "trackId" : "c_elegans_PRJNA13758_polya_clusters_minus_strand",
+ "description" : "https://polyasite.unibas.ch/atlas - Clusters of polyA sites using a bespoke clustering procedure which groups together closely-spaced poly(A) sites, that most likely are due to imprecision in cleavage or processing. Construction of the clusters was broadened to include sites with lower read support that were located from -12 to +12 nucleotides around sites with strong support. In another pass, sites that were located within 25 nucleotides of each other were clustered together, and finally, for clusters with no annotated poly(A) signals a more permissive distance of 50 nucleotides was used in clustering.",
"type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/RNASeq Splice Junctions (common)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "name" : "RNASeq Splice Junctions (common)",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
"category" : [
- "Expression"
- ],
- "trackId" : "c_elegans_PRJNA13758_rnaseq_splice_junctions_(common)",
- "displays" : [
- {
- "renderer" : {
- "color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "showDescriptions" : false
- },
- "mouseover" : "jexl:get(feature,'score')+' reads'",
- "type" : "LinearBasicDisplay",
- "displayId" : "rnaseq_splice_junctions_(common)-c_elegans_PRJNA13758-LinearBasicDisplay"
- }
+ "Externally Sourced Resources",
+ "Atlas"
]
},
{
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "name" : "RNASeq Splice Junctions (rare)",
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "maxHeight" : 5000,
- "color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
- "showDescriptions" : false,
- "height" : "jexl:4"
- },
- "mouseover" : "jexl:get(feature,'score')+' reads'",
- "displayId" : "rnaseq_splice_junctions_(rare)-c_elegans_PRJNA13758-LinearBasicDisplay"
- }
- ],
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
- "Expression"
+ "Misc",
+ "Transcription Start Sites"
],
- "trackId" : "c_elegans_PRJNA13758_rnaseq_splice_junctions_(rare)"
- },
- {
- "description" : "This is a set of Transcription Start Sites (TSS) in the Forward sense identified in short read data from the paper: The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures. Chen RA, Down TA, Stempor P, Chen QB, Egelhofer TA, Hillier LW, Jeffers TE, Ahringer J. Genome Res. 2013 Jun 20.; PubMed 23550086; WBPaper00042246. The RNASeq data was obtained from the NCBI Sequence Read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra) under accession number SRA062711. This was aligned to the current version of the assembly and the number of reads aligned to the forward sense of the genome were counted at the genomic position of the 5' end of the aligned read. The count at each genomic position was then normalised by dividing by the number of millions of aligned reads, giving a value in units of Reads Per Million (RPM).",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/TSS_Chen.Forward.bw",
- "locationType" : "UriLocation"
- }
- },
- "type" : "QuantitativeTrack",
+ "trackId" : "c_elegans_PRJNA13758_tss_(chen)_forward",
"name" : "TSS (Chen) Forward",
+ "description" : "This is a set of Transcription Start Sites (TSS) in the Forward sense identified in short read data from the paper: The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures. Chen RA, Down TA, Stempor P, Chen QB, Egelhofer TA, Hillier LW, Jeffers TE, Ahringer J. Genome Res. 2013 Jun 20.; PubMed 23550086; WBPaper00042246. The RNASeq data was obtained from the NCBI Sequence Read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra) under accession number SRA062711. This was aligned to the current version of the assembly and the number of reads aligned to the forward sense of the genome were counted at the genomic position of the 5' end of the aligned read. The count at each genomic position was then normalised by dividing by the number of millions of aligned reads, giving a value in units of Reads Per Million (RPM).",
"displays" : [
{
"type" : "LinearWiggleDisplay",
"renderers" : {
- "LinePlotRenderer" : {
- "color" : "black",
- "type" : "LinePlotRenderer"
+ "XYPlotRenderer" : {
+ "type" : "XYPlotRenderer",
+ "color" : "black"
},
"DensityRenderer" : {
"type" : "DensityRenderer",
"color" : "black"
},
- "XYPlotRenderer" : {
- "color" : "black",
- "type" : "XYPlotRenderer"
+ "LinePlotRenderer" : {
+ "type" : "LinePlotRenderer",
+ "color" : "black"
}
},
"maxScore" : 25,
- "minScore" : 0,
- "displayId" : "tss_(chen)_forward-c_elegans_PRJNA13758-LinearWiggleDisplay"
+ "displayId" : "tss_(chen)_forward-c_elegans_PRJNA13758-LinearWiggleDisplay",
+ "minScore" : 0
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/TSS_Chen.Forward.bw"
+ },
+ "type" : "BigWigAdapter"
+ }
+ },
+ {
"category" : [
"Misc",
"Transcription Start Sites"
],
- "trackId" : "c_elegans_PRJNA13758_tss_(chen)_forward"
- },
- {
- "description" : "This is a set of Transcription Start Sites (TSS) in the Reverse sense identified in short read data from the paper: The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures. Chen RA, Down TA, Stempor P, Chen QB, Egelhofer TA, Hillier LW, Jeffers TE, Ahringer J. Genome Res. 2013 Jun 20.; PubMed 23550086; WBPaper00042246. The RNASeq data was obtained from the NCBI Sequence Read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra) under accession number SRA062711. This was aligned to the current version of the assembly and the number of reads aligned to the reverse sense of the genome were counted at the genomic position of the 5' end of the aligned read. The count at each genomic position was then normalised by dividing by the number of millions of aligned reads, giving a value in units of Reads Per Million (RPM).",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/TSS_Chen.Reverse.bw",
- "locationType" : "UriLocation"
- }
- },
"type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "This is a set of Transcription Start Sites (TSS) in the Reverse sense identified in short read data from the paper: The landscape of RNA polymerase II transcription initiation in C. elegans reveals promoter and enhancer architectures. Chen RA, Down TA, Stempor P, Chen QB, Egelhofer TA, Hillier LW, Jeffers TE, Ahringer J. Genome Res. 2013 Jun 20.; PubMed 23550086; WBPaper00042246. The RNASeq data was obtained from the NCBI Sequence Read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra) under accession number SRA062711. This was aligned to the current version of the assembly and the number of reads aligned to the reverse sense of the genome were counted at the genomic position of the 5' end of the aligned read. The count at each genomic position was then normalised by dividing by the number of millions of aligned reads, giving a value in units of Reads Per Million (RPM).",
"name" : "TSS (Chen) Reverse",
+ "trackId" : "c_elegans_PRJNA13758_tss_(chen)_reverse",
"displays" : [
{
- "displayId" : "tss_(chen)_reverse-c_elegans_PRJNA13758-LinearWiggleDisplay",
- "minScore" : 0,
"type" : "LinearWiggleDisplay",
- "maxScore" : 25,
"renderers" : {
- "LinePlotRenderer" : {
- "type" : "LinePlotRenderer",
- "color" : "black"
- },
"XYPlotRenderer" : {
"type" : "XYPlotRenderer",
"color" : "black"
},
+ "LinePlotRenderer" : {
+ "color" : "black",
+ "type" : "LinePlotRenderer"
+ },
"DensityRenderer" : {
- "type" : "DensityRenderer",
- "color" : "black"
+ "color" : "black",
+ "type" : "DensityRenderer"
}
- }
+ },
+ "maxScore" : 25,
+ "displayId" : "tss_(chen)_reverse-c_elegans_PRJNA13758-LinearWiggleDisplay",
+ "minScore" : 0
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "Misc",
- "Transcription Start Sites"
- ],
- "trackId" : "c_elegans_PRJNA13758_tss_(chen)_reverse"
- },
- {
- "displays" : [
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/TSS_Chen.Reverse.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ }
+ },
+ {
+ "category" : [
+ "Misc",
+ "Transcription Start Sites"
+ ],
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "description" : "This is a set of Transcription Start Sites (TSS) in the Forward sense identified in short read data from the paper: The transcription start site landscape of C. elegans. Saito TL, Hashimoto S, Gu SG, Morton JJ, Stadler M, Blumenthal T, Fire A, Morishita S. Genome Res. 2013 Aug;23(8):1348-61. PubMed 23636945, WBPaper00042354. The RNASeq data was obtained from the NCBI Sequence Read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra) under accession number SRA060670. This was aligned to the current version of the assembly and the number of reads aligned to the forward sense of the genome were counted at the genomic position of the 5' end of the aligned read. The count at each genomic position was then normalised by dividing by the number of millions of aligned reads, giving a value in units of Reads Per Million (RPM). The paper describes a http://wormtss.utgenome.org/ genome browser showing further analyses of this data.",
+ "name" : "TSS (Saito) Forward",
+ "trackId" : "c_elegans_PRJNA13758_tss_(saito)_forward",
+ "displays" : [
{
- "displayId" : "tss_(saito)_forward-c_elegans_PRJNA13758-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
"renderers" : {
- "DensityRenderer" : {
- "color" : "black",
- "type" : "DensityRenderer"
- },
"XYPlotRenderer" : {
"color" : "black",
"type" : "XYPlotRenderer"
},
+ "DensityRenderer" : {
+ "color" : "black",
+ "type" : "DensityRenderer"
+ },
"LinePlotRenderer" : {
"type" : "LinePlotRenderer",
"color" : "black"
}
},
"maxScore" : 25,
- "minScore" : 0
+ "minScore" : 0,
+ "displayId" : "tss_(saito)_forward-c_elegans_PRJNA13758-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_tss_(saito)_forward",
- "category" : [
- "Misc",
- "Transcription Start Sites"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : "This is a set of Transcription Start Sites (TSS) in the Forward sense identified in short read data from the paper: The transcription start site landscape of C. elegans. Saito TL, Hashimoto S, Gu SG, Morton JJ, Stadler M, Blumenthal T, Fire A, Morishita S. Genome Res. 2013 Aug;23(8):1348-61. PubMed 23636945, WBPaper00042354. The RNASeq data was obtained from the NCBI Sequence Read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra) under accession number SRA060670. This was aligned to the current version of the assembly and the number of reads aligned to the forward sense of the genome were counted at the genomic position of the 5' end of the aligned read. The count at each genomic position was then normalised by dividing by the number of millions of aligned reads, giving a value in units of Reads Per Million (RPM). The paper describes a http://wormtss.utgenome.org/ genome browser showing further analyses of this data.",
- "name" : "TSS (Saito) Forward",
- "type" : "QuantitativeTrack",
"adapter" : {
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/TSS_Saito.Forward.bw",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/TSS_Saito.Forward.bw"
},
"type" : "BigWigAdapter"
}
},
{
- "type" : "QuantitativeTrack",
"adapter" : {
+ "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/TSS_Saito.Reverse.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/TSS_Saito.Reverse.bw"
+ }
},
- "name" : "TSS (Saito) Reverse",
- "description" : "This is a set of Transcription Start Sites (TSS) in the Reverse sense identified in short read data from the paper: The transcription start site landscape of C. elegans. Saito TL, Hashimoto S, Gu SG, Morton JJ, Stadler M, Blumenthal T, Fire A, Morishita S. Genome Res. 2013 Aug;23(8):1348-61. PubMed 23636945, WBPaper00042354. The RNASeq data was obtained from the NCBI Sequence Read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra) under accession number SRA060670. This was aligned to the current version of the assembly and the number of reads aligned to the reverse sense of the genome were counted at the genomic position of the 5' end of the aligned read. The count at each genomic position was then normalised by dividing by the number of millions of aligned reads, giving a value in units of Reads Per Million (RPM). The paper describes a http://wormtss.utgenome.org/ genome browser showing further analyses of this data.",
- "category" : [
- "Misc",
- "Transcription Start Sites"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_tss_(saito)_reverse",
"displays" : [
{
+ "displayId" : "tss_(saito)_reverse-c_elegans_PRJNA13758-LinearWiggleDisplay",
"minScore" : 0,
+ "maxScore" : 25,
"renderers" : {
"LinePlotRenderer" : {
"color" : "black",
"type" : "LinePlotRenderer"
},
"DensityRenderer" : {
- "type" : "DensityRenderer",
- "color" : "black"
+ "color" : "black",
+ "type" : "DensityRenderer"
},
"XYPlotRenderer" : {
"color" : "black",
"type" : "XYPlotRenderer"
}
},
- "maxScore" : 25,
- "type" : "LinearWiggleDisplay",
- "displayId" : "tss_(saito)_reverse-c_elegans_PRJNA13758-LinearWiggleDisplay"
+ "type" : "LinearWiggleDisplay"
}
- ]
+ ],
+ "description" : "This is a set of Transcription Start Sites (TSS) in the Reverse sense identified in short read data from the paper: The transcription start site landscape of C. elegans. Saito TL, Hashimoto S, Gu SG, Morton JJ, Stadler M, Blumenthal T, Fire A, Morishita S. Genome Res. 2013 Aug;23(8):1348-61. PubMed 23636945, WBPaper00042354. The RNASeq data was obtained from the NCBI Sequence Read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra) under accession number SRA060670. This was aligned to the current version of the assembly and the number of reads aligned to the reverse sense of the genome were counted at the genomic position of the 5' end of the aligned read. The count at each genomic position was then normalised by dividing by the number of millions of aligned reads, giving a value in units of Reads Per Million (RPM). The paper describes a http://wormtss.utgenome.org/ genome browser showing further analyses of this data.",
+ "trackId" : "c_elegans_PRJNA13758_tss_(saito)_reverse",
+ "name" : "TSS (Saito) Reverse",
+ "category" : [
+ "Misc",
+ "Transcription Start Sites"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack"
},
{
+ "trackId" : "c_elegans_PRJNA13758_tss_(gu)_reverse",
+ "name" : "TSS (Gu) Reverse",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
+ "type" : "QuantitativeTrack",
"category" : [
"Misc",
"Transcription Start Sites"
],
- "trackId" : "c_elegans_PRJNA13758_tss_(gu)_reverse",
+ "adapter" : {
+ "type" : "BigWigAdapter",
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/TSS_Gu.Reverse.bw"
+ }
+ },
"displays" : [
{
- "displayId" : "tss_(Gu)_reverse-c_elegans_PRJNA13758-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay",
"renderers" : {
"XYPlotRenderer" : {
- "color" : "black",
- "type" : "XYPlotRenderer"
- },
- "DensityRenderer" : {
- "type" : "DensityRenderer",
+ "type" : "XYPlotRenderer",
"color" : "black"
},
"LinePlotRenderer" : {
"type" : "LinePlotRenderer",
"color" : "black"
+ },
+ "DensityRenderer" : {
+ "type" : "DensityRenderer",
+ "color" : "black"
}
},
"maxScore" : 1000,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
- }
- ],
- "type" : "QuantitativeTrack",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/TSS_Gu.Reverse.bw",
- "locationType" : "UriLocation"
+ "minScore" : 0,
+ "displayId" : "tss_(Gu)_reverse-c_elegans_PRJNA13758-LinearWiggleDisplay"
}
- },
- "name" : "TSS (Gu) Reverse"
+ ]
},
{
- "name" : "TSS (Gu) Forward",
- "type" : "QuantitativeTrack",
"adapter" : {
- "type" : "BigWigAdapter",
"bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/TSS_Gu.Forward.bw",
- "locationType" : "UriLocation"
- }
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/TSS_Gu.Forward.bw"
+ },
+ "type" : "BigWigAdapter"
},
+ "name" : "TSS (Gu) Forward",
"trackId" : "c_elegans_PRJNA13758_tss_(gu)_forward",
+ "type" : "QuantitativeTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "category" : [
- "Misc",
- "Transcription Start Sites"
- ],
"displays" : [
{
"type" : "LinearWiggleDisplay",
@@ -44576,12 +43864,24 @@
"minScore" : 0,
"displayId" : "tss_(Gu)_forward-c_elegans_PRJNA13758-LinearWiggleDisplay"
}
+ ],
+ "category" : [
+ "Misc",
+ "Transcription Start Sites"
]
},
{
- "description" : "This is a set of Transcription Start Sites (TSS) in the Forward sense identified in short read data from the paper: Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation. Kruesi WS, Core LJ, Waters CT, Lis JT, Meyer BJ. Elife. 2013 Jun 18;2:e00808. PubMed 23795297, WBPaper00042529. The RNASeq data was obtained from the NCBI Sequence Read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra) under accession number SRP017636. The TAP+ and TAP- reads were aligned to the current version of the assembly and the number of reads aligned to the forward sense of the genome were counted at the genomic position of the 5' end of the aligned read. The number of TAP- (control) reads were subtracted from the TAP+ reads at each position. The count at each genomic position was then normalised by dividing by the number of millions of aligned reads, giving a value in units of Reads Per Million (RPM).",
"name" : "TSS (Kruesi) Forward",
+ "trackId" : "c_elegans_PRJNA13758_tss_(kruesi)_forward",
+ "description" : "This is a set of Transcription Start Sites (TSS) in the Forward sense identified in short read data from the paper: Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation. Kruesi WS, Core LJ, Waters CT, Lis JT, Meyer BJ. Elife. 2013 Jun 18;2:e00808. PubMed 23795297, WBPaper00042529. The RNASeq data was obtained from the NCBI Sequence Read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra) under accession number SRP017636. The TAP+ and TAP- reads were aligned to the current version of the assembly and the number of reads aligned to the forward sense of the genome were counted at the genomic position of the 5' end of the aligned read. The number of TAP- (control) reads were subtracted from the TAP+ reads at each position. The count at each genomic position was then normalised by dividing by the number of millions of aligned reads, giving a value in units of Reads Per Million (RPM).",
"type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "Misc",
+ "Transcription Start Sites"
+ ],
"adapter" : {
"bigWigLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/TSS_Kruesi.Forward.bw",
@@ -44592,204 +43892,219 @@
"displays" : [
{
"displayId" : "tss_kruesi()_forward-c_elegans_PRJNA13758-LinearWiggleDisplay",
- "type" : "LinearWiggleDisplay",
+ "minScore" : 0,
"renderers" : {
- "XYPlotRenderer" : {
- "type" : "XYPlotRenderer",
+ "LinePlotRenderer" : {
+ "type" : "LinePlotRenderer",
"color" : "black"
},
"DensityRenderer" : {
- "type" : "DensityRenderer",
- "color" : "black"
+ "color" : "black",
+ "type" : "DensityRenderer"
},
- "LinePlotRenderer" : {
- "type" : "LinePlotRenderer",
+ "XYPlotRenderer" : {
+ "type" : "XYPlotRenderer",
"color" : "black"
}
},
"maxScore" : 25,
- "minScore" : 0
+ "type" : "LinearWiggleDisplay"
}
- ],
- "trackId" : "c_elegans_PRJNA13758_tss_(kruesi)_forward",
- "category" : [
- "Misc",
- "Transcription Start Sites"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
]
},
{
- "description" : "This is a set of Transcription Start Sites (TSS) in the Reverse sense identified in short read data from the paper: Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation. Kruesi WS, Core LJ, Waters CT, Lis JT, Meyer BJ. Elife. 2013 Jun 18;2:e00808. PubMed 23795297, WBPaper00042529. The RNASeq data was obtained from the NCBI Sequence Read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra) under accession number SRP017636. The TAP+ and TAP- reads were aligned to the current version of the assembly and the number of reads aligned to the reverse sense of the genome were counted at the genomic position of the 5' end of the aligned read. The number of TAP- (control) reads were subtracted from the TAP+ reads at each position. The count at each genomic position was then normalised by dividing by the number of millions of aligned reads, giving a value in units of Reads Per Million (RPM).",
- "name" : "TSS (Kruesi) Reverse",
- "adapter" : {
- "type" : "BigWigAdapter",
- "bigWigLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/TSS_Kruesi.Reverse.bw"
- }
- },
- "type" : "QuantitativeTrack",
"displays" : [
{
- "displayId" : "tss_kruesi()_reverse-c_elegans_PRJNA13758-LinearWiggleDisplay",
+ "type" : "LinearWiggleDisplay",
"renderers" : {
- "XYPlotRenderer" : {
- "type" : "XYPlotRenderer",
+ "LinePlotRenderer" : {
+ "type" : "LinePlotRenderer",
"color" : "black"
},
"DensityRenderer" : {
- "color" : "black",
- "type" : "DensityRenderer"
+ "type" : "DensityRenderer",
+ "color" : "black"
},
- "LinePlotRenderer" : {
+ "XYPlotRenderer" : {
"color" : "black",
- "type" : "LinePlotRenderer"
+ "type" : "XYPlotRenderer"
}
},
"maxScore" : 25,
- "type" : "LinearWiggleDisplay",
- "minScore" : 0
+ "minScore" : 0,
+ "displayId" : "tss_kruesi()_reverse-c_elegans_PRJNA13758-LinearWiggleDisplay"
}
],
- "trackId" : "c_elegans_PRJNA13758_tss_(kruesi)_reverse",
+ "adapter" : {
+ "bigWigLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/wiggle_binaries/TSS_Kruesi.Reverse.bw"
+ },
+ "type" : "BigWigAdapter"
+ },
+ "type" : "QuantitativeTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"Misc",
"Transcription Start Sites"
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ]
+ "name" : "TSS (Kruesi) Reverse",
+ "trackId" : "c_elegans_PRJNA13758_tss_(kruesi)_reverse",
+ "description" : "This is a set of Transcription Start Sites (TSS) in the Reverse sense identified in short read data from the paper: Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation. Kruesi WS, Core LJ, Waters CT, Lis JT, Meyer BJ. Elife. 2013 Jun 18;2:e00808. PubMed 23795297, WBPaper00042529. The RNASeq data was obtained from the NCBI Sequence Read Archive (SRA) (http://www.ncbi.nlm.nih.gov/sra) under accession number SRP017636. The TAP+ and TAP- reads were aligned to the current version of the assembly and the number of reads aligned to the reverse sense of the genome were counted at the genomic position of the 5' end of the aligned read. The number of TAP- (control) reads were subtracted from the TAP+ reads at each position. The count at each genomic position was then normalised by dividing by the number of millions of aligned reads, giving a value in units of Reads Per Million (RPM)."
},
{
+ "category" : [
+ "Externally Sourced Resources",
+ "Other"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "QuantitativeTrack",
"description" : "UCSC Nematode conservation calculated across 26 species. For more information about these data, see the README at UCSC (http://hgdownload.soe.ucsc.edu/goldenPath/ce11/phastCons26way/).",
+ "trackId" : "c_elegans_PRJNA13758_ucsc_conservation",
"name" : "UCSC Conservation",
- "adapter" : {
- "bigWigLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/UCSC/ce11.phastCons26way.bw",
- "locationType" : "UriLocation"
- },
- "type" : "BigWigAdapter"
- },
- "type" : "QuantitativeTrack",
"displays" : [
{
- "minScore" : 0,
+ "type" : "LinearWiggleDisplay",
"maxScore" : 1,
"renderers" : {
"DensityRenderer" : {
- "posColor" : "grey",
"type" : "DensityRenderer",
+ "posColor" : "grey",
"color" : "grey"
},
"XYPlotRenderer" : {
- "bicolorPivot" : "none",
- "type" : "XYPlotRenderer",
- "color" : "grey",
"summaryScoreMode" : "avg",
- "posColor" : "grey"
+ "type" : "XYPlotRenderer",
+ "bicolorPivot" : "none",
+ "posColor" : "grey",
+ "color" : "grey"
}
},
- "type" : "LinearWiggleDisplay",
- "displayId" : "ucsc_conservation-c_elegans_PRJNA13758-LinearWiggleDisplay"
+ "displayId" : "ucsc_conservation-c_elegans_PRJNA13758-LinearWiggleDisplay",
+ "minScore" : 0
}
],
- "trackId" : "c_elegans_PRJNA13758_ucsc_conservation",
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "category" : [
- "Externally Sourced Resources",
- "Other"
- ]
+ "adapter" : {
+ "bigWigLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/UCSC/ce11.phastCons26way.bw",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BigWigAdapter"
+ }
},
{
- "description" : "MiRanda prediction with stringent filters (score>=156 and energy <-7). This file contains the best predictions and is the reference file. From http://utrome.org",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/jbrowse/data/c_elegans/tracks/miRanda predicted binding site (stringent)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/jbrowse/data/c_elegans/tracks/miRanda predicted binding site (stringent)/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
},
- "name" : "miRanda predicted binding site (restricted)",
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "miranda_predicted_binding_site_(restricted)-c_elegans_PRJNA13758-LinearBasicDisplay",
"renderer" : {
- "height" : 5,
+ "color1" : "deeppink",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "deeppink"
+ "height" : 5,
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "miranda_predicted_binding_site_(restricted)-c_elegans_PRJNA13758-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
+ "name" : "miRanda predicted binding site (restricted)",
+ "trackId" : "c_elegans_PRJNA13758_miranda_predicted_binding_site_(restricted)",
+ "description" : "MiRanda prediction with stringent filters (score>=156 and energy <-7). This file contains the best predictions and is the reference file. From http://utrome.org",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
"category" : [
"Externally Sourced Resources",
"UTRome v2"
- ],
+ ]
+ },
+ {
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_miranda_predicted_binding_site_(restricted)"
- },
- {
+ "type" : "FeatureTrack",
+ "category" : [
+ "Externally Sourced Resources",
+ "UTRome v2"
+ ],
+ "trackId" : "c_elegans_PRJNA13758_miranda_predicted_binding_site_(generic)",
+ "name" : "miRanda predicted binding site (generic)",
+ "description" : "All MiRanda predictions (a lot of predictions, also with very low scores, but informative). From http://utrome.org",
"displays" : [
{
- "displayId" : "miranda_predicted_binding_site_(generic)-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 5,
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "pink"
+ "color1" : "pink",
+ "height" : 5,
+ "showLabels" : false
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "miranda_predicted_binding_site_(generic)-c_elegans_PRJNA13758-LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "trackId" : "c_elegans_PRJNA13758_miranda_predicted_binding_site_(generic)",
- "category" : [
- "Externally Sourced Resources",
- "UTRome v2"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "description" : "All MiRanda predictions (a lot of predictions, also with very low scores, but informative). From http://utrome.org",
- "name" : "miRanda predicted binding site (generic)",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/jbrowse/data/c_elegans/tracks/miRanda predicted binding site (all)/{refseq}/trackData.jsonz"
}
- },
- "type" : "FeatureTrack"
+ }
},
{
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/jbrowse/data/c_elegans/tracks/Predicted 3prime UTR (filtered)/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
"displays" : [
{
- "displayId" : "predicted_3prime_utr_(filtered)-c_elegans_PRJNA13758-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "deepskyblue",
+ "height" : 5,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 5
- }
+ "color1" : "deepskyblue",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "predicted_3prime_utr_(filtered)-c_elegans_PRJNA13758-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
+ "name" : "Predicted 3prime UTR (filtered)",
+ "trackId" : "c_elegans_PRJNA13758_predicted_3prime_utr_(filtered)",
+ "description" : "3’UTRs we have identified using filtered by score. From http://utrome.org",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "category" : [
+ "Externally Sourced Resources",
+ "UTRome v2"
+ ]
+ },
+ {
+ "description" : "Database with all the 3’UTRs we have identified using relaxed filters (a lot of 3’UTR isoforms for each gene). From http://utrome.org",
+ "trackId" : "c_elegans_PRJNA13758_predicted_3prime_utr_(mild)",
+ "name" : "Predicted 3prime UTR (mild)",
"category" : [
"Externally Sourced Resources",
"UTRome v2"
@@ -44797,20 +44112,7 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_predicted_3prime_utr_(filtered)",
- "description" : "3’UTRs we have identified using filtered by score. From http://utrome.org",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/jbrowse/data/c_elegans/tracks/Predicted 3prime UTR (filtered)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
"type" : "FeatureTrack",
- "name" : "Predicted 3prime UTR (filtered)"
- },
- {
- "description" : "Database with all the 3’UTRs we have identified using relaxed filters (a lot of 3’UTR isoforms for each gene). From http://utrome.org",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -44818,23 +44120,26 @@
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "name" : "Predicted 3prime UTR (mild)",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
"displays" : [
{
- "displayId" : "predicted_3prime_utr_(mild)-c_elegans_PRJNA13758-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "skyblue",
- "type" : "SvgFeatureRenderer",
+ "height" : 5,
"showLabels" : false,
- "height" : 5
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "predicted_3prime_utr_(mild)-c_elegans_PRJNA13758-LinearBasicDisplay"
}
],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ }
+ },
+ {
+ "description" : "Predictions of 3’UTRs from a previous version of UTRome. From http://utrome.org",
+ "trackId" : "c_elegans_PRJNA13758_predicted_3prime_utr_(v1-historical)",
+ "name" : "Predicted 3prime UTR (v1-historical)",
"category" : [
"Externally Sourced Resources",
"UTRome v2"
@@ -44842,9 +44147,7 @@
"assemblyNames" : [
"c_elegans_PRJNA13758"
],
- "trackId" : "c_elegans_PRJNA13758_predicted_3prime_utr_(mild)"
- },
- {
+ "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -44852,79 +44155,60 @@
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "name" : "Predicted 3prime UTR (v1-historical)",
- "description" : "Predictions of 3’UTRs from a previous version of UTRome. From http://utrome.org",
- "category" : [
- "Externally Sourced Resources",
- "UTRome v2"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758"
- ],
- "trackId" : "c_elegans_PRJNA13758_predicted_3prime_utr_(v1-historical)",
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
"displays" : [
{
"displayId" : "predicted_3prime_utr_(v1-historical)-c_elegans_PRJNA13758-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
+ "color3" : "skyblue",
"type" : "SvgFeatureRenderer",
"color1" : "skyblue",
"height" : 5,
- "color3" : "skyblue"
- }
+ "showLabels" : false
+ },
+ "type" : "LinearBasicDisplay"
}
]
},
{
- "assemblyNames" : [
- "c_elegans_PRJNA275000"
- ],
- "category" : [
- "Genes",
- "Ab-initio predictions"
- ],
- "trackId" : "c_elegans_PRJNA275000_genblastg_cds_predictions",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/genBlastG CDS predictions/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
},
"displays" : [
{
+ "displayId" : "genblastg_cds_predictions-c_elegans_PRJNA275000-LinearBasicDisplay",
"renderer" : {
"height" : 7,
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "genblastg_cds_predictions-c_elegans_PRJNA275000-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/genBlastG CDS predictions/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "type" : "FeatureTrack",
+ "description" : "Data from 'genBlastG: using BLAST searches to build homologous gene models' (WBPaper00040677).",
+ "trackId" : "c_elegans_PRJNA275000_genblastg_cds_predictions",
"name" : "genBlastG CDS predictions",
- "description" : "Data from 'genBlastG: using BLAST searches to build homologous gene models' (WBPaper00040677)."
+ "category" : [
+ "Genes",
+ "Ab-initio predictions"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA275000"
+ ],
+ "type" : "FeatureTrack"
},
{
- "name" : "Other UniProt proteins",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/Other UniProt proteins/{refseq}/trackData.jsonz"
- }
- },
- "type" : "FeatureTrack",
"description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"trackId" : "c_elegans_PRJNA275000_other_uniprot_proteins",
+ "name" : "Other UniProt proteins",
"category" : [
"Sequence Similarity",
"Proteins"
@@ -44932,31 +44216,32 @@
"assemblyNames" : [
"c_elegans_PRJNA275000"
],
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/Other UniProt proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "other_uniprot_proteins-c_elegans_PRJNA275000-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "orange",
+ "showLabels" : false,
"showDescriptions" : false,
"height" : 4
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "other_uniprot_proteins-c_elegans_PRJNA275000-LinearBasicDisplay"
+ }
}
]
},
{
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/C. briggsae proteins/{refseq}/trackData.jsonz"
- }
- },
- "type" : "FeatureTrack",
- "name" : "C. briggsae proteins",
"description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_elegans_PRJNA275000_C_briggsae_proteins",
+ "name" : "C. briggsae proteins",
"category" : [
"Sequence Similarity",
"Proteins"
@@ -44964,45 +44249,49 @@
"assemblyNames" : [
"c_elegans_PRJNA275000"
],
- "trackId" : "c_elegans_PRJNA275000_C_briggsae_proteins",
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/C. briggsae proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
+ "displayId" : "C_briggsae_proteins-c_elegans_PRJNA275000-LinearBasicDisplay",
"renderer" : {
- "color1" : "orange",
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "height" : 4
+ "height" : 4,
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
},
"mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
- "displayId" : "C_briggsae_proteins-c_elegans_PRJNA275000-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
]
},
{
- "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/H. sapiens proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "H. sapiens proteins",
"displays" : [
{
- "mouseover" : "jexl:get(feature,'clone')",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "color1" : "orange",
+ "showLabels" : false,
+ "height" : 4
},
- "type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"displayId" : "H_sapiens_proteins-c_elegans_PRJNA275000-LinearBasicDisplay"
}
],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/H. sapiens proteins/{refseq}/trackData.jsonz"
+ }
+ },
"category" : [
"Sequence Similarity",
"Proteins"
@@ -45010,43 +44299,55 @@
"assemblyNames" : [
"c_elegans_PRJNA275000"
],
- "trackId" : "c_elegans_PRJNA275000_H_sapiens_proteins"
+ "type" : "FeatureTrack",
+ "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_elegans_PRJNA275000_H_sapiens_proteins",
+ "name" : "H. sapiens proteins"
},
{
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "Repeat Region (RepeatMasker)",
- "description" : "Repetitive regions identified by RepeatMasker.",
"assemblyNames" : [
"c_elegans_PRJNA275000"
],
+ "type" : "FeatureTrack",
"category" : [
"Genome Structure",
"Repeats"
],
"trackId" : "c_elegans_PRJNA275000_repeat_region_(repeatmasker)",
+ "name" : "Repeat Region (RepeatMasker)",
+ "description" : "Repetitive regions identified by RepeatMasker.",
"displays" : [
{
- "displayId" : "repeat_region_(repeatmasker)-c_elegans_PRJNA275000-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "height" : 4,
+ "showDescriptions" : false,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "bisque",
- "showDescriptions" : false,
- "height" : 4
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "repeat_region_(repeatmasker)-c_elegans_PRJNA275000-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
"description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_elegans_PRJNA275000_P_pacificus_proteins",
+ "name" : "P. pacificus proteins",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA275000"
+ ],
"type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
@@ -45055,59 +44356,50 @@
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/P. pacificus proteins/{refseq}/trackData.jsonz"
}
},
- "name" : "P. pacificus proteins",
"displays" : [
{
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
"type" : "SvgFeatureRenderer",
"showLabels" : false,
+ "height" : 4,
"color1" : "orange"
},
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
- "displayId" : "P_pacificus_proteins-c_elegans_PRJNA275000-LinearBasicDisplay"
+ "displayId" : "P_pacificus_proteins-c_elegans_PRJNA275000-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA275000"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "trackId" : "c_elegans_PRJNA275000_P_pacificus_proteins"
+ ]
},
{
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz"
- }
- },
- "type" : "FeatureTrack",
+ "trackId" : "c_elegans_PRJNA275000_D_melanogaster_proteins",
"name" : "D. melanogaster proteins",
"description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"assemblyNames" : [
"c_elegans_PRJNA275000"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "trackId" : "c_elegans_PRJNA275000_D_melanogaster_proteins",
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
- "displayId" : "D_melanogaster_proteins-c_elegans_PRJNA275000-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "orange"
+ "height" : 4,
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "D_melanogaster_proteins-c_elegans_PRJNA275000-LinearBasicDisplay"
}
]
},
@@ -45115,112 +44407,89 @@
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/B. malayi proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/B. malayi proteins/{refseq}/trackData.jsonz"
}
},
- "type" : "FeatureTrack",
- "name" : "B. malayi proteins",
- "description" : "Matches to WormBase B. malayi proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "assemblyNames" : [
- "c_elegans_PRJNA275000"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "trackId" : "c_elegans_PRJNA275000_B_malayi_proteins",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "B_malayi_proteins-c_elegans_PRJNA275000-LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
"color1" : "orange",
+ "height" : 4,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 4
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "B_malayi_proteins-c_elegans_PRJNA275000-LinearBasicDisplay"
+ "type" : "SvgFeatureRenderer"
+ }
}
- ]
- },
- {
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/C. brenneri proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "C. brenneri proteins",
- "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ ],
+ "description" : "Matches to WormBase B. malayi proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_elegans_PRJNA275000_B_malayi_proteins",
+ "name" : "B. malayi proteins",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
"assemblyNames" : [
"c_elegans_PRJNA275000"
],
+ "type" : "FeatureTrack"
+ },
+ {
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA275000"
+ ],
+ "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "C. brenneri proteins",
"trackId" : "c_elegans_PRJNA275000_C_brenneri_proteins",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "orange",
- "height" : 4
+ "showLabels" : false,
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')",
"displayId" : "C_brenneri_proteins-c_elegans_PRJNA275000-LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/C. brenneri proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
"displays" : [
{
- "displayId" : "S_ratti_proteins-c_elegans_PRJNA275000-LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "color1" : "orange",
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "height" : 4
+ "height" : 4,
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
},
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "S_ratti_proteins-c_elegans_PRJNA275000-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA275000"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "trackId" : "c_elegans_PRJNA275000_S_ratti_proteins",
- "description" : "Matches to WormBase S. ratti proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/S. ratti proteins/{refseq}/trackData.jsonz"
- }
- },
- "type" : "FeatureTrack",
- "name" : "S. ratti proteins"
- },
- {
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/S. ratti proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "name" : "S. cerevisiae proteins",
- "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"category" : [
"Sequence Similarity",
"Proteins"
@@ -45228,45 +44497,68 @@
"assemblyNames" : [
"c_elegans_PRJNA275000"
],
- "trackId" : "c_elegans_PRJNA275000_S_cerevisiae_proteins",
+ "type" : "FeatureTrack",
+ "description" : "Matches to WormBase S. ratti proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_elegans_PRJNA275000_S_ratti_proteins",
+ "name" : "S. ratti proteins"
+ },
+ {
"displays" : [
{
- "displayId" : "S_cerevisiae_proteins-c_elegans_PRJNA275000-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "S_cerevisiae_proteins-c_elegans_PRJNA275000-LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
+ "color1" : "orange",
+ "height" : 4,
"showLabels" : false
}
}
- ]
- },
- {
- "description" : "cDNAs from this species from INSDC that have been aligned to the genome using STAR.",
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/$ASEMBLY/tracks/INSDC nematode cDNAs/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz"
}
},
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
"type" : "FeatureTrack",
- "name" : "INSDC nematode cDNAs",
+ "assemblyNames" : [
+ "c_elegans_PRJNA275000"
+ ],
+ "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "S. cerevisiae proteins",
+ "trackId" : "c_elegans_PRJNA275000_S_cerevisiae_proteins"
+ },
+ {
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/$ASEMBLY/tracks/INSDC nematode cDNAs/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "$ASEMBLY_insdc_nematode_cdnas-LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
"height" : 4,
+ "showDescriptions" : false,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "grey"
- },
- "type" : "LinearBasicDisplay"
+ "color1" : "grey",
+ "type" : "SvgFeatureRenderer"
+ }
}
],
+ "description" : "cDNAs from this species from INSDC that have been aligned to the genome using STAR.",
+ "trackId" : "$ASEMBLY_insdc_nematode_cdnas",
+ "name" : "INSDC nematode cDNAs",
"category" : [
"Sequence Similarity",
"Nucleotide"
@@ -45274,31 +44566,22 @@
"assemblyNames" : [
"$ASEMBLY"
],
- "trackId" : "$ASEMBLY_insdc_nematode_cdnas"
+ "type" : "FeatureTrack"
},
{
- "trackId" : "c_elegans_PRJNA275000_low_complextity_region_(dust)",
- "assemblyNames" : [
- "c_elegans_PRJNA275000"
- ],
- "category" : [
- "Genome Structure",
- "Repeats"
- ],
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "low_complextity_region_(dust)-c_elegans_PRJNA275000-LinearBasicDisplay",
"renderer" : {
+ "color1" : "bisque",
"height" : 4,
"showDescriptions" : false,
- "color1" : "bisque",
"showLabels" : false,
"type" : "SvgFeatureRenderer"
- },
- "displayId" : "low_complextity_region_(dust)-c_elegans_PRJNA275000-LinearBasicDisplay"
+ }
}
],
- "name" : "Low complextity region (Dust)",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -45307,54 +44590,52 @@
}
},
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA275000"
+ ],
+ "category" : [
+ "Genome Structure",
+ "Repeats"
+ ],
+ "name" : "Low complextity region (Dust)",
+ "trackId" : "c_elegans_PRJNA275000_low_complextity_region_(dust)",
"description" : "Low-complexity regions identified by Dust."
},
{
"name" : "O. volvulus proteins",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/O. volvulus proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "description" : "Matches to WormBase O. volvulus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"trackId" : "c_elegans_PRJNA275000_O_volvulus_proteins",
+ "description" : "Matches to WormBase O. volvulus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA275000"
+ ],
"category" : [
"Sequence Similarity",
"Proteins"
],
- "assemblyNames" : [
- "c_elegans_PRJNA275000"
- ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/O. volvulus proteins/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
- "displayId" : "O_volvulus_proteins-c_elegans_PRJNA275000-LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "color1" : "orange",
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "height" : 4
+ "height" : 4,
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
},
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "O_volvulus_proteins-c_elegans_PRJNA275000-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
]
},
{
- "displays" : [
- {
- "displayId" : "tandem_and_inverted_repeats-c_elegans_PRJNA275000-LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "bisque",
- "showDescriptions" : false
- },
- "type" : "LinearBasicDisplay"
- }
- ],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA275000"
],
@@ -45362,29 +44643,50 @@
"Genome Structure",
"Repeats"
],
+ "name" : "Tandem and Inverted Repeats",
"trackId" : "c_elegans_PRJNA275000_tandem_and_inverted_repeats",
"description" : "Exact tandem and inverted repetitive elements.",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "tandem_and_inverted_repeats-c_elegans_PRJNA275000-LinearBasicDisplay",
+ "renderer" : {
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "color1" : "bisque",
+ "type" : "SvgFeatureRenderer"
+ }
+ }
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/Tandem and Inverted Repeats/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/Tandem and Inverted Repeats/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
}
- },
- "type" : "FeatureTrack",
- "name" : "Tandem and Inverted Repeats"
+ }
},
{
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "orange",
+ "showLabels" : false,
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
+ },
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "C_remanei_proteins-c_elegans_PRJNA275000-LinearBasicDisplay"
+ }
+ ],
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/C. remanei proteins/{refseq}/trackData.jsonz"
- }
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/C. remanei proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "name" : "C. remanei proteins",
- "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"category" : [
"Sequence Similarity",
"Proteins"
@@ -45392,46 +44694,36 @@
"assemblyNames" : [
"c_elegans_PRJNA275000"
],
+ "type" : "FeatureTrack",
+ "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"trackId" : "c_elegans_PRJNA275000_C_remanei_proteins",
- "displays" : [
- {
- "displayId" : "C_remanei_proteins-c_elegans_PRJNA275000-LinearBasicDisplay",
- "renderer" : {
- "height" : 4,
- "color1" : "orange",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay"
- }
- ]
+ "name" : "C. remanei proteins"
},
{
- "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "C. japonica proteins",
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/C. japonica proteins/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/C. japonica proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "C_japonica_proteins-c_elegans_PRJNA275000-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
"color1" : "orange",
- "height" : 4
+ "height" : 4,
+ "showLabels" : false
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "C_japonica_proteins-c_elegans_PRJNA275000-LinearBasicDisplay"
}
],
+ "name" : "C. japonica proteins",
"trackId" : "c_elegans_PRJNA275000_C_japonica_proteins",
+ "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA275000"
],
@@ -45441,68 +44733,57 @@
]
},
{
- "name" : "C. elegans proteins",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "C_elegans_proteins-c_elegans_PRJNA275000-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "orange",
+ "height" : 4,
+ "showLabels" : false
+ }
+ }
+ ],
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/tracks/C. elegans proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ }
},
- "type" : "FeatureTrack",
- "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "trackId" : "c_elegans_PRJNA275000_C_elegans_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA275000"
],
- "displays" : [
- {
- "mouseover" : "jexl:get(feature,'clone')",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "orange",
- "height" : 4
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "C_elegans_proteins-c_elegans_PRJNA275000-LinearBasicDisplay"
- }
- ]
+ "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "C. elegans proteins",
+ "trackId" : "c_elegans_PRJNA275000_C_elegans_proteins"
},
{
"displays" : [
{
- "displayId" : "TTCN_sequence_search_c_elegans_PRJNA275000-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
"showDescriptions" : false,
"height" : 4,
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "SlateBlue"
+ "color1" : "SlateBlue",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "TTCN_sequence_search_c_elegans_PRJNA275000-LinearBasicDisplay"
}
],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA275000"
- ],
- "trackId" : "c_elegans_PRJNA275000_TTCN_sequence_search",
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
"adapter" : {
- "search" : "TTC.",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
"fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA275000.WS284.genomic.fa.gz"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA275000.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
},
"faiLocation" : {
"locationType" : "UriLocation",
@@ -45511,28 +44792,26 @@
"gziLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA275000.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BgzipFastaAdapter"
},
- "type" : "SequenceSearchAdapter"
+ "type" : "SequenceSearchAdapter",
+ "search" : "TTC."
},
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA275000"
+ ],
"type" : "FeatureTrack",
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
+ "trackId" : "c_elegans_PRJNA275000_TTCN_sequence_search",
"name" : "Cas12e TTCN PAM sites"
},
{
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "Indigo",
- "showDescriptions" : false,
- "height" : 4
- },
- "displayId" : "TTN_sequence_search_c_elegans_PRJNA275000-LinearBasicDisplay"
- }
- ],
- "trackId" : "c_elegans_PRJNA275000_TTN_sequence_search",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA275000"
],
@@ -45540,30 +44819,47 @@
"Externally Sourced Resources",
"CRISPR predictions"
],
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
"name" : "Cas12a TTN PAM sites",
- "type" : "FeatureTrack",
+ "trackId" : "c_elegans_PRJNA275000_TTN_sequence_search",
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
+ "displays" : [
+ {
+ "renderer" : {
+ "height" : 4,
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "color1" : "Indigo",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "TTN_sequence_search_c_elegans_PRJNA275000-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
+ "search" : "TT.",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA275000.WS284.genomic.fa.gz.gzi",
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA275000.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
"fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA275000.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA275000.WS284.genomic.fa.gz"
},
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA275000.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA275000.WS284.genomic.fa.gz.gzi"
},
"type" : "BgzipFastaAdapter"
- },
- "search" : "TT.",
- "type" : "SequenceSearchAdapter"
+ }
}
},
{
+ "name" : "SaCas9 NNGRRT PAM sites",
+ "trackId" : "c_elegans_PRJNA275000_NNGRRT_sequence_search",
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_elegans_PRJNA275000"
],
@@ -45571,55 +44867,72 @@
"Externally Sourced Resources",
"CRISPR predictions"
],
- "trackId" : "c_elegans_PRJNA275000_NNGRRT_sequence_search",
- "displays" : [
- {
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "DarkViolet",
- "showDescriptions" : false,
- "height" : 4
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "NNGRRT_sequence_search_c_elegans_PRJNA275000-LinearBasicDisplay"
- }
- ],
- "type" : "FeatureTrack",
"adapter" : {
"search" : "..G[AG][AG]T",
"sequenceAdapter" : {
"type" : "BgzipFastaAdapter",
- "fastaLocation" : {
+ "gziLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA275000.WS284.genomic.fa.gz"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA275000.WS284.genomic.fa.gz.gzi"
},
"faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA275000.WS284.genomic.fa.gz.fai"
- },
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA275000.WS284.genomic.fa.gz.gzi",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA275000.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
- }
+ },
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA275000.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
+ }
},
"type" : "SequenceSearchAdapter"
},
- "name" : "SaCas9 NNGRRT PAM sites",
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time."
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "showLabels" : false,
+ "height" : 4,
+ "showDescriptions" : false,
+ "color1" : "DarkViolet",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "NNGRRT_sequence_search_c_elegans_PRJNA275000-LinearBasicDisplay"
+ }
+ ]
},
{
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA275000"
+ ],
"description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
"name" : "SpCas9 NGG PAM sites",
- "type" : "FeatureTrack",
+ "trackId" : "c_elegans_PRJNA275000_NGG_sequence_search",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "height" : 4,
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "color1" : "RebeccaPurple"
+ },
+ "displayId" : "NGG_sequence_search_c_elegans_PRJNA275000-LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"search" : ".GG",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
"gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA275000.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA275000.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
},
+ "type" : "BgzipFastaAdapter",
"faiLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA275000.WS284.genomic.fa.gz.fai"
@@ -45630,32 +44943,9 @@
}
},
"type" : "SequenceSearchAdapter"
- },
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "RebeccaPurple",
- "showDescriptions" : false,
- "height" : 4
- },
- "displayId" : "NGG_sequence_search_c_elegans_PRJNA275000-LinearBasicDisplay"
- }
- ],
- "trackId" : "c_elegans_PRJNA275000_NGG_sequence_search",
- "assemblyNames" : [
- "c_elegans_PRJNA275000"
- ],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ]
+ }
},
{
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
- "name" : "Curated Genes (protein coding)",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -45663,207 +44953,195 @@
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
"displays" : [
{
- "displayId" : "curated_genes_(protein_coding)-c_inopinata_PRJDB5687-LinearBasicDisplay",
"renderer" : {
"color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
- "maxHeight" : 5000,
"type" : "SvgFeatureRenderer",
+ "maxHeight" : 5000,
"color3" : "#965567"
},
+ "displayId" : "curated_genes_(protein_coding)-c_inopinata_PRJDB5687-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
+ "name" : "Curated Genes (protein coding)",
"trackId" : "c_inopinata_PRJDB5687_curated_genes_protein_coding",
"category" : [
"Genes",
"Curated Genes"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_inopinata_PRJDB5687"
]
},
{
- "name" : "Curated Genes",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_inopinata_PRJDB5687/tracks/Curated_Genes/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
- "trackId" : "c_inopinata_PRJDB5687_curated_genes",
"category" : [
"Genes",
"Curated Genes"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_inopinata_PRJDB5687"
],
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
+ "name" : "Curated Genes",
+ "trackId" : "c_inopinata_PRJDB5687_curated_genes",
"displays" : [
{
- "displayId" : "curated_genes-c_inopinata_PRJDB5687-LinearBasicDisplay",
"renderer" : {
- "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
- "maxHeight" : 5000,
"type" : "SvgFeatureRenderer",
+ "maxHeight" : 5000,
+ "color3" : "#965567",
+ "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
- },
- "color3" : "#965567"
+ }
},
+ "displayId" : "curated_genes-c_inopinata_PRJDB5687-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
+ },
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_inopinata_PRJDB5687/tracks/Curated_Genes/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
}
},
{
- "category" : [
- "Genome Structure",
- "Repeats"
- ],
- "assemblyNames" : [
- "c_inopinata_PRJDB5687"
- ],
- "trackId" : "c_inopinata_PRJDB5687_low_complextity_region_(dust)",
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_inopinata_PRJDB5687/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
"renderer" : {
- "height" : 4,
+ "showLabels" : false,
"showDescriptions" : false,
+ "height" : 4,
"color1" : "bisque",
- "showLabels" : false,
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "low_complextity_region_(dust)-c_inopinata_PRJDB5687-LinearBasicDisplay"
+ "displayId" : "low_complextity_region_(dust)-c_inopinata_PRJDB5687-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_inopinata_PRJDB5687/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz"
- }
- },
- "type" : "FeatureTrack",
+ "trackId" : "c_inopinata_PRJDB5687_low_complextity_region_(dust)",
"name" : "Low complextity region (Dust)",
- "description" : "Low-complexity regions identified by Dust."
+ "description" : "Low-complexity regions identified by Dust.",
+ "assemblyNames" : [
+ "c_inopinata_PRJDB5687"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Genome Structure",
+ "Repeats"
+ ]
},
{
+ "name" : "Cas12e TTCN PAM sites",
+ "trackId" : "c_inopinata_PRJDB5687_TTCN_sequence_search",
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_inopinata_PRJDB5687"
+ ],
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
"adapter" : {
- "type" : "SequenceSearchAdapter",
"search" : "TTC.",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
"type" : "BgzipFastaAdapter",
- "faiLocation" : {
+ "gziLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_inopinata.PRJDB5687.WS284.genomic.fa.gz.fai"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_inopinata.PRJDB5687.WS284.genomic.fa.gz.gzi"
},
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_inopinata.PRJDB5687.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
- "gziLocation" : {
+ "faiLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_inopinata.PRJDB5687.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_inopinata.PRJDB5687.WS284.genomic.fa.gz.fai"
}
}
},
- "name" : "Cas12e TTCN PAM sites",
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "assemblyNames" : [
- "c_inopinata_PRJDB5687"
- ],
- "trackId" : "c_inopinata_PRJDB5687_TTCN_sequence_search",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "SlateBlue",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
"height" : 4,
- "showDescriptions" : false
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "TTCN_sequence_search_c_inopinata_PRJDB5687-LinearBasicDisplay"
}
]
},
{
- "adapter" : {
- "search" : "TT.",
- "sequenceAdapter" : {
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_inopinata.PRJDB5687.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
- },
- "faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_inopinata.PRJDB5687.WS284.genomic.fa.gz.fai"
- },
- "gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_inopinata.PRJDB5687.WS284.genomic.fa.gz.gzi"
- },
- "type" : "BgzipFastaAdapter"
- },
- "type" : "SequenceSearchAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "Cas12a TTN PAM sites",
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
- "assemblyNames" : [
- "c_inopinata_PRJDB5687"
- ],
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
+ "assemblyNames" : [
+ "c_inopinata_PRJDB5687"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
"trackId" : "c_inopinata_PRJDB5687_TTN_sequence_search",
+ "name" : "Cas12a TTN PAM sites",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "Indigo",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
"height" : 4,
- "showDescriptions" : false
+ "showLabels" : false,
+ "color1" : "Indigo",
+ "type" : "SvgFeatureRenderer"
},
"displayId" : "TTN_sequence_search_c_inopinata_PRJDB5687-LinearBasicDisplay"
}
- ]
- },
- {
- "displays" : [
- {
- "renderer" : {
- "height" : 4,
- "showDescriptions" : false,
- "color1" : "DarkViolet",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ ],
+ "adapter" : {
+ "search" : "TT.",
+ "type" : "SequenceSearchAdapter",
+ "sequenceAdapter" : {
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_inopinata.PRJDB5687.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "NNGRRT_sequence_search_c_inopinata_PRJDB5687-LinearBasicDisplay"
+ "fastaLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_inopinata.PRJDB5687.WS284.genomic.fa.gz"
+ },
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_inopinata.PRJDB5687.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ }
}
- ],
- "trackId" : "c_inopinata_PRJDB5687_NNGRRT_sequence_search",
+ }
+ },
+ {
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
@@ -45871,12 +45149,32 @@
"assemblyNames" : [
"c_inopinata_PRJDB5687"
],
+ "type" : "FeatureTrack",
"description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
+ "trackId" : "c_inopinata_PRJDB5687_NNGRRT_sequence_search",
"name" : "SaCas9 NNGRRT PAM sites",
+ "displays" : [
+ {
+ "displayId" : "NNGRRT_sequence_search_c_inopinata_PRJDB5687-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "DarkViolet",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 4
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
- "type" : "SequenceSearchAdapter",
"search" : "..G[AG][AG]T",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_inopinata.PRJDB5687.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BgzipFastaAdapter",
"faiLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_inopinata.PRJDB5687.WS284.genomic.fa.gz.fai"
@@ -45884,142 +45182,136 @@
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_inopinata.PRJDB5687.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
- },
- "gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_inopinata.PRJDB5687.WS284.genomic.fa.gz.gzi"
- },
- "type" : "BgzipFastaAdapter"
+ }
}
- },
- "type" : "FeatureTrack"
+ }
},
{
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
+ "trackId" : "c_inopinata_PRJDB5687_NGG_sequence_search",
+ "name" : "SpCas9 NGG PAM sites",
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
+ "assemblyNames" : [
+ "c_inopinata_PRJDB5687"
+ ],
"type" : "FeatureTrack",
"adapter" : {
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_inopinata.PRJDB5687.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_inopinata.PRJDB5687.WS284.genomic.fa.gz.gzi"
},
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_inopinata.PRJDB5687.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
- "gziLocation" : {
+ "faiLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_inopinata.PRJDB5687.WS284.genomic.fa.gz.gzi"
- },
- "type" : "BgzipFastaAdapter"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_inopinata.PRJDB5687.WS284.genomic.fa.gz.fai"
+ }
},
- "search" : ".GG",
- "type" : "SequenceSearchAdapter"
+ "search" : ".GG"
},
- "name" : "SpCas9 NGG PAM sites",
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "assemblyNames" : [
- "c_inopinata_PRJDB5687"
- ],
- "trackId" : "c_inopinata_PRJDB5687_NGG_sequence_search",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "NGG_sequence_search_c_inopinata_PRJDB5687-LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "RebeccaPurple",
+ "showLabels" : false,
+ "height" : 4,
"showDescriptions" : false,
- "height" : 4
+ "color1" : "RebeccaPurple"
},
- "displayId" : "NGG_sequence_search_c_inopinata_PRJDB5687-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
]
},
{
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"labels" : {
"description" : "jexl:get(feature,'type')"
},
- "type" : "SvgFeatureRenderer",
"color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'"
},
- "displayId" : "gene_models_(historical)-c_japonica_PRJNA12591-LinearBasicDisplay"
+ "displayId" : "gene_models_(historical)-c_japonica_PRJNA12591-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Gene Models (historical)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"category" : [
"Genes",
"Curated Genes"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_japonica_PRJNA12591"
],
- "trackId" : "c_japonica_PRJNA12591_gene_models_(historical)",
"description" : "Historical gene predictions.",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Gene Models (historical)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "name" : "Gene Models (historical)"
+ "name" : "Gene Models (historical)",
+ "trackId" : "c_japonica_PRJNA12591_gene_models_(historical)"
},
{
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"Genes",
"Curated Genes"
],
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ],
"trackId" : "c_japonica_PRJNA12591_curated_genes_pseudogenes",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
+ "name" : "Curated Genes (pseudogenes)",
+ "description" : "A subset of the full Curated Genes set limited to pseudogenes only. Pseudogenes of tRNA are lighter gray and pseudogenes of rRNA are darker gray than pseudogenes of protein coding genes.",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "curated_genes_(pseudogenes)-c_japonica_PRJNA12591-LinearBasicDisplay",
"renderer" : {
"height" : 6,
"color1" : "gray",
"type" : "SvgFeatureRenderer"
- },
- "displayId" : "curated_genes_(pseudogenes)-c_japonica_PRJNA12591-LinearBasicDisplay"
+ }
}
],
- "type" : "FeatureTrack",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Curated Genes (pseudogenes)/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
}
- },
- "name" : "Curated Genes (pseudogenes)",
- "description" : "A subset of the full Curated Genes set limited to pseudogenes only. Pseudogenes of tRNA are lighter gray and pseudogenes of rRNA are darker gray than pseudogenes of protein coding genes."
+ }
},
{
+ "category" : [
+ "Reagents"
+ ],
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
+ ],
+ "type" : "FeatureTrack",
"description" : "This track shows the locations of the cosmids, fosmids, and YACs used for the physical mapping and sequencing of the C. elegans genome. The clone termini do not necessarily correspond to the termini of submitted GenBank/EMBL entries. In some cases the exact termini of the clones is not known. For example, YACs were sequenced using PCR amplification across gaps in the cosmid maps. When a clone end is not known, it is shown as an arrow extending to the end of the display. Such data is to be treated with caution. The Vancouver fosmids can be ordered directly from GeneService.",
+ "trackId" : "c_japonica_PRJNA12591_yacs_fosmids_cosmids",
"name" : "YACs, Fosmids, & Cosmids",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/YACs, Fosmids, & Cosmids/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
"displays" : [
{
"renderer" : {
@@ -46027,99 +45319,110 @@
"color1" : "black",
"height" : 3
},
- "type" : "LinearBasicDisplay",
- "displayId" : "yacs,_fosmids,_&_cosmids-c_japonica_PRJNA12591-LinearBasicDisplay"
+ "displayId" : "yacs,_fosmids,_&_cosmids-c_japonica_PRJNA12591-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "trackId" : "c_japonica_PRJNA12591_yacs_fosmids_cosmids",
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ],
- "category" : [
- "Reagents"
- ]
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/YACs, Fosmids, & Cosmids/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
"trackId" : "c_japonica_PRJNA12591_curated_genes_protein_coding",
+ "name" : "Curated Genes (protein coding)",
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
"assemblyNames" : [
"c_japonica_PRJNA12591"
],
+ "type" : "FeatureTrack",
"category" : [
"Genes",
"Curated Genes"
],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "displayId" : "curated_genes_(protein_coding)-c_japonica_PRJNA12591-LinearBasicDisplay",
"renderer" : {
- "maxHeight" : 5000,
"color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
+ "color3" : "#965567",
"type" : "SvgFeatureRenderer",
- "color3" : "#965567"
+ "maxHeight" : 5000
},
+ "displayId" : "curated_genes_(protein_coding)-c_japonica_PRJNA12591-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
- "name" : "Curated Genes (protein coding)",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track."
+ }
},
{
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"type" : "SvgFeatureRenderer",
+ "color1" : "jexl:startsWith(get(feature,'source'),'BLAT_mRNA_')==true?'yellow':'gray'",
"outline" : "black",
- "color1" : "jexl:startsWith(get(feature,'source'),'BLAT_mRNA_')==true?'yellow':'gray'"
+ "height" : 6
},
- "type" : "LinearBasicDisplay",
"displayId" : "mrnas/ncrnas_(best)-c_japonica_PRJNA12591-LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/mRNAs_ncRNAs (best)/{refseq}/trackData.jsonz"
+ }
},
- "trackId" : "c_japonica_PRJNA12591_mrnas/ncrnas_(best)",
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"Genes",
"Supporting Evidence"
],
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ],
- "description" : "Native (same species) full length cDNAs and ncRNAs aligned to the genome using BLAT. This track shows the best unique location for each cDNA.",
+ "trackId" : "c_japonica_PRJNA12591_mrnas/ncrnas_(best)",
"name" : "mRNAs/ncRNAs (best)",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/mRNAs_ncRNAs (best)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- }
+ "description" : "Native (same species) full length cDNAs and ncRNAs aligned to the genome using BLAT. This track shows the best unique location for each cDNA."
},
{
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
+ ],
+ "category" : [
+ "Sequence Features",
+ "Translated Features"
+ ],
+ "name" : "Protein motifs",
+ "trackId" : "c_japonica_PRJNA12591_protein_motifs",
+ "description" : "This track shows the extent of predicted protein motifs. Note these spans correspond to amino acid coordinates interpolated onto the physical map. Included are signal peptide (signalp), coiled coil (ncoils) and transmembrane (tmhmm) domains, regions of low complexity (seg), and Pfam annotated motif homologies.",
"displays" : [
{
"displayId" : "protein_motifs-c_japonica_PRJNA12591-LinearBasicDisplay",
"renderer" : {
- "color1" : "jexl:parent(feature)=='undefined'?'purple':get(parent(feature),'predictiontype')=='tmhmm'?'magenta':get(parent(feature),'predictiontype')=='seg'?'lightseagreen':get(parent(feature),'predictiontype')=='signalp'?'aquamarine':get(parent(feature),'predictiontype')=='ncoils'?'chartreuse':\nget(parent(feature),'predictiontype')=='pfam'?'lightsalmon':'purple'",
"type" : "SvgFeatureRenderer",
- "height" : 7
+ "height" : 7,
+ "color1" : "jexl:parent(feature)=='undefined'?'purple':get(parent(feature),'predictiontype')=='tmhmm'?'magenta':get(parent(feature),'predictiontype')=='seg'?'lightseagreen':get(parent(feature),'predictiontype')=='signalp'?'aquamarine':get(parent(feature),'predictiontype')=='ncoils'?'chartreuse':\nget(parent(feature),'predictiontype')=='pfam'?'lightsalmon':'purple'"
},
"type" : "LinearBasicDisplay"
}
@@ -46127,181 +45430,179 @@
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "trackId" : "c_japonica_PRJNA12591_protein_motifs",
- "category" : [
- "Sequence Features",
- "Translated Features"
- ],
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ],
- "description" : "This track shows the extent of predicted protein motifs. Note these spans correspond to amino acid coordinates interpolated onto the physical map. Included are signal peptide (signalp), coiled coil (ncoils) and transmembrane (tmhmm) domains, regions of low complexity (seg), and Pfam annotated motif homologies.",
- "name" : "Protein motifs",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Protein motifs/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- }
- }
- },
- {
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
- "name" : "Curated Genes",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Curated_Genes/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
- },
+ }
+ },
+ {
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
+ ],
"type" : "FeatureTrack",
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
+ "trackId" : "c_japonica_PRJNA12591_curated_genes",
+ "name" : "Curated Genes",
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
"displays" : [
{
"renderer" : {
- "color3" : "#965567",
+ "maxHeight" : 5000,
"type" : "SvgFeatureRenderer",
+ "color3" : "#965567",
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
},
- "maxHeight" : 5000,
"color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "curated_genes-c_japonica_PRJNA12591-LinearBasicDisplay"
+ "displayId" : "curated_genes-c_japonica_PRJNA12591-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
},
- "trackId" : "c_japonica_PRJNA12591_curated_genes",
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ],
- "category" : [
- "Genes",
- "Curated Genes"
- ]
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Curated_Genes/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
- "trackId" : "c_japonica_PRJNA12591_trans-spliced_acceptor",
- "category" : [
- "Sequence Features",
- "Signals & Motifs"
- ],
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "trans-spliced_acceptor-c_japonica_PRJNA12591-LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "jexl:get(feature,'source')=='SL1'?'red':get(feature,'source')=='SL2'?'green':'black'",
"labels" : {
"description" : "jexl:get(feature,'source') || get(feature,'description')"
- },
- "type" : "SvgFeatureRenderer",
- "color1" : "jexl:get(feature,'source')=='SL1'?'red':get(feature,'source')=='SL2'?'green':'black'"
+ }
},
- "displayId" : "trans-spliced_acceptor-c_japonica_PRJNA12591-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
- "name" : "Trans-spliced acceptor",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Trans-spliced acceptor/{refseq}/trackData.jsonz"
- }
+ },
+ "type" : "NCListAdapter"
},
- "description" : "This track contains SL1 and SL2 trans-spliced acceptors from a variety of sources: SL1 and SL2 trans-spliced acceptors published by Blumenthal et al, Nature (2002), Trans-Spliced Exon Coupled RNA End Determination (TEC-RED) Hwang et al, PNAS (2004), EST/mRNA sequence data, RNASeq read data from ENA. SL1 acceptors are show in red, SL2 in green. Direction of transcription is indicated by arrow direction."
+ "category" : [
+ "Sequence Features",
+ "Signals & Motifs"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
+ ],
+ "description" : "This track contains SL1 and SL2 trans-spliced acceptors from a variety of sources: SL1 and SL2 trans-spliced acceptors published by Blumenthal et al, Nature (2002), Trans-Spliced Exon Coupled RNA End Determination (TEC-RED) Hwang et al, PNAS (2004), EST/mRNA sequence data, RNASeq read data from ENA. SL1 acceptors are show in red, SL2 in green. Direction of transcription is indicated by arrow direction.",
+ "name" : "Trans-spliced acceptor",
+ "trackId" : "c_japonica_PRJNA12591_trans-spliced_acceptor"
},
{
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/genBlastG CDS predictions/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "name" : "genBlastG CDS predictions",
"description" : "Data from 'genBlastG: using BLAST searches to build homologous gene models' (WBPaper00040677).",
+ "name" : "genBlastG CDS predictions",
+ "trackId" : "c_japonica_PRJNA12591_genblastg_cds_predictions",
"category" : [
"Genes",
"Ab-initio predictions"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_japonica_PRJNA12591"
],
- "trackId" : "c_japonica_PRJNA12591_genblastg_cds_predictions",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/genBlastG CDS predictions/{refseq}/trackData.jsonz"
+ }
+ },
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "genblastg_cds_predictions-c_japonica_PRJNA12591-LinearBasicDisplay",
"renderer" : {
"height" : 7,
"type" : "SvgFeatureRenderer"
- },
- "displayId" : "genblastg_cds_predictions-c_japonica_PRJNA12591-LinearBasicDisplay"
+ }
}
]
},
{
"name" : "Curated Genes (noncoding)",
+ "trackId" : "c_japonica_PRJNA12591_curated_genes_noncoding",
+ "description" : "Non-coding curated gene models, including ncRNA, tRNA, miRNA, snRNA, snoRNA, piRNA, lincRNA and antisense RNA.",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
+ ],
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Curated Genes (noncoding)/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Curated Genes (noncoding)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
}
},
- "description" : "Non-coding curated gene models, including ncRNA, tRNA, miRNA, snRNA, snoRNA, piRNA, lincRNA and antisense RNA.",
- "trackId" : "c_japonica_PRJNA12591_curated_genes_noncoding",
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
"displays" : [
{
"displayId" : "curated_genes_(noncoding)-c_japonica_PRJNA12591-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "height" : 6,
"color1" : "gray",
- "type" : "SvgFeatureRenderer",
- "height" : 6
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
}
- ],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- }
+ ]
},
{
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
"displayId" : "repeat_region_(repeatmasker)-c_japonica_PRJNA12591-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"color1" : "bisque",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"height" : 4,
"showDescriptions" : false
- }
+ },
+ "type" : "LinearBasicDisplay"
}
],
+ "description" : "Repetitive regions identified by RepeatMasker.",
"trackId" : "c_japonica_PRJNA12591_repeat_region_(repeatmasker)",
+ "name" : "Repeat Region (RepeatMasker)",
"category" : [
"Genome Structure",
"Repeats"
@@ -46309,21 +45610,20 @@
"assemblyNames" : [
"c_japonica_PRJNA12591"
],
- "description" : "Repetitive regions identified by RepeatMasker.",
- "name" : "Repeat Region (RepeatMasker)",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
"type" : "FeatureTrack"
},
{
"description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"name" : "C. brenneri proteins",
+ "trackId" : "c_japonica_PRJNA12591_C_brenneri_proteins",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
+ ],
"adapter" : {
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/C. brenneri proteins/{refseq}/trackData.jsonz",
@@ -46333,71 +45633,40 @@
},
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "C_brenneri_proteins-c_japonica_PRJNA12591-LinearBasicDisplay",
"renderer" : {
+ "color1" : "orange",
"height" : 4,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "orange"
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
- "displayId" : "C_brenneri_proteins-c_japonica_PRJNA12591-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')"
}
- ],
- "trackId" : "c_japonica_PRJNA12591_C_brenneri_proteins",
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
]
},
{
- "name" : "P. pacificus proteins",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/P. pacificus proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "trackId" : "c_japonica_PRJNA12591_P_pacificus_proteins",
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ],
"displays" : [
{
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
+ "showLabels" : false,
"height" : 4,
"color1" : "orange",
- "showLabels" : false,
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "P_pacificus_proteins-c_japonica_PRJNA12591-LinearBasicDisplay"
+ "displayId" : "P_pacificus_proteins-c_japonica_PRJNA12591-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ]
- },
- {
- "name" : "C. japonica proteins",
- "type" : "FeatureTrack",
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/C. japonica proteins/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/P. pacificus proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
}
},
- "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "trackId" : "c_japonica_PRJNA12591_C_japonica_proteins",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_japonica_PRJNA12591"
],
@@ -46405,35 +45674,48 @@
"Sequence Similarity",
"Proteins"
],
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
- "renderer" : {
- "height" : 4,
- "color1" : "orange",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "displayId" : "C_japonica_proteins-c_japonica_PRJNA12591-LinearBasicDisplay"
- }
- ]
+ "name" : "P. pacificus proteins",
+ "trackId" : "c_japonica_PRJNA12591_P_pacificus_proteins",
+ "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
},
{
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/C. japonica proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
"renderer" : {
- "color1" : "orange",
+ "height" : 4,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 4
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
},
"mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
- "displayId" : "T_muris_proteins-c_japonica_PRJNA12591-LinearBasicDisplay"
+ "displayId" : "C_japonica_proteins-c_japonica_PRJNA12591-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
+ "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_japonica_PRJNA12591_C_japonica_proteins",
+ "name" : "C. japonica proteins",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
+ ],
+ "type" : "FeatureTrack"
+ },
+ {
+ "name" : "T. muris proteins",
"trackId" : "c_japonica_PRJNA12591_T_muris_proteins",
+ "description" : "Matches to WormBase T. muris proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_japonica_PRJNA12591"
],
@@ -46441,20 +45723,28 @@
"Sequence Similarity",
"Proteins"
],
- "description" : "Matches to WormBase T. muris proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "T. muris proteins",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/T. muris proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "NCListAdapter"
},
- "type" : "FeatureTrack"
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "orange",
+ "showLabels" : false,
+ "height" : 4
+ },
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "T_muris_proteins-c_japonica_PRJNA12591-LinearBasicDisplay"
+ }
+ ]
},
{
- "name" : "Low complextity region (Dust)",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -46462,431 +45752,430 @@
"locationType" : "UriLocation"
}
},
- "description" : "Low-complexity regions identified by Dust.",
- "trackId" : "c_japonica_PRJNA12591_low_complextity_region_(dust)",
- "category" : [
- "Genome Structure",
- "Repeats"
- ],
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ],
"displays" : [
{
"renderer" : {
- "color1" : "bisque",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
+ "showDescriptions" : false,
"height" : 4,
- "showDescriptions" : false
+ "showLabels" : false,
+ "color1" : "bisque",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "low_complextity_region_(dust)-c_japonica_PRJNA12591-LinearBasicDisplay"
+ "displayId" : "low_complextity_region_(dust)-c_japonica_PRJNA12591-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
+ ],
+ "trackId" : "c_japonica_PRJNA12591_low_complextity_region_(dust)",
+ "name" : "Low complextity region (Dust)",
+ "description" : "Low-complexity regions identified by Dust.",
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Genome Structure",
+ "Repeats"
]
},
{
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/B. malayi proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "displayId" : "B_malayi_proteins-c_japonica_PRJNA12591-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
+ "color1" : "orange",
"showLabels" : false,
"height" : 4
- }
+ },
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "B_malayi_proteins-c_japonica_PRJNA12591-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
+ "description" : "Matches to WormBase B. malayi proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "B. malayi proteins",
"trackId" : "c_japonica_PRJNA12591_B_malayi_proteins",
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ],
"category" : [
"Sequence Similarity",
"Proteins"
],
- "description" : "Matches to WormBase B. malayi proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "B. malayi proteins",
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/B. malayi proteins/{refseq}/trackData.jsonz"
- }
- }
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
+ ]
},
{
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/S. ratti proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ }
},
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "S_ratti_proteins-c_japonica_PRJNA12591-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "orange",
+ "height" : 4,
+ "showLabels" : false
+ },
+ "mouseover" : "jexl:get(feature,'clone')"
+ }
+ ],
"name" : "S. ratti proteins",
+ "trackId" : "c_japonica_PRJNA12591_S_ratti_proteins",
"description" : "Matches to WormBase S. ratti proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_japonica_PRJNA12591"
],
"category" : [
"Sequence Similarity",
"Proteins"
- ],
- "trackId" : "c_japonica_PRJNA12591_S_ratti_proteins",
- "displays" : [
- {
- "displayId" : "S_ratti_proteins-c_japonica_PRJNA12591-LinearBasicDisplay",
- "renderer" : {
- "height" : 4,
- "color1" : "orange",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
- },
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay"
- }
]
},
{
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Contig submissions/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
- "displayId" : "contig_submissions-c_japonica_PRJNA12591-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "contig_submissions-c_japonica_PRJNA12591-LinearBasicDisplay",
"renderer" : {
- "height" : 7,
+ "type" : "SvgFeatureRenderer",
"color1" : "sienna",
- "type" : "SvgFeatureRenderer"
+ "height" : 7
}
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
+ "description" : "This track shows the location and coordinates of contigs (mostly cosmids) submitted to GenBank/EMBL.",
"trackId" : "c_japonica_PRJNA12591_contig_submissions",
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ],
+ "name" : "Contig submissions",
"category" : [
"Genome Structure",
"Assembly & Curation"
],
- "description" : "This track shows the location and coordinates of contigs (mostly cosmids) submitted to GenBank/EMBL.",
- "name" : "Contig submissions",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Contig submissions/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
+ ],
"type" : "FeatureTrack"
},
{
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
+ ],
+ "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "S. cerevisiae proteins",
+ "trackId" : "c_japonica_PRJNA12591_S_cerevisiae_proteins",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
+ "height" : 4,
"color1" : "orange",
- "height" : 4
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')",
"displayId" : "S_cerevisiae_proteins-c_japonica_PRJNA12591-LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "trackId" : "c_japonica_PRJNA12591_S_cerevisiae_proteins",
- "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz"
}
- },
- "name" : "S. cerevisiae proteins"
+ }
},
{
- "name" : "WormBase nematode mRNAs/ESTs (best)",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/WormBase nematode mRNAs_ESTs (best)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/WormBase nematode mRNAs_ESTs (best)/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "description" : "ESTs and mRNAs from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each cDNA sequence. mRNAs are shown in light blue; ESTs in green.",
- "trackId" : "wormbase_nematode_mrnas/ests_(best)-c_japonica_PRJNA12591",
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ],
- "category" : [
- "Sequence Similarity",
- "Nucleotide"
- ],
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
"height" : 4,
+ "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA_BEST'?'lightblue':get(feature,'source')=='BLAT_Caen_EST_BEST'?'green':'black'",
"labels" : {
"name" : "jexl:get(feature,'species') || get(feature,'id')"
},
- "type" : "SvgFeatureRenderer",
- "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA_BEST'?'lightblue':get(feature,'source')=='BLAT_Caen_EST_BEST'?'green':'black'"
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "wormbase_nematode_mrnas/ests_(best)-c_japonica_PRJNA12591-LinearBasicDisplay"
}
- ]
- },
- {
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
],
+ "description" : "ESTs and mRNAs from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each cDNA sequence. mRNAs are shown in light blue; ESTs in green.",
+ "trackId" : "wormbase_nematode_mrnas/ests_(best)-c_japonica_PRJNA12591",
+ "name" : "WormBase nematode mRNAs/ESTs (best)",
"category" : [
- "Genes",
- "Supporting Evidence"
+ "Sequence Similarity",
+ "Nucleotide"
],
- "trackId" : "c_japonica_PRJNA12591_trinity-assembled_rnaseq",
- "displays" : [
- {
- "displayId" : "trinity-assembled_rnaseq-c_japonica_PRJNA12591-LinearBasicDisplay",
- "renderer" : {
- "color1" : "mediumpurple",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 5
- },
- "type" : "LinearBasicDisplay"
- }
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
],
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Trinity-assembled RNAseq/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "Trinity-assembled RNAseq",
- "description" : "Native (same species) RNAseq data was assembled with Trinity and then aligned to the genome with BLAT"
+ "type" : "FeatureTrack"
},
{
+ "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "rnaseq_asymmetries-c_japonica_PRJNA12591-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "jexl:get(feature,'source')=='RNASeq_R_asymmetry'?'red': get(feature,'source')=='RNASeq_F_asymmetry'?'green':'black'",
"type" : "SvgFeatureRenderer",
+ "color1" : "mediumpurple",
"showLabels" : false,
- "height" : 24,
- "displayMode" : "collapse"
+ "height" : 5
},
- "mouseover" : "jexl:'Score: '+get(feature,'score')",
- "type" : "LinearBasicDisplay"
+ "displayId" : "trinity-assembled_rnaseq-c_japonica_PRJNA12591-LinearBasicDisplay"
}
],
"assemblyNames" : [
"c_japonica_PRJNA12591"
],
"category" : [
- "Expression"
+ "Genes",
+ "Supporting Evidence"
],
- "trackId" : "c_japonica_PRJNA12591_rnaseq_asymmetries",
- "description" : "Red boxes indicate regions where there are more than 2 times as many forward sense RNASeq reads aligned to the genome as reverse sense reads. This asymmetrical signal has been found empirically to be a sensitive marker for the ends of transcripts. Green boxes indicate regions where there are more than 2 times as many reverse sense RNASeq reads aligned to the genome as forward sense reads. This asymmetrical signal has been found empirically to be sensitive marker for the ends of transcripts. The height of all boxes indicates the relative score of the feature.",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/RNASeq Asymmetries/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Trinity-assembled RNAseq/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "name" : "RNASeq Asymmetries"
+ "name" : "Trinity-assembled RNAseq",
+ "trackId" : "c_japonica_PRJNA12591_trinity-assembled_rnaseq",
+ "description" : "Native (same species) RNAseq data was assembled with Trinity and then aligned to the genome with BLAT"
},
{
- "trackId" : "c_japonica_PRJNA12591_rnaseq_introns",
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ],
+ "description" : "Red boxes indicate regions where there are more than 2 times as many forward sense RNASeq reads aligned to the genome as reverse sense reads. This asymmetrical signal has been found empirically to be a sensitive marker for the ends of transcripts. Green boxes indicate regions where there are more than 2 times as many reverse sense RNASeq reads aligned to the genome as forward sense reads. This asymmetrical signal has been found empirically to be sensitive marker for the ends of transcripts. The height of all boxes indicates the relative score of the feature.",
+ "trackId" : "c_japonica_PRJNA12591_rnaseq_asymmetries",
+ "name" : "RNASeq Asymmetries",
"category" : [
"Expression"
],
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
+ ],
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/RNASeq Asymmetries/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
- "mouseover" : "jexl:get(feature,'score')+' reads'",
"renderer" : {
- "showLabels" : false,
+ "displayMode" : "collapse",
"type" : "SvgFeatureRenderer",
- "color1" : "green",
- "showDescriptions" : false,
- "height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)"
+ "height" : 24,
+ "showLabels" : false,
+ "color1" : "jexl:get(feature,'source')=='RNASeq_R_asymmetry'?'red': get(feature,'source')=='RNASeq_F_asymmetry'?'green':'black'"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "rnaseq_introns-c_japonica_PRJNA12591-LinearBasicDisplay"
- }
- ],
- "name" : "RNASeq introns",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/RNASeq introns/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "mouseover" : "jexl:'Score: '+get(feature,'score')",
+ "displayId" : "rnaseq_asymmetries-c_japonica_PRJNA12591-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- },
- "type" : "FeatureTrack",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display."
+ ]
},
{
- "name" : "RNASeq Splice Junctions (common)",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/RNASeq Splice Junctions (common)/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/RNASeq introns/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
- "trackId" : "c_japonica_PRJNA12591_rnaseq_splice_junctions_(common)",
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ],
- "category" : [
- "Expression"
- ],
"displays" : [
{
- "mouseover" : "jexl:get(feature,'score')+' reads'",
+ "type" : "LinearBasicDisplay",
+ "displayId" : "rnaseq_introns-c_japonica_PRJNA12591-LinearBasicDisplay",
"renderer" : {
- "color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "showDescriptions" : false
+ "showDescriptions" : false,
+ "height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)",
+ "showLabels" : false,
+ "color1" : "green"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "rnaseq_splice_junctions_(common)-c_japonica_PRJNA12591-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'score')+' reads'"
}
+ ],
+ "name" : "RNASeq introns",
+ "trackId" : "c_japonica_PRJNA12591_rnaseq_introns",
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
+ ],
+ "category" : [
+ "Expression"
]
},
{
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "RNASeq Splice Junctions (rare)",
"displays" : [
{
- "displayId" : "rnaseq_splice_junctions_(rare)-c_japonica_PRJNA12591-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'score')+' reads'",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "height" : "jexl:4",
"color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
- "maxHeight" : 5000,
- "showLabels" : false,
- "showDescriptions" : false
- }
+ "showDescriptions" : false,
+ "showLabels" : false
+ },
+ "displayId" : "rnaseq_splice_junctions_(common)-c_japonica_PRJNA12591-LinearBasicDisplay"
}
],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/RNASeq Splice Junctions (common)/{refseq}/trackData.jsonz"
+ }
+ },
"category" : [
"Expression"
],
"assemblyNames" : [
"c_japonica_PRJNA12591"
],
- "trackId" : "c_japonica_PRJNA12591_rnaseq_splice_junctions_(rare)"
+ "type" : "FeatureTrack",
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
+ "trackId" : "c_japonica_PRJNA12591_rnaseq_splice_junctions_(common)",
+ "name" : "RNASeq Splice Junctions (common)"
},
{
- "name" : "Nanopore matches",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Nanopore matches/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "description" : "This Nanopore transcript data is from the paper 'The full-length transcriptome of C. elegans using direct RNA sequencing' Roach et al. https://doi.org/10.1101/598763. Where several transcripts are nearly identical, they are represented by a single transcript and the number of transcripts is recorded in the read coverage. Sequencing is from 3' to 5' and randomly terminates, so the 5' end of transcripts is often incomplete.",
- "trackId" : "c_japonica_PRJNA12591_nanopore_matches",
"category" : [
- "Genes",
- "Supporting Evidence"
+ "Expression"
],
"assemblyNames" : [
"c_japonica_PRJNA12591"
],
+ "type" : "FeatureTrack",
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
+ "trackId" : "c_japonica_PRJNA12591_rnaseq_splice_junctions_(rare)",
+ "name" : "RNASeq Splice Junctions (rare)",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA'?'lightblue':'green'",
"maxHeight" : 5000,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "type" : "SvgFeatureRenderer",
+ "color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
+ "showDescriptions" : false,
+ "height" : "jexl:4",
+ "showLabels" : false
},
- "type" : "LinearBasicDisplay",
- "displayId" : "nanopore_matches-c_japonica_PRJNA12591-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'score')+' reads'",
+ "displayId" : "rnaseq_splice_junctions_(rare)-c_japonica_PRJNA12591-LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
- "name" : "RNASeq",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/RNASeq/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Nanopore matches/{refseq}/trackData.jsonz"
}
},
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "showLabels" : false,
+ "height" : 4,
+ "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA'?'lightblue':'green'",
+ "type" : "SvgFeatureRenderer",
+ "maxHeight" : 5000
+ },
+ "displayId" : "nanopore_matches-c_japonica_PRJNA12591-LinearBasicDisplay"
+ }
+ ],
+ "name" : "Nanopore matches",
+ "trackId" : "c_japonica_PRJNA12591_nanopore_matches",
+ "description" : "This Nanopore transcript data is from the paper 'The full-length transcriptome of C. elegans using direct RNA sequencing' Roach et al. https://doi.org/10.1101/598763. Where several transcripts are nearly identical, they are represented by a single transcript and the number of transcripts is recorded in the read coverage. Sequencing is from 3' to 5' and randomly terminates, so the 5' end of transcripts is often incomplete.",
"type" : "FeatureTrack",
- "description" : "These boxes indicate alignments of short read sequences from all available RNASeq projects. The number of reads has been normalised by averaging over the number of libraries. The height of all boxes indicates the relative score of the feature.",
- "trackId" : "c_japonica_PRJNA12591_rnaseq",
"assemblyNames" : [
"c_japonica_PRJNA12591"
],
+ "category" : [
+ "Genes",
+ "Supporting Evidence"
+ ]
+ },
+ {
"category" : [
"Expression"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
+ ],
+ "description" : "These boxes indicate alignments of short read sequences from all available RNASeq projects. The number of reads has been normalised by averaging over the number of libraries. The height of all boxes indicates the relative score of the feature.",
+ "name" : "RNASeq",
+ "trackId" : "c_japonica_PRJNA12591_rnaseq",
"displays" : [
{
"type" : "LinearBasicDisplay",
"mouseover" : "jexl:'Score: '+get(feature,'score')",
"renderer" : {
- "height" : "jexl:get(feature,'score')>100?50:floor(get(feature,'score')/2)>4?floor(get(feature,'score')/2):4",
"displayMode" : "collapse",
- "showDescriptions" : false,
"color1" : "black",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : "jexl:get(feature,'score')>100?50:floor(get(feature,'score')/2)>4?floor(get(feature,'score')/2):4",
+ "type" : "SvgFeatureRenderer"
},
"displayId" : "rnaseq-c_japonica_PRJNA12591-LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/RNASeq/{refseq}/trackData.jsonz"
+ }
+ }
},
{
- "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "H. sapiens proteins",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -46897,102 +46186,116 @@
"displays" : [
{
"displayId" : "H_sapiens_proteins-c_japonica_PRJNA12591-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
+ "height" : 4,
"color1" : "orange",
- "height" : 4
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')"
+ "mouseover" : "jexl:get(feature,'clone')",
+ "type" : "LinearBasicDisplay"
}
],
+ "name" : "H. sapiens proteins",
"trackId" : "c_japonica_PRJNA12591_H_sapiens_proteins",
+ "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
+ ],
"category" : [
"Sequence Similarity",
"Proteins"
- ],
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
]
},
{
- "name" : "Links and Superlinks",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Links and Superlinks/{refseq}/trackData.jsonz"
- }
+ },
+ "type" : "NCListAdapter"
+ },
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "type" : "FeatureTrack",
- "description" : "This track shows the location and coordinates of contigs created during the assembly of the C. elegans genome.",
- "trackId" : "c_japonica_PRJNA12591_links_and_superlinks",
- "category" : [
- "Genome Structure",
- "Assembly & Curation"
- ],
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ],
"displays" : [
{
+ "displayId" : "links_and_superlinks-c_japonica_PRJNA12591-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
"color1" : "black",
+ "height" : 4,
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "links_and_superlinks-c_japonica_PRJNA12591-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- }
+ "trackId" : "c_japonica_PRJNA12591_links_and_superlinks",
+ "name" : "Links and Superlinks",
+ "description" : "This track shows the location and coordinates of contigs created during the assembly of the C. elegans genome.",
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Genome Structure",
+ "Assembly & Curation"
+ ]
},
{
- "name" : "Tandem and Inverted Repeats",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Tandem and Inverted Repeats/{refseq}/trackData.jsonz"
- }
- },
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
+ ],
"type" : "FeatureTrack",
- "description" : "Exact tandem and inverted repetitive elements.",
- "trackId" : "c_japonica_PRJNA12591_tandem_and_inverted_repeats",
"category" : [
"Genome Structure",
"Repeats"
],
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ],
+ "trackId" : "c_japonica_PRJNA12591_tandem_and_inverted_repeats",
+ "name" : "Tandem and Inverted Repeats",
+ "description" : "Exact tandem and inverted repetitive elements.",
"displays" : [
{
+ "displayId" : "tandem_and_inverted_repeats-c_japonica_PRJNA12591-LinearBasicDisplay",
"renderer" : {
- "color1" : "bisque",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "showDescriptions" : false
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "color1" : "bisque"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "tandem_and_inverted_repeats-c_japonica_PRJNA12591-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
- ]
- },
- {
- "type" : "FeatureTrack",
+ ],
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/O. volvulus proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Tandem and Inverted Repeats/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
+ }
+ },
+ {
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "orange",
+ "showLabels" : false,
+ "height" : 4
+ },
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "O_volvulus_proteins-c_japonica_PRJNA12591-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/O. volvulus proteins/{refseq}/trackData.jsonz"
+ }
},
- "name" : "O. volvulus proteins",
- "description" : "Matches to WormBase O. volvulus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_japonica_PRJNA12591"
],
@@ -47000,65 +46303,47 @@
"Sequence Similarity",
"Proteins"
],
+ "name" : "O. volvulus proteins",
"trackId" : "c_japonica_PRJNA12591_O_volvulus_proteins",
- "displays" : [
- {
- "displayId" : "O_volvulus_proteins-c_japonica_PRJNA12591-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
- "renderer" : {
- "height" : 4,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "orange"
- }
- }
- ]
+ "description" : "Matches to WormBase O. volvulus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
},
{
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Microarray oligo probes/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
"displays" : [
{
- "displayId" : "microarray_oligo_probes-c_japonica_PRJNA12591-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "black",
"type" : "SvgFeatureRenderer",
- "height" : 4
- }
+ "height" : 4,
+ "color1" : "black"
+ },
+ "displayId" : "microarray_oligo_probes-c_japonica_PRJNA12591-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "category" : [
- "Reagents"
- ],
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ],
+ "name" : "Microarray oligo probes",
"trackId" : "c_japonica_PRJNA12591_microarray_oligo_probes",
"description" : "This track contains Affymetrix GeneChip and Washington University GSC microarray probe sets.",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Microarray oligo probes/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
"type" : "FeatureTrack",
- "name" : "Microarray oligo probes"
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
+ ],
+ "category" : [
+ "Reagents"
+ ]
},
{
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Other UniProt proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "Other UniProt proteins",
"description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_japonica_PRJNA12591_other_uniprot_proteins",
+ "name" : "Other UniProt proteins",
"category" : [
"Sequence Similarity",
"Proteins"
@@ -47066,109 +46351,116 @@
"assemblyNames" : [
"c_japonica_PRJNA12591"
],
- "trackId" : "c_japonica_PRJNA12591_other_uniprot_proteins",
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Other UniProt proteins/{refseq}/trackData.jsonz"
+ }
+ },
"displays" : [
{
- "displayId" : "other_uniprot_proteins-c_japonica_PRJNA12591-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "showLabels" : false,
"showDescriptions" : false,
"height" : 4,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "orange"
- }
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "other_uniprot_proteins-c_japonica_PRJNA12591-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
]
},
{
- "description" : "IsoSeq from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each IsoSeqsequence.",
+ "trackId" : "non-c._elegans_isoseq_collection_(best)-c_japonica_PRJNA12591",
"name" : "Non-C. elegans Isoseq collection (best)",
+ "description" : "IsoSeq from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each IsoSeqsequence.",
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Sequence Similarity",
+ "Nucleotide"
+ ],
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Non-C. elegans Isoseq collection (best)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Non-C. elegans Isoseq collection (best)/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
+ "height" : 4,
"color1" : "green",
- "type" : "SvgFeatureRenderer",
- "height" : 4
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "non-c._elegans_isoseq_collection_(best)-c_japonica_PRJNA12591-LinearBasicDisplay"
}
- ],
- "trackId" : "non-c._elegans_isoseq_collection_(best)-c_japonica_PRJNA12591",
+ ]
+ },
+ {
"category" : [
"Sequence Similarity",
- "Nucleotide"
+ "Proteins"
],
"assemblyNames" : [
"c_japonica_PRJNA12591"
- ]
- },
- {
- "name" : "C. briggsae proteins",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/C. briggsae proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
+ ],
"type" : "FeatureTrack",
"description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"trackId" : "c_japonica_PRJNA12591_C_briggsae_proteins",
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
+ "name" : "C. briggsae proteins",
"displays" : [
{
- "mouseover" : "jexl:get(feature,'clone')",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "orange",
- "type" : "SvgFeatureRenderer",
+ "height" : 4,
"showLabels" : false,
- "height" : 4
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"displayId" : "C_briggsae_proteins-c_japonica_PRJNA12591-LinearBasicDisplay"
}
- ]
- },
- {
- "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "type" : "FeatureTrack",
+ ],
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/C. briggsae proteins/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
+ }
+ },
+ {
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz"
+ }
},
- "name" : "D. melanogaster proteins",
"displays" : [
{
- "displayId" : "D_melanogaster_proteins-c_japonica_PRJNA12591-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
"color1" : "orange",
+ "height" : 4,
"showLabels" : false,
"type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')"
+ "displayId" : "D_melanogaster_proteins-c_japonica_PRJNA12591-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
+ "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_japonica_PRJNA12591_D_melanogaster_proteins",
+ "name" : "D. melanogaster proteins",
"category" : [
"Sequence Similarity",
"Proteins"
@@ -47176,54 +46468,53 @@
"assemblyNames" : [
"c_japonica_PRJNA12591"
],
- "trackId" : "c_japonica_PRJNA12591_D_melanogaster_proteins"
+ "type" : "FeatureTrack"
},
{
+ "trackId" : "c_japonica_PRJNA12591_ests",
+ "name" : "ESTs",
+ "description" : "Native (same-species) Expressed Sequence Tags (ESTs), aligned to the genome using BLAT. This track shows the best unique location for each EST. The paired 5' and 3' ESTs from the same cDNA clone are connected by a dashed line and a colored light green. ESTs with no mate are yellow, and ESTs with a mate that is 'far away' are dark green.",
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"Genes",
"Supporting Evidence"
],
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ],
- "trackId" : "c_japonica_PRJNA12591_ests",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/ESTs (best)/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
},
"displays" : [
{
- "displayId" : "ests-c_japonica_PRJNA12591-LinearBasicDisplay",
"renderer" : {
"color1" : "jexl:parent(feature)=='undefined'?'red':get(parent(feature),'has_mate')==1?'limegreen':get(parent(feature),'has_mate')==2?'green':get(parent(feature),'has_mate')==0?'gold':'black'",
"maxHeight" : 5000,
"type" : "SvgFeatureRenderer"
},
+ "displayId" : "ests-c_japonica_PRJNA12591-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/ESTs (best)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "ESTs",
- "description" : "Native (same-species) Expressed Sequence Tags (ESTs), aligned to the genome using BLAT. This track shows the best unique location for each EST. The paired 5' and 3' ESTs from the same cDNA clone are connected by a dashed line and a colored light green. ESTs with no mate are yellow, and ESTs with a mate that is 'far away' are dark green."
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ }
},
{
+ "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_japonica_PRJNA12591_C_elegans_proteins",
"name" : "C. elegans proteins",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/C. elegans proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/C. elegans proteins/{refseq}/trackData.jsonz"
+ }
},
- "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "trackId" : "c_japonica_PRJNA12591_C_elegans_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
@@ -47233,481 +46524,428 @@
],
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
+ "height" : 4,
"color1" : "orange",
- "height" : 4
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "C_elegans_proteins-c_japonica_PRJNA12591-LinearBasicDisplay"
}
- ]
+ ],
+ "type" : "FeatureTrack"
},
{
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ],
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"trackId" : "c_japonica_PRJNA12591_C_remanei_proteins",
+ "name" : "C. remanei proteins",
"displays" : [
{
"displayId" : "C_remanei_proteins-c_japonica_PRJNA12591-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "orange",
- "height" : 4
+ "showLabels" : false,
+ "height" : 4,
+ "color1" : "orange"
},
- "mouseover" : "jexl:get(feature,'clone')",
"type" : "LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/C. remanei proteins/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/C. remanei proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
- },
- "name" : "C. remanei proteins",
- "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ }
},
{
- "name" : "Genbank submissions",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Genbank submissions/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/Genbank submissions/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "description" : "The C. elegans genome was submitted to the GenBank and EMBL databases in in the form of a set of minimally-overlapping segments. This track shows the position of these accessioned entries.",
- "trackId" : "c_japonica_PRJNA12591_genbank_submissions",
- "category" : [
- "Genome Structure",
- "Assembly & Curation"
- ],
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"displays" : [
{
"displayId" : "genbank_submissions-c_japonica_PRJNA12591-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'genbank')",
"renderer" : {
- "type" : "SvgFeatureRenderer",
+ "height" : 4,
"color1" : "sienna",
- "height" : 4
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- }
- },
- {
- "trackId" : "c_japonica_PRJNA12591_TTCN_sequence_search",
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
+ "name" : "Genbank submissions",
+ "trackId" : "c_japonica_PRJNA12591_genbank_submissions",
+ "description" : "The C. elegans genome was submitted to the GenBank and EMBL databases in in the form of a set of minimally-overlapping segments. This track shows the position of these accessioned entries.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_japonica_PRJNA12591"
],
+ "category" : [
+ "Genome Structure",
+ "Assembly & Curation"
+ ]
+ },
+ {
"displays" : [
{
- "displayId" : "TTCN_sequence_search_c_japonica_PRJNA12591-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 4,
"type" : "SvgFeatureRenderer",
"showLabels" : false,
+ "height" : 4,
+ "showDescriptions" : false,
"color1" : "SlateBlue"
- }
+ },
+ "displayId" : "TTCN_sequence_search_c_japonica_PRJNA12591-LinearBasicDisplay"
}
],
- "name" : "Cas12e TTCN PAM sites",
"adapter" : {
"type" : "SequenceSearchAdapter",
- "search" : "TTC.",
"sequenceAdapter" : {
- "gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz.gzi"
- },
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
"faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz.fai"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
},
- "type" : "BgzipFastaAdapter"
- }
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz.gzi"
+ }
+ },
+ "search" : "TTC."
},
- "type" : "FeatureTrack",
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time."
- },
- {
- "trackId" : "c_japonica_PRJNA12591_TTN_sequence_search",
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ],
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "displays" : [
- {
- "displayId" : "TTN_sequence_search_c_japonica_PRJNA12591-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "Indigo",
- "showDescriptions" : false,
- "height" : 4
- }
- }
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
],
- "name" : "Cas12a TTN PAM sites",
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "SequenceSearchAdapter",
- "sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
- },
- "faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz.fai"
- },
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
- }
- },
- "search" : "TT."
- },
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time."
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
+ "trackId" : "c_japonica_PRJNA12591_TTCN_sequence_search",
+ "name" : "Cas12e TTCN PAM sites"
},
{
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
"adapter" : {
+ "search" : "TT.",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
- "faiLocation" : {
+ "gziLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz.fai"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz.gzi"
},
+ "type" : "BgzipFastaAdapter",
"fastaLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz"
},
- "gziLocation" : {
+ "faiLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz.fai"
}
},
- "search" : "..G[AG][AG]T",
"type" : "SequenceSearchAdapter"
},
- "type" : "FeatureTrack",
- "name" : "SaCas9 NNGRRT PAM sites",
"displays" : [
{
- "displayId" : "NNGRRT_sequence_search_c_japonica_PRJNA12591-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "DarkViolet",
+ "color1" : "Indigo",
"showDescriptions" : false,
- "height" : 4
- }
+ "height" : 4,
+ "showLabels" : false
+ },
+ "displayId" : "TTN_sequence_search_c_japonica_PRJNA12591-LinearBasicDisplay"
}
],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
+ "trackId" : "c_japonica_PRJNA12591_TTN_sequence_search",
+ "name" : "Cas12a TTN PAM sites",
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
"assemblyNames" : [
"c_japonica_PRJNA12591"
],
- "trackId" : "c_japonica_PRJNA12591_NNGRRT_sequence_search"
+ "type" : "FeatureTrack",
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ]
},
{
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "NNGRRT_sequence_search_c_japonica_PRJNA12591-LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 4,
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "RebeccaPurple"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "NGG_sequence_search_c_japonica_PRJNA12591-LinearBasicDisplay"
+ "color1" : "DarkViolet",
+ "height" : 4,
+ "showDescriptions" : false,
+ "showLabels" : false
+ }
}
],
- "trackId" : "c_japonica_PRJNA12591_NGG_sequence_search",
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
- ],
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
- "name" : "SpCas9 NGG PAM sites",
"adapter" : {
+ "search" : "..G[AG][AG]T",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
"type" : "BgzipFastaAdapter",
- "faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz.fai"
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
},
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
- "gziLocation" : {
+ "faiLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz.fai"
}
- },
- "search" : ".GG",
- "type" : "SequenceSearchAdapter"
- },
- "type" : "FeatureTrack"
- },
- {
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display.",
- "name" : "RNASeq introns",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/RNASeq introns/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ }
},
"type" : "FeatureTrack",
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'score')+' reads'",
- "renderer" : {
- "showDescriptions" : false,
- "height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "green"
- },
- "displayId" : "rnaseq_introns-c_japonica_PRJNA12591-LinearBasicDisplay"
- }
- ],
- "trackId" : "c_japonica_PRJNA12591_rnaseq_introns",
"assemblyNames" : [
"c_japonica_PRJNA12591"
],
"category" : [
- "Expression"
- ]
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
+ "name" : "SaCas9 NNGRRT PAM sites",
+ "trackId" : "c_japonica_PRJNA12591_NNGRRT_sequence_search",
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time."
},
{
- "displays" : [
- {
- "renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "jexl:get(feature,'score')>1000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/1000))))+'00'+hex(round(255-(140*(get(feature,'score')/1000)))):'#00'+hex(round(255-(140*(get(feature,'score')/1000))))+hex(round(255-(140*(get(feature,'score')/1000))))",
- "showDescriptions" : false
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
+ "trackId" : "c_japonica_PRJNA12591_NGG_sequence_search",
+ "name" : "SpCas9 NGG PAM sites",
+ "adapter" : {
+ "search" : ".GG",
+ "sequenceAdapter" : {
+ "fastaLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz"
},
- "mouseover" : "jexl:get(feature,'score')+' reads'",
- "type" : "LinearBasicDisplay",
- "displayId" : "rnaseq_splice_junctions_(common)-c_japonica_PRJNA12591-LinearBasicDisplay"
- }
- ],
+ "faiLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz.fai"
+ },
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BgzipFastaAdapter"
+ },
+ "type" : "SequenceSearchAdapter"
+ },
"category" : [
- "Expression"
- ],
- "assemblyNames" : [
- "c_japonica_PRJNA12591"
+ "Externally Sourced Resources",
+ "CRISPR predictions"
],
- "trackId" : "c_japonica_PRJNA12591_rnaseq_splice_junctions_(common)",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/RNASeq Splice Junctions (common)/{refseq}/trackData.jsonz"
- }
- },
- "type" : "FeatureTrack",
- "name" : "RNASeq Splice Junctions (common)"
- },
- {
"assemblyNames" : [
"c_japonica_PRJNA12591"
],
- "category" : [
- "Expression"
- ],
- "trackId" : "c_japonica_PRJNA12591_rnaseq_splice_junctions_(rare)",
"displays" : [
{
"type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'score')+' reads'",
"renderer" : {
- "showDescriptions" : false,
- "height" : "jexl:4",
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "jexl:get(feature,'score')>1000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/1000))))+'00'+hex(round(255-(140*(get(feature,'score')/1000)))):'#00'+hex(round(255-(140*(get(feature,'score')/1000))))+hex(round(255-(140*(get(feature,'score')/1000))))",
- "maxHeight" : 5000
+ "color1" : "RebeccaPurple",
+ "height" : 4,
+ "showDescriptions" : false,
+ "showLabels" : false
},
- "displayId" : "rnaseq_splice_junctions_(rare)-c_japonica_PRJNA12591-LinearBasicDisplay"
+ "displayId" : "NGG_sequence_search_c_japonica_PRJNA12591-LinearBasicDisplay"
}
],
+ "type" : "FeatureTrack"
+ },
+ {
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_latens_PRJNA248912/tracks/Curated_Genes/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "name" : "RNASeq Splice Junctions (rare)",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads."
- },
- {
- "trackId" : "c_latens_PRJNA248912_curated_genes",
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "assemblyNames" : [
- "c_latens_PRJNA248912"
- ],
"displays" : [
{
- "displayId" : "curated_genes-c_latens_PRJNA248912-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
- "maxHeight" : 5000,
- "type" : "SvgFeatureRenderer",
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
},
+ "type" : "SvgFeatureRenderer",
+ "maxHeight" : 5000,
"color3" : "#965567"
- }
+ },
+ "displayId" : "curated_genes-c_latens_PRJNA248912-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
},
+ "trackId" : "c_latens_PRJNA248912_curated_genes",
"name" : "Curated Genes",
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
+ "assemblyNames" : [
+ "c_latens_PRJNA248912"
+ ],
"type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_latens_PRJNA248912/tracks/Curated_Genes/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes."
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ]
},
{
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_latens_PRJNA248912/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "Curated Genes (protein coding)",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ }
},
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "curated_genes_(protein_coding)-c_latens_PRJNA248912-LinearBasicDisplay",
"renderer" : {
"color3" : "#965567",
"type" : "SvgFeatureRenderer",
"maxHeight" : 5000,
"color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'"
- },
- "displayId" : "curated_genes_(protein_coding)-c_latens_PRJNA248912-LinearBasicDisplay"
+ }
}
],
- "assemblyNames" : [
- "c_latens_PRJNA248912"
- ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
+ "trackId" : "c_latens_PRJNA248912_curated_genes_protein_coding",
+ "name" : "Curated Genes (protein coding)",
"category" : [
"Genes",
"Curated Genes"
],
- "trackId" : "c_latens_PRJNA248912_curated_genes_protein_coding"
+ "assemblyNames" : [
+ "c_latens_PRJNA248912"
+ ],
+ "type" : "FeatureTrack"
},
{
- "description" : "Low-complexity regions identified by Dust.",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_latens_PRJNA248912/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_latens_PRJNA248912/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
},
- "name" : "Low complextity region (Dust)",
"displays" : [
{
+ "displayId" : "low_complextity_region_(dust)-c_latens_PRJNA248912-LinearBasicDisplay",
"renderer" : {
+ "showLabels" : false,
"height" : 4,
"showDescriptions" : false,
"color1" : "bisque",
- "showLabels" : false,
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "low_complextity_region_(dust)-c_latens_PRJNA248912-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
+ "name" : "Low complextity region (Dust)",
+ "trackId" : "c_latens_PRJNA248912_low_complextity_region_(dust)",
+ "description" : "Low-complexity regions identified by Dust.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_latens_PRJNA248912"
+ ],
"category" : [
"Genome Structure",
"Repeats"
+ ]
+ },
+ {
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_latens_PRJNA248912"
],
- "trackId" : "c_latens_PRJNA248912_low_complextity_region_(dust)"
- },
- {
"description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
"name" : "Cas12e TTCN PAM sites",
+ "trackId" : "c_latens_PRJNA248912_TTCN_sequence_search",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "TTCN_sequence_search_c_latens_PRJNA248912-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "SlateBlue",
+ "height" : 4,
+ "showDescriptions" : false,
+ "showLabels" : false
+ }
+ }
+ ],
+ "adapter" : {
+ "sequenceAdapter" : {
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_latens.PRJNA248912.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ },
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_latens.PRJNA248912.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
+ },
+ "fastaLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_latens.PRJNA248912.WS284.genomic.fa.gz"
+ }
+ },
+ "type" : "SequenceSearchAdapter",
+ "search" : "TTC."
+ }
+ },
+ {
"adapter" : {
+ "search" : "TT.",
"type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
"gziLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_latens.PRJNA248912.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
},
+ "type" : "BgzipFastaAdapter",
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_latens.PRJNA248912.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
@@ -47715,181 +46953,126 @@
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_latens.PRJNA248912.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
- },
- "type" : "BgzipFastaAdapter"
- },
- "search" : "TTC."
+ }
+ }
},
- "type" : "FeatureTrack",
"displays" : [
{
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showLabels" : false,
"showDescriptions" : false,
"height" : 4,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "SlateBlue"
+ "color1" : "Indigo"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "TTCN_sequence_search_c_latens_PRJNA248912-LinearBasicDisplay"
+ "displayId" : "TTN_sequence_search_c_latens_PRJNA248912-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_latens_PRJNA248912_TTCN_sequence_search",
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
+ "name" : "Cas12a TTN PAM sites",
+ "trackId" : "c_latens_PRJNA248912_TTN_sequence_search",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_latens_PRJNA248912"
]
},
{
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
"adapter" : {
+ "search" : "..G[AG][AG]T",
"sequenceAdapter" : {
"type" : "BgzipFastaAdapter",
"gziLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_latens.PRJNA248912.WS284.genomic.fa.gz.gzi"
},
- "faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_latens.PRJNA248912.WS284.genomic.fa.gz.fai"
- },
"fastaLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_latens.PRJNA248912.WS284.genomic.fa.gz"
+ },
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_latens.PRJNA248912.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
}
},
- "search" : "TT.",
"type" : "SequenceSearchAdapter"
},
- "type" : "FeatureTrack",
- "name" : "Cas12a TTN PAM sites",
"displays" : [
{
- "displayId" : "TTN_sequence_search_c_latens_PRJNA248912-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
+ "displayId" : "NNGRRT_sequence_search_c_latens_PRJNA248912-LinearBasicDisplay",
"renderer" : {
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "Indigo",
"showDescriptions" : false,
- "height" : 4
- }
+ "height" : 4,
+ "color1" : "DarkViolet",
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
}
],
+ "trackId" : "c_latens_PRJNA248912_NNGRRT_sequence_search",
+ "name" : "SaCas9 NNGRRT PAM sites",
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
"assemblyNames" : [
"c_latens_PRJNA248912"
],
+ "type" : "FeatureTrack",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
- ],
- "trackId" : "c_latens_PRJNA248912_TTN_sequence_search"
+ ]
},
{
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
- "name" : "SaCas9 NNGRRT PAM sites",
- "adapter" : {
- "type" : "SequenceSearchAdapter",
- "search" : "..G[AG][AG]T",
- "sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_latens.PRJNA248912.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
- },
- "fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_latens.PRJNA248912.WS284.genomic.fa.gz"
- },
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_latens.PRJNA248912.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
- }
- }
- },
- "type" : "FeatureTrack",
- "displays" : [
- {
- "displayId" : "NNGRRT_sequence_search_c_latens_PRJNA248912-LinearBasicDisplay",
- "renderer" : {
- "height" : 4,
- "showDescriptions" : false,
- "color1" : "DarkViolet",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "type" : "LinearBasicDisplay"
- }
- ],
- "trackId" : "c_latens_PRJNA248912_NNGRRT_sequence_search",
"assemblyNames" : [
"c_latens_PRJNA248912"
],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ]
- },
- {
- "name" : "SpCas9 NGG PAM sites",
- "adapter" : {
- "sequenceAdapter" : {
- "fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_latens.PRJNA248912.WS284.genomic.fa.gz"
- },
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_latens.PRJNA248912.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
- },
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_latens.PRJNA248912.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
- },
- "type" : "BgzipFastaAdapter"
- },
- "search" : ".GG",
- "type" : "SequenceSearchAdapter"
- },
"type" : "FeatureTrack",
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
- "trackId" : "c_latens_PRJNA248912_NGG_sequence_search",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "assemblyNames" : [
- "c_latens_PRJNA248912"
- ],
+ "trackId" : "c_latens_PRJNA248912_NGG_sequence_search",
+ "name" : "SpCas9 NGG PAM sites",
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
"displays" : [
{
- "displayId" : "NGG_sequence_search_c_latens_PRJNA248912-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"showDescriptions" : false,
"height" : 4,
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
"color1" : "RebeccaPurple"
- }
+ },
+ "displayId" : "NGG_sequence_search_c_latens_PRJNA248912-LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "search" : ".GG",
+ "sequenceAdapter" : {
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_latens.PRJNA248912.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BgzipFastaAdapter",
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_latens.PRJNA248912.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
+ },
+ "faiLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_latens.PRJNA248912.WS284.genomic.fa.gz.fai"
+ }
+ },
+ "type" : "SequenceSearchAdapter"
+ }
},
{
- "name" : "Curated Genes",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_nigoni_PRJNA384657/tracks/Curated_Genes/{refseq}/trackData.jsonz"
- }
- },
"type" : "FeatureTrack",
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
- "trackId" : "c_nigoni_PRJNA384657_curated_genes",
"assemblyNames" : [
"c_nigoni_PRJNA384657"
],
@@ -47897,83 +47080,84 @@
"Genes",
"Curated Genes"
],
+ "name" : "Curated Genes",
+ "trackId" : "c_nigoni_PRJNA384657_curated_genes",
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
+ "formatDetails" : {
+ "feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
+ },
"displays" : [
{
"renderer" : {
- "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
- "maxHeight" : 5000,
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
},
+ "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
+ "color3" : "#965567",
"type" : "SvgFeatureRenderer",
- "color3" : "#965567"
+ "maxHeight" : 5000
},
- "type" : "LinearBasicDisplay",
- "displayId" : "curated_genes-c_nigoni_PRJNA384657-LinearBasicDisplay"
+ "displayId" : "curated_genes-c_nigoni_PRJNA384657-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_nigoni_PRJNA384657/tracks/Curated_Genes/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
}
},
{
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color3" : "#965567",
- "type" : "SvgFeatureRenderer",
- "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
- "maxHeight" : 5000
- },
- "displayId" : "curated_genes_(protein_coding)-c_nigoni_PRJNA384657-LinearBasicDisplay"
- }
- ],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
"trackId" : "c_nigoni_PRJNA384657_curated_genes_protein_coding",
- "category" : [
- "Genes",
- "Curated Genes"
- ],
+ "name" : "Curated Genes (protein coding)",
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
"assemblyNames" : [
"c_nigoni_PRJNA384657"
],
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
- "name" : "Curated Genes (protein coding)",
"type" : "FeatureTrack",
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_nigoni_PRJNA384657/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_nigoni_PRJNA384657/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz"
}
- }
+ },
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
+ "displays" : [
+ {
+ "renderer" : {
+ "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
+ "color3" : "#965567",
+ "type" : "SvgFeatureRenderer",
+ "maxHeight" : 5000
+ },
+ "displayId" : "curated_genes_(protein_coding)-c_nigoni_PRJNA384657-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "orange",
+ "height" : 4,
"showDescriptions" : false,
- "height" : 4
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "other_uniprot_proteins-c_nigoni_PRJNA384657-LinearBasicDisplay"
+ "displayId" : "other_uniprot_proteins-c_nigoni_PRJNA384657-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "c_nigoni_PRJNA384657"
- ],
- "trackId" : "c_nigoni_PRJNA384657_other_uniprot_proteins",
- "description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -47981,13 +47165,19 @@
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_nigoni_PRJNA384657/tracks/Other UniProt proteins/{refseq}/trackData.jsonz"
}
},
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
"type" : "FeatureTrack",
- "name" : "Other UniProt proteins"
+ "assemblyNames" : [
+ "c_nigoni_PRJNA384657"
+ ],
+ "description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "Other UniProt proteins",
+ "trackId" : "c_nigoni_PRJNA384657_other_uniprot_proteins"
},
{
- "description" : "Low-complexity regions identified by Dust.",
- "name" : "Low complextity region (Dust)",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
"locationType" : "UriLocation",
@@ -47997,37 +47187,31 @@
},
"displays" : [
{
- "displayId" : "low_complextity_region_(dust)-c_nigoni_PRJNA384657-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer",
"color1" : "bisque",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
- }
+ "height" : 4,
+ "showDescriptions" : false
+ },
+ "displayId" : "low_complextity_region_(dust)-c_nigoni_PRJNA384657-LinearBasicDisplay"
}
],
"trackId" : "c_nigoni_PRJNA384657_low_complextity_region_(dust)",
+ "name" : "Low complextity region (Dust)",
+ "description" : "Low-complexity regions identified by Dust.",
+ "assemblyNames" : [
+ "c_nigoni_PRJNA384657"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"Genome Structure",
"Repeats"
- ],
- "assemblyNames" : [
- "c_nigoni_PRJNA384657"
]
},
{
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_nigoni_PRJNA384657/tracks/C. briggsae proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "name" : "C. briggsae proteins",
- "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"assemblyNames" : [
"c_nigoni_PRJNA384657"
],
@@ -48035,177 +47219,176 @@
"Sequence Similarity",
"Proteins"
],
+ "name" : "C. briggsae proteins",
"trackId" : "c_nigoni_PRJNA384657_C_briggsae_proteins",
+ "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"displays" : [
{
- "displayId" : "C_briggsae_proteins-c_nigoni_PRJNA384657-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
"showLabels" : false,
- "height" : 4
+ "height" : 4,
+ "color1" : "orange"
},
"mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay"
+ "displayId" : "C_briggsae_proteins-c_nigoni_PRJNA384657-LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_nigoni_PRJNA384657/tracks/C. briggsae proteins/{refseq}/trackData.jsonz"
+ }
+ }
},
{
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_nigoni_PRJNA384657"
+ ],
"category" : [
"Sequence Similarity",
"Proteins"
],
- "assemblyNames" : [
- "c_nigoni_PRJNA384657"
- ],
+ "name" : "C. elegans proteins",
"trackId" : "c_nigoni_PRJNA384657_C_elegans_proteins",
+ "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "C_elegans_proteins-c_nigoni_PRJNA384657-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
+ "height" : 4,
"color1" : "orange",
- "height" : 4
- },
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay"
+ "type" : "SvgFeatureRenderer"
+ }
}
],
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_nigoni_PRJNA384657/tracks/C. elegans proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "C. elegans proteins",
- "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
- },
- {
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_nigoni_PRJNA384657/tracks/C. remanei proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "C. remanei proteins",
- "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ }
+ },
+ {
"assemblyNames" : [
"c_nigoni_PRJNA384657"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
],
"trackId" : "c_nigoni_PRJNA384657_C_remanei_proteins",
+ "name" : "C. remanei proteins",
+ "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "C_remanei_proteins-c_nigoni_PRJNA384657-LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "orange",
- "height" : 4
+ "height" : 4,
+ "showLabels" : false
},
- "displayId" : "C_remanei_proteins-c_nigoni_PRJNA384657-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
- ]
- },
- {
- "name" : "P. pacificus proteins",
- "type" : "FeatureTrack",
+ ],
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_nigoni_PRJNA384657/tracks/P. pacificus proteins/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_nigoni_PRJNA384657/tracks/C. remanei proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
- },
+ }
+ },
+ {
"description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "P. pacificus proteins",
"trackId" : "c_nigoni_PRJNA384657_P_pacificus_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_nigoni_PRJNA384657"
],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_nigoni_PRJNA384657/tracks/P. pacificus proteins/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "P_pacificus_proteins-c_nigoni_PRJNA384657-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
"showLabels" : false,
- "height" : 4
+ "height" : 4,
+ "color1" : "orange"
},
- "mouseover" : "jexl:get(feature,'clone')",
- "displayId" : "P_pacificus_proteins-c_nigoni_PRJNA384657-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
]
},
{
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_nigoni_PRJNA384657/tracks/C. japonica proteins/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "height" : 4,
+ "showLabels" : false,
+ "color1" : "orange"
},
- "displayId" : "C_japonica_proteins-c_nigoni_PRJNA384657-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "C_japonica_proteins-c_nigoni_PRJNA384657-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_nigoni_PRJNA384657_C_japonica_proteins",
- "assemblyNames" : [
- "c_nigoni_PRJNA384657"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
"description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"name" : "C. japonica proteins",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_nigoni_PRJNA384657/tracks/C. japonica proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- }
- },
- {
- "trackId" : "c_nigoni_PRJNA384657_S_cerevisiae_proteins",
+ "trackId" : "c_nigoni_PRJNA384657_C_japonica_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_nigoni_PRJNA384657"
- ],
+ ]
+ },
+ {
"displays" : [
{
"type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
"height" : 4,
- "color1" : "orange",
"showLabels" : false,
+ "color1" : "orange",
"type" : "SvgFeatureRenderer"
},
+ "mouseover" : "jexl:get(feature,'clone')",
"displayId" : "S_cerevisiae_proteins-c_nigoni_PRJNA384657-LinearBasicDisplay"
}
],
- "name" : "S. cerevisiae proteins",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -48213,52 +47396,52 @@
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_nigoni_PRJNA384657/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz"
}
},
- "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
- },
- {
- "trackId" : "c_nigoni_PRJNA384657_D_melanogaster_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_nigoni_PRJNA384657"
],
+ "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "S. cerevisiae proteins",
+ "trackId" : "c_nigoni_PRJNA384657_S_cerevisiae_proteins"
+ },
+ {
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "D_melanogaster_proteins-c_nigoni_PRJNA384657-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
"height" : 4,
- "color1" : "orange",
"showLabels" : false,
+ "color1" : "orange",
"type" : "SvgFeatureRenderer"
- },
- "mouseover" : "jexl:get(feature,'clone')",
- "displayId" : "D_melanogaster_proteins-c_nigoni_PRJNA384657-LinearBasicDisplay"
+ }
}
],
- "name" : "D. melanogaster proteins",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_nigoni_PRJNA384657/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_nigoni_PRJNA384657/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
},
- "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "assemblyNames" : [
+ "c_nigoni_PRJNA384657"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_nigoni_PRJNA384657_D_melanogaster_proteins",
+ "name" : "D. melanogaster proteins"
},
{
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_nigoni_PRJNA384657/tracks/C. brenneri proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "name" : "C. brenneri proteins",
- "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"category" : [
"Sequence Similarity",
"Proteins"
@@ -48266,69 +47449,68 @@
"assemblyNames" : [
"c_nigoni_PRJNA384657"
],
+ "type" : "FeatureTrack",
+ "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"trackId" : "c_nigoni_PRJNA384657_C_brenneri_proteins",
+ "name" : "C. brenneri proteins",
"displays" : [
{
"renderer" : {
- "height" : 4,
- "type" : "SvgFeatureRenderer",
+ "color1" : "orange",
"showLabels" : false,
- "color1" : "orange"
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
},
"mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
- "displayId" : "C_brenneri_proteins-c_nigoni_PRJNA384657-LinearBasicDisplay"
+ "displayId" : "C_brenneri_proteins-c_nigoni_PRJNA384657-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_nigoni_PRJNA384657/tracks/C. brenneri proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
"displays" : [
{
"renderer" : {
- "height" : 4,
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
+ "color1" : "orange",
+ "height" : 4,
"showLabels" : false
},
"mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
- "displayId" : "H_sapiens_proteins-c_nigoni_PRJNA384657-LinearBasicDisplay"
+ "displayId" : "H_sapiens_proteins-c_nigoni_PRJNA384657-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_nigoni_PRJNA384657_H_sapiens_proteins",
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "c_nigoni_PRJNA384657"
- ],
- "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "H. sapiens proteins",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_nigoni_PRJNA384657/tracks/H. sapiens proteins/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
- }
+ },
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_nigoni_PRJNA384657"
+ ],
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "name" : "H. sapiens proteins",
+ "trackId" : "c_nigoni_PRJNA384657_H_sapiens_proteins",
+ "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
},
{
- "displays" : [
- {
- "displayId" : "TTCN_sequence_search_c_nigoni_PRJNA384657-LinearBasicDisplay",
- "renderer" : {
- "showDescriptions" : false,
- "height" : 4,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "SlateBlue"
- },
- "type" : "LinearBasicDisplay"
- }
- ],
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
"trackId" : "c_nigoni_PRJNA384657_TTCN_sequence_search",
+ "name" : "Cas12e TTCN PAM sites",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
@@ -48336,79 +47518,73 @@
"assemblyNames" : [
"c_nigoni_PRJNA384657"
],
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
- "name" : "Cas12e TTCN PAM sites",
"type" : "FeatureTrack",
"adapter" : {
"search" : "TTC.",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_nigoni.PRJNA384657.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
"fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_nigoni.PRJNA384657.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_nigoni.PRJNA384657.WS284.genomic.fa.gz"
},
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_nigoni.PRJNA384657.WS284.genomic.fa.gz.gzi"
}
- },
- "type" : "SequenceSearchAdapter"
- }
- },
- {
+ }
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "TTCN_sequence_search_c_nigoni_PRJNA384657-LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showLabels" : false,
"height" : 4,
"showDescriptions" : false,
- "color1" : "Indigo",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "color1" : "SlateBlue"
},
- "displayId" : "TTN_sequence_search_c_nigoni_PRJNA384657-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
- ],
- "assemblyNames" : [
- "c_nigoni_PRJNA384657"
- ],
+ ]
+ },
+ {
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "trackId" : "c_nigoni_PRJNA384657_TTN_sequence_search",
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
+ "assemblyNames" : [
+ "c_nigoni_PRJNA384657"
+ ],
"type" : "FeatureTrack",
- "adapter" : {
- "sequenceAdapter" : {
- "fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_nigoni.PRJNA384657.WS284.genomic.fa.gz"
- },
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_nigoni.PRJNA384657.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
+ "trackId" : "c_nigoni_PRJNA384657_TTN_sequence_search",
+ "name" : "Cas12a TTN PAM sites",
+ "displays" : [
+ {
+ "renderer" : {
+ "showDescriptions" : false,
+ "height" : 4,
+ "showLabels" : false,
+ "color1" : "Indigo",
+ "type" : "SvgFeatureRenderer"
},
+ "displayId" : "TTN_sequence_search_c_nigoni_PRJNA384657-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
+ "adapter" : {
+ "search" : "TT.",
+ "sequenceAdapter" : {
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_nigoni.PRJNA384657.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
},
- "type" : "BgzipFastaAdapter"
- },
- "search" : "TT.",
- "type" : "SequenceSearchAdapter"
- },
- "name" : "Cas12a TTN PAM sites"
- },
- {
- "adapter" : {
- "search" : "..G[AG][AG]T",
- "sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
"fastaLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_nigoni.PRJNA384657.WS284.genomic.fa.gz"
@@ -48416,95 +47592,105 @@
"faiLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_nigoni.PRJNA384657.WS284.genomic.fa.gz.fai"
- },
- "gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_nigoni.PRJNA384657.WS284.genomic.fa.gz.gzi"
}
},
"type" : "SequenceSearchAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "SaCas9 NNGRRT PAM sites",
+ }
+ },
+ {
"description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
+ "name" : "SaCas9 NNGRRT PAM sites",
+ "trackId" : "c_nigoni_PRJNA384657_NNGRRT_sequence_search",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_nigoni_PRJNA384657"
],
- "trackId" : "c_nigoni_PRJNA384657_NNGRRT_sequence_search",
+ "adapter" : {
+ "sequenceAdapter" : {
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_nigoni.PRJNA384657.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
+ },
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_nigoni.PRJNA384657.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_nigoni.PRJNA384657.WS284.genomic.fa.gz.gzi"
+ }
+ },
+ "type" : "SequenceSearchAdapter",
+ "search" : "..G[AG][AG]T"
+ },
"displays" : [
{
- "displayId" : "NNGRRT_sequence_search_c_nigoni_PRJNA384657-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "NNGRRT_sequence_search_c_nigoni_PRJNA384657-LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 4,
"type" : "SvgFeatureRenderer",
"showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 4,
"color1" : "DarkViolet"
}
}
]
},
{
+ "assemblyNames" : [
+ "c_nigoni_PRJNA384657"
+ ],
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "SequenceSearchAdapter",
- "search" : ".GG",
- "sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_nigoni.PRJNA384657.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
- },
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_nigoni.PRJNA384657.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
- },
- "faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_nigoni.PRJNA384657.WS284.genomic.fa.gz.fai"
- }
- }
- },
- "name" : "SpCas9 NGG PAM sites",
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "assemblyNames" : [
- "c_nigoni_PRJNA384657"
- ],
"trackId" : "c_nigoni_PRJNA384657_NGG_sequence_search",
+ "name" : "SpCas9 NGG PAM sites",
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "NGG_sequence_search_c_nigoni_PRJNA384657-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "showDescriptions" : false,
- "color1" : "RebeccaPurple",
"type" : "SvgFeatureRenderer",
+ "color1" : "RebeccaPurple",
+ "showDescriptions" : false,
+ "height" : 4,
"showLabels" : false
+ }
+ }
+ ],
+ "adapter" : {
+ "search" : ".GG",
+ "type" : "SequenceSearchAdapter",
+ "sequenceAdapter" : {
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_nigoni.PRJNA384657.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "NGG_sequence_search_c_nigoni_PRJNA384657-LinearBasicDisplay"
+ "fastaLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_nigoni.PRJNA384657.WS284.genomic.fa.gz"
+ },
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_nigoni.PRJNA384657.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BgzipFastaAdapter"
}
- ]
+ }
},
{
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_panamensis_PRJEB28259/tracks/Curated_Genes/{refseq}/trackData.jsonz"
- }
- },
- "name" : "Curated Genes",
"description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
+ "trackId" : "c_panamensis_PRJEB28259_curated_genes",
+ "name" : "Curated Genes",
"category" : [
"Genes",
"Curated Genes"
@@ -48512,7 +47698,14 @@
"assemblyNames" : [
"c_panamensis_PRJEB28259"
],
- "trackId" : "c_panamensis_PRJEB28259_curated_genes",
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_panamensis_PRJEB28259/tracks/Curated_Genes/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"formatDetails" : {
"feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
},
@@ -48520,65 +47713,55 @@
{
"displayId" : "curated_genes-c_panamensis_PRJEB28259-LinearBasicDisplay",
"renderer" : {
- "color3" : "#965567",
+ "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
},
"type" : "SvgFeatureRenderer",
- "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
- "maxHeight" : 5000
+ "maxHeight" : 5000,
+ "color3" : "#965567"
},
"type" : "LinearBasicDisplay"
}
]
},
{
+ "trackId" : "c_panamensis_PRJEB28259_curated_genes_protein_coding",
+ "name" : "Curated Genes (protein coding)",
"description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
+ "assemblyNames" : [
+ "c_panamensis_PRJEB28259"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_panamensis_PRJEB28259/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "Curated Genes (protein coding)",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_panamensis_PRJEB28259/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz"
+ }
},
"displays" : [
{
- "displayId" : "curated_genes_(protein_coding)-c_panamensis_PRJEB28259-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
"maxHeight" : 5000,
"type" : "SvgFeatureRenderer",
"color3" : "#965567"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "curated_genes_(protein_coding)-c_panamensis_PRJEB28259-LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_panamensis_PRJEB28259"
- ],
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "trackId" : "c_panamensis_PRJEB28259_curated_genes_protein_coding"
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ }
},
{
- "name" : "Low complextity region (Dust)",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_panamensis_PRJEB28259/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
"type" : "FeatureTrack",
- "description" : "Low-complexity regions identified by Dust.",
- "trackId" : "c_panamensis_PRJEB28259_low_complextity_region_(dust)",
"assemblyNames" : [
"c_panamensis_PRJEB28259"
],
@@ -48586,34 +47769,34 @@
"Genome Structure",
"Repeats"
],
+ "name" : "Low complextity region (Dust)",
+ "trackId" : "c_panamensis_PRJEB28259_low_complextity_region_(dust)",
+ "description" : "Low-complexity regions identified by Dust.",
"displays" : [
{
- "displayId" : "low_complextity_region_(dust)-c_panamensis_PRJEB28259-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "showDescriptions" : false,
"color1" : "bisque",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- }
- }
- ]
- },
- {
- "displays" : [
- {
- "displayId" : "TTCN_sequence_search_c_panamensis_PRJEB28259-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
+ "showLabels" : false,
"height" : 4,
"showDescriptions" : false,
- "color1" : "SlateBlue",
- "showLabels" : false,
"type" : "SvgFeatureRenderer"
- }
+ },
+ "displayId" : "low_complextity_region_(dust)-c_panamensis_PRJEB28259-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_panamensis_PRJEB28259/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz"
+ }
+ }
+ },
+ {
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
+ "trackId" : "c_panamensis_PRJEB28259_TTCN_sequence_search",
+ "name" : "Cas12e TTCN PAM sites",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
@@ -48621,261 +47804,262 @@
"assemblyNames" : [
"c_panamensis_PRJEB28259"
],
- "trackId" : "c_panamensis_PRJEB28259_TTCN_sequence_search",
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
"type" : "FeatureTrack",
"adapter" : {
- "search" : "TTC.",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
- "fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz"
- },
"faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz.fai"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
},
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz.gzi",
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
+ },
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz.gzi"
}
},
- "type" : "SequenceSearchAdapter"
+ "search" : "TTC."
},
- "name" : "Cas12e TTCN PAM sites"
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "SlateBlue",
+ "height" : 4,
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "TTCN_sequence_search_c_panamensis_PRJEB28259-LinearBasicDisplay"
+ }
+ ]
},
{
- "assemblyNames" : [
- "c_panamensis_PRJEB28259"
- ],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "trackId" : "c_panamensis_PRJEB28259_TTN_sequence_search",
"displays" : [
{
- "displayId" : "TTN_sequence_search_c_panamensis_PRJEB28259-LinearBasicDisplay",
"renderer" : {
- "color1" : "Indigo",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
+ "showLabels" : false,
"height" : 4,
- "showDescriptions" : false
+ "showDescriptions" : false,
+ "color1" : "Indigo"
},
+ "displayId" : "TTN_sequence_search_c_panamensis_PRJEB28259-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
"adapter" : {
- "search" : "TT.",
"sequenceAdapter" : {
- "fastaLocation" : {
+ "faiLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz.fai"
},
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz.fai",
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
- },
- "type" : "BgzipFastaAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz.gzi"
+ }
},
- "type" : "SequenceSearchAdapter"
+ "type" : "SequenceSearchAdapter",
+ "search" : "TT."
},
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_panamensis_PRJEB28259"
+ ],
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
"name" : "Cas12a TTN PAM sites",
+ "trackId" : "c_panamensis_PRJEB28259_TTN_sequence_search",
"description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time."
},
{
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
+ "name" : "SaCas9 NNGRRT PAM sites",
+ "trackId" : "c_panamensis_PRJEB28259_NNGRRT_sequence_search",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_panamensis_PRJEB28259"
],
- "trackId" : "c_panamensis_PRJEB28259_NNGRRT_sequence_search",
+ "adapter" : {
+ "search" : "..G[AG][AG]T",
+ "type" : "SequenceSearchAdapter",
+ "sequenceAdapter" : {
+ "faiLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz.fai"
+ },
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
+ },
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz.gzi"
+ },
+ "type" : "BgzipFastaAdapter"
+ }
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "NNGRRT_sequence_search_c_panamensis_PRJEB28259-LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 4,
"showDescriptions" : false,
- "color1" : "DarkViolet",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "NNGRRT_sequence_search_c_panamensis_PRJEB28259-LinearBasicDisplay"
+ "color1" : "DarkViolet"
+ }
}
- ],
- "type" : "FeatureTrack",
+ ]
+ },
+ {
"adapter" : {
- "search" : "..G[AG][AG]T",
+ "search" : ".GG",
"sequenceAdapter" : {
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz.gzi"
},
- "faiLocation" : {
+ "fastaLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz.fai"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz"
},
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz.gzi",
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
- },
- "type" : "BgzipFastaAdapter"
+ }
},
"type" : "SequenceSearchAdapter"
},
- "name" : "SaCas9 NNGRRT PAM sites",
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time."
- },
- {
"displays" : [
{
"displayId" : "NGG_sequence_search_c_panamensis_PRJEB28259-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "RebeccaPurple",
+ "height" : 4,
"showDescriptions" : false,
- "height" : 4
+ "showLabels" : false,
+ "color1" : "RebeccaPurple"
},
"type" : "LinearBasicDisplay"
}
],
+ "name" : "SpCas9 NGG PAM sites",
"trackId" : "c_panamensis_PRJEB28259_NGG_sequence_search",
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_panamensis_PRJEB28259"
],
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
- ],
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
- "name" : "SpCas9 NGG PAM sites",
- "type" : "FeatureTrack",
- "adapter" : {
- "sequenceAdapter" : {
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
- },
- "faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz.fai"
- },
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
- },
- "type" : "BgzipFastaAdapter"
- },
- "search" : ".GG",
- "type" : "SequenceSearchAdapter"
- }
+ ]
},
{
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_parvicauda_PRJEB12595/tracks/Curated_Genes/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
"name" : "Curated Genes",
+ "trackId" : "c_parvicauda_PRJEB12595_curated_genes",
"description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_parvicauda_PRJEB12595"
+ ],
"category" : [
"Genes",
"Curated Genes"
],
- "assemblyNames" : [
- "c_parvicauda_PRJEB12595"
- ],
- "trackId" : "c_parvicauda_PRJEB12595_curated_genes",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_parvicauda_PRJEB12595/tracks/Curated_Genes/{refseq}/trackData.jsonz"
+ }
+ },
"formatDetails" : {
"feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
},
"displays" : [
{
- "displayId" : "curated_genes-c_parvicauda_PRJEB12595-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
+ "maxHeight" : 5000,
+ "type" : "SvgFeatureRenderer",
+ "color3" : "#965567",
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
},
- "type" : "SvgFeatureRenderer",
- "maxHeight" : 5000,
- "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
- "color3" : "#965567"
+ "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "curated_genes-c_parvicauda_PRJEB12595-LinearBasicDisplay"
}
]
},
{
- "name" : "Curated Genes (protein coding)",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_parvicauda_PRJEB12595/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
- "trackId" : "c_parvicauda_PRJEB12595_curated_genes_protein_coding",
- "assemblyNames" : [
- "c_parvicauda_PRJEB12595"
- ],
- "category" : [
- "Genes",
- "Curated Genes"
- ],
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "curated_genes_(protein_coding)-c_parvicauda_PRJEB12595-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
"maxHeight" : 5000,
- "color3" : "#965567"
- },
- "displayId" : "curated_genes_(protein_coding)-c_parvicauda_PRJEB12595-LinearBasicDisplay"
+ "color3" : "#965567",
+ "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'"
+ }
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- }
- },
- {
- "trackId" : "c_parvicauda_PRJEB12595_low_complextity_region_(dust)",
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_parvicauda_PRJEB12595/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"category" : [
- "Genome Structure",
- "Repeats"
+ "Genes",
+ "Curated Genes"
],
"assemblyNames" : [
"c_parvicauda_PRJEB12595"
],
+ "type" : "FeatureTrack",
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
+ "trackId" : "c_parvicauda_PRJEB12595_curated_genes_protein_coding",
+ "name" : "Curated Genes (protein coding)"
+ },
+ {
"displays" : [
{
- "displayId" : "low_complextity_region_(dust)-c_parvicauda_PRJEB12595-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
"color1" : "bisque",
- "showDescriptions" : false,
- "height" : 4
- }
+ "showLabels" : false,
+ "height" : 4,
+ "showDescriptions" : false
+ },
+ "displayId" : "low_complextity_region_(dust)-c_parvicauda_PRJEB12595-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "name" : "Low complextity region (Dust)",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -48884,59 +48068,39 @@
}
},
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_parvicauda_PRJEB12595"
+ ],
+ "category" : [
+ "Genome Structure",
+ "Repeats"
+ ],
+ "name" : "Low complextity region (Dust)",
+ "trackId" : "c_parvicauda_PRJEB12595_low_complextity_region_(dust)",
"description" : "Low-complexity regions identified by Dust."
},
{
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
- "type" : "FeatureTrack",
- "adapter" : {
- "sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
- "fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_parvicauda.PRJEB12595.WS284.genomic.fa.gz"
- },
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_parvicauda.PRJEB12595.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
- },
- "gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_parvicauda.PRJEB12595.WS284.genomic.fa.gz.gzi"
- }
- },
- "search" : "TTC.",
- "type" : "SequenceSearchAdapter"
- },
- "name" : "Cas12e TTCN PAM sites",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "TTCN_sequence_search_c_parvicauda_PRJEB12595-LinearBasicDisplay",
"renderer" : {
- "color1" : "SlateBlue",
"type" : "SvgFeatureRenderer",
"showLabels" : false,
+ "showDescriptions" : false,
"height" : 4,
- "showDescriptions" : false
- },
- "displayId" : "TTCN_sequence_search_c_parvicauda_PRJEB12595-LinearBasicDisplay"
+ "color1" : "SlateBlue"
+ }
}
],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "assemblyNames" : [
- "c_parvicauda_PRJEB12595"
- ],
- "trackId" : "c_parvicauda_PRJEB12595_TTCN_sequence_search"
- },
- {
"adapter" : {
- "type" : "SequenceSearchAdapter",
- "search" : "TT.",
+ "search" : "TTC.",
"sequenceAdapter" : {
"type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_parvicauda.PRJEB12595.WS284.genomic.fa.gz.gzi"
+ },
"faiLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_parvicauda.PRJEB12595.WS284.genomic.fa.gz.fai"
@@ -48944,265 +48108,295 @@
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_parvicauda.PRJEB12595.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
- },
- "gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_parvicauda.PRJEB12595.WS284.genomic.fa.gz.gzi"
}
- }
+ },
+ "type" : "SequenceSearchAdapter"
},
- "type" : "FeatureTrack",
- "name" : "Cas12a TTN PAM sites",
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_parvicauda_PRJEB12595"
],
- "trackId" : "c_parvicauda_PRJEB12595_TTN_sequence_search",
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
+ "name" : "Cas12e TTCN PAM sites",
+ "trackId" : "c_parvicauda_PRJEB12595_TTCN_sequence_search"
+ },
+ {
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "showDescriptions" : false,
- "color1" : "Indigo",
"type" : "SvgFeatureRenderer",
+ "color1" : "Indigo",
+ "showDescriptions" : false,
+ "height" : 4,
"showLabels" : false
},
- "displayId" : "TTN_sequence_search_c_parvicauda_PRJEB12595-LinearBasicDisplay"
+ "displayId" : "TTN_sequence_search_c_parvicauda_PRJEB12595-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ]
- },
- {
- "name" : "SaCas9 NNGRRT PAM sites",
- "type" : "FeatureTrack",
+ ],
"adapter" : {
- "search" : "..G[AG][AG]T",
"sequenceAdapter" : {
"gziLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_parvicauda.PRJEB12595.WS284.genomic.fa.gz.gzi"
},
- "fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_parvicauda.PRJEB12595.WS284.genomic.fa.gz"
- },
+ "type" : "BgzipFastaAdapter",
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_parvicauda.PRJEB12595.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
- "type" : "BgzipFastaAdapter"
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_parvicauda.PRJEB12595.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
+ }
},
- "type" : "SequenceSearchAdapter"
+ "type" : "SequenceSearchAdapter",
+ "search" : "TT."
},
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
- "trackId" : "c_parvicauda_PRJEB12595_NNGRRT_sequence_search",
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_parvicauda_PRJEB12595"
],
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
+ "name" : "Cas12a TTN PAM sites",
+ "trackId" : "c_parvicauda_PRJEB12595_TTN_sequence_search"
+ },
+ {
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_parvicauda_PRJEB12595"
+ ],
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
+ "name" : "SaCas9 NNGRRT PAM sites",
+ "trackId" : "c_parvicauda_PRJEB12595_NNGRRT_sequence_search",
"displays" : [
{
- "displayId" : "NNGRRT_sequence_search_c_parvicauda_PRJEB12595-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "showDescriptions" : false,
"color1" : "DarkViolet",
"showLabels" : false,
+ "height" : 4,
+ "showDescriptions" : false,
"type" : "SvgFeatureRenderer"
},
+ "displayId" : "NNGRRT_sequence_search_c_parvicauda_PRJEB12595-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
- ]
- },
- {
- "name" : "SpCas9 NGG PAM sites",
- "type" : "FeatureTrack",
+ ],
"adapter" : {
- "type" : "SequenceSearchAdapter",
- "search" : ".GG",
+ "search" : "..G[AG][AG]T",
"sequenceAdapter" : {
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_parvicauda.PRJEB12595.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
+ "faiLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_parvicauda.PRJEB12595.WS284.genomic.fa.gz.fai"
},
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_parvicauda.PRJEB12595.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_parvicauda.PRJEB12595.WS284.genomic.fa.gz.gzi"
+ },
+ "type" : "BgzipFastaAdapter"
+ },
+ "type" : "SequenceSearchAdapter"
+ }
+ },
+ {
+ "adapter" : {
+ "type" : "SequenceSearchAdapter",
+ "sequenceAdapter" : {
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_parvicauda.PRJEB12595.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
+ "fastaLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_parvicauda.PRJEB12595.WS284.genomic.fa.gz"
+ },
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_parvicauda.PRJEB12595.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ },
"type" : "BgzipFastaAdapter"
- }
+ },
+ "search" : ".GG"
},
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "height" : 4,
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "color1" : "RebeccaPurple"
+ },
+ "displayId" : "NGG_sequence_search_c_parvicauda_PRJEB12595-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"trackId" : "c_parvicauda_PRJEB12595_NGG_sequence_search",
+ "name" : "SpCas9 NGG PAM sites",
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
"assemblyNames" : [
"c_parvicauda_PRJEB12595"
],
+ "type" : "FeatureTrack",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
- ],
- "displays" : [
- {
- "displayId" : "NGG_sequence_search_c_parvicauda_PRJEB12595-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "RebeccaPurple",
- "showDescriptions" : false,
- "height" : 4
- }
- }
]
},
{
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
"displays" : [
{
- "displayId" : "curated_genes_(protein_coding)-c_quiockensis_PRJEB11354-LinearBasicDisplay",
"renderer" : {
- "color3" : "#965567",
"color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
- "maxHeight" : 5000,
- "type" : "SvgFeatureRenderer"
+ "color3" : "#965567",
+ "type" : "SvgFeatureRenderer",
+ "maxHeight" : 5000
},
+ "displayId" : "curated_genes_(protein_coding)-c_quiockensis_PRJEB11354-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "assemblyNames" : [
- "c_quiockensis_PRJEB11354"
- ],
- "trackId" : "c_quiockensis_PRJEB11354_curated_genes_protein_coding",
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_quiockensis_PRJEB11354/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz"
- }
+ },
+ "type" : "NCListAdapter"
},
"type" : "FeatureTrack",
- "name" : "Curated Genes (protein coding)"
+ "assemblyNames" : [
+ "c_quiockensis_PRJEB11354"
+ ],
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
+ "name" : "Curated Genes (protein coding)",
+ "trackId" : "c_quiockensis_PRJEB11354_curated_genes_protein_coding",
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track."
},
{
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
- "name" : "Curated Genes",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_quiockensis_PRJEB11354/tracks/Curated_Genes/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "curated_genes-c_quiockensis_PRJEB11354-LinearBasicDisplay",
"renderer" : {
- "color3" : "#965567",
- "maxHeight" : 5000,
- "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
},
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "curated_genes-c_quiockensis_PRJEB11354-LinearBasicDisplay"
+ "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
+ "type" : "SvgFeatureRenderer",
+ "maxHeight" : 5000,
+ "color3" : "#965567"
+ }
}
],
"formatDetails" : {
"feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
},
- "trackId" : "c_quiockensis_PRJEB11354_curated_genes",
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_quiockensis_PRJEB11354/tracks/Curated_Genes/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_quiockensis_PRJEB11354"
+ ],
"category" : [
"Genes",
"Curated Genes"
],
- "assemblyNames" : [
- "c_quiockensis_PRJEB11354"
- ]
+ "name" : "Curated Genes",
+ "trackId" : "c_quiockensis_PRJEB11354_curated_genes",
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes."
},
{
+ "trackId" : "c_quiockensis_PRJEB11354_low_complextity_region_(dust)",
+ "name" : "Low complextity region (Dust)",
+ "description" : "Low-complexity regions identified by Dust.",
"assemblyNames" : [
"c_quiockensis_PRJEB11354"
],
+ "type" : "FeatureTrack",
"category" : [
"Genome Structure",
"Repeats"
],
- "trackId" : "c_quiockensis_PRJEB11354_low_complextity_region_(dust)",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_quiockensis_PRJEB11354/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
"renderer" : {
- "height" : 4,
- "showDescriptions" : false,
- "color1" : "bisque",
+ "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "showDescriptions" : false,
+ "height" : 4,
+ "color1" : "bisque"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "low_complextity_region_(dust)-c_quiockensis_PRJEB11354-LinearBasicDisplay"
- }
- ],
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_quiockensis_PRJEB11354/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz"
+ "displayId" : "low_complextity_region_(dust)-c_quiockensis_PRJEB11354-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- },
- "type" : "FeatureTrack",
- "name" : "Low complextity region (Dust)",
- "description" : "Low-complexity regions identified by Dust."
+ ]
},
{
- "assemblyNames" : [
- "c_quiockensis_PRJEB11354"
- ],
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_quiockensis_PRJEB11354"
+ ],
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
+ "name" : "Cas12e TTCN PAM sites",
"trackId" : "c_quiockensis_PRJEB11354_TTCN_sequence_search",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "SlateBlue",
"showDescriptions" : false,
- "height" : 4
+ "height" : 4,
+ "color1" : "SlateBlue",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "TTCN_sequence_search_c_quiockensis_PRJEB11354-LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
"gziLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_quiockensis.PRJEB11354.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
},
+ "type" : "BgzipFastaAdapter",
"faiLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_quiockensis.PRJEB11354.WS284.genomic.fa.gz.fai"
@@ -49212,267 +48406,269 @@
"locationType" : "UriLocation"
}
},
+ "type" : "SequenceSearchAdapter",
"search" : "TTC."
- },
- "name" : "Cas12e TTCN PAM sites",
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time."
+ }
},
{
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
- "name" : "Cas12a TTN PAM sites",
- "type" : "FeatureTrack",
"adapter" : {
"search" : "TT.",
"sequenceAdapter" : {
"type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_quiockensis.PRJEB11354.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ },
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_quiockensis.PRJEB11354.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
"faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_quiockensis.PRJEB11354.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
- },
- "gziLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_quiockensis.PRJEB11354.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_quiockensis.PRJEB11354.WS284.genomic.fa.gz.fai"
}
},
"type" : "SequenceSearchAdapter"
},
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 4,
"showDescriptions" : false,
+ "height" : 4,
+ "showLabels" : false,
"color1" : "Indigo",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "TTN_sequence_search_c_quiockensis_PRJEB11354-LinearBasicDisplay"
+ "displayId" : "TTN_sequence_search_c_quiockensis_PRJEB11354-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
"trackId" : "c_quiockensis_PRJEB11354_TTN_sequence_search",
+ "name" : "Cas12a TTN PAM sites",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
"assemblyNames" : [
"c_quiockensis_PRJEB11354"
- ]
+ ],
+ "type" : "FeatureTrack"
},
{
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_quiockensis_PRJEB11354"
+ ],
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
+ "name" : "SaCas9 NNGRRT PAM sites",
+ "trackId" : "c_quiockensis_PRJEB11354_NNGRRT_sequence_search",
"displays" : [
{
"displayId" : "NNGRRT_sequence_search_c_quiockensis_PRJEB11354-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "showLabels" : false,
"height" : 4,
"showDescriptions" : false,
"color1" : "DarkViolet",
- "showLabels" : false,
"type" : "SvgFeatureRenderer"
- }
+ },
+ "type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_quiockensis_PRJEB11354"
- ],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "trackId" : "c_quiockensis_PRJEB11354_NNGRRT_sequence_search",
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
"adapter" : {
+ "search" : "..G[AG][AG]T",
"type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
"faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_quiockensis.PRJEB11354.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_quiockensis.PRJEB11354.WS284.genomic.fa.gz.fai"
},
"fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_quiockensis.PRJEB11354.WS284.genomic.fa.gz"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_quiockensis.PRJEB11354.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
},
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_quiockensis.PRJEB11354.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_quiockensis.PRJEB11354.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
}
- },
- "search" : "..G[AG][AG]T"
- },
- "type" : "FeatureTrack",
- "name" : "SaCas9 NNGRRT PAM sites"
+ }
+ }
},
{
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
"trackId" : "c_quiockensis_PRJEB11354_NGG_sequence_search",
- "assemblyNames" : [
- "c_quiockensis_PRJEB11354"
- ],
+ "name" : "SpCas9 NGG PAM sites",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "displays" : [
- {
- "renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "RebeccaPurple",
- "showDescriptions" : false,
- "height" : 4
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "NGG_sequence_search_c_quiockensis_PRJEB11354-LinearBasicDisplay"
- }
+ "assemblyNames" : [
+ "c_quiockensis_PRJEB11354"
],
- "name" : "SpCas9 NGG PAM sites",
"type" : "FeatureTrack",
"adapter" : {
"search" : ".GG",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
"fastaLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_quiockensis.PRJEB11354.WS284.genomic.fa.gz"
},
"faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_quiockensis.PRJEB11354.WS284.genomic.fa.gz.fai"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_quiockensis.PRJEB11354.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
},
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_quiockensis.PRJEB11354.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_quiockensis.PRJEB11354.WS284.genomic.fa.gz.gzi"
}
- },
- "type" : "SequenceSearchAdapter"
+ }
},
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time."
+ "displays" : [
+ {
+ "displayId" : "NGG_sequence_search_c_quiockensis_PRJEB11354-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "RebeccaPurple",
+ "height" : 4,
+ "showDescriptions" : false,
+ "showLabels" : false
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Curated_Genes/{refseq}/trackData.jsonz"
+ }
+ },
"displays" : [
{
- "displayId" : "curated_genes-c_remanei_PRJNA53967-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "color3" : "#965567",
- "maxHeight" : 5000,
- "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
- "type" : "SvgFeatureRenderer",
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
- }
- }
+ },
+ "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
+ "maxHeight" : 5000,
+ "type" : "SvgFeatureRenderer",
+ "color3" : "#965567"
+ },
+ "displayId" : "curated_genes-c_remanei_PRJNA53967-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
},
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
+ "name" : "Curated Genes",
"trackId" : "c_remanei_PRJNA53967_curated_genes",
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ],
"category" : [
"Genes",
"Curated Genes"
],
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
- "name" : "Curated Genes",
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Curated_Genes/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- }
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
+ ]
},
{
- "name" : "Protein motifs",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Protein motifs/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
+ ],
"type" : "FeatureTrack",
- "description" : "This track shows the extent of predicted protein motifs. Note these spans correspond to amino acid coordinates interpolated onto the physical map. Included are signal peptide (signalp), coiled coil (ncoils) and transmembrane (tmhmm) domains, regions of low complexity (seg), and Pfam annotated motif homologies.",
- "trackId" : "c_remanei_PRJNA53967_protein_motifs",
"category" : [
"Sequence Features",
"Translated Features"
],
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ],
+ "trackId" : "c_remanei_PRJNA53967_protein_motifs",
+ "name" : "Protein motifs",
+ "description" : "This track shows the extent of predicted protein motifs. Note these spans correspond to amino acid coordinates interpolated onto the physical map. Included are signal peptide (signalp), coiled coil (ncoils) and transmembrane (tmhmm) domains, regions of low complexity (seg), and Pfam annotated motif homologies.",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
+ "height" : 7,
"color1" : "jexl:parent(feature)=='undefined'?'purple':get(parent(feature),'predictiontype')=='tmhmm'?'magenta':get(parent(feature),'predictiontype')=='seg'?'lightseagreen':get(parent(feature),'predictiontype')=='signalp'?'aquamarine':get(parent(feature),'predictiontype')=='ncoils'?'chartreuse':\nget(parent(feature),'predictiontype')=='pfam'?'lightsalmon':'purple'",
- "height" : 7
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "protein_motifs-c_remanei_PRJNA53967-LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Protein motifs/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
}
},
{
- "name" : "Curated Genes (noncoding)",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Curated Genes (noncoding)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Non-coding curated gene models, including ncRNA, tRNA, miRNA, snRNA, snoRNA, piRNA, lincRNA and antisense RNA.",
- "trackId" : "c_remanei_PRJNA53967_curated_genes_noncoding",
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
"displays" : [
{
"displayId" : "curated_genes_(noncoding)-c_remanei_PRJNA53967-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 6,
"color1" : "gray",
+ "height" : 6,
"type" : "SvgFeatureRenderer"
- }
+ },
+ "type" : "LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- }
- },
- {
- "trackId" : "c_remanei_PRJNA53967_yacs_fosmids_cosmids",
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Curated Genes (noncoding)/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
+ ],
"category" : [
- "Reagents"
+ "Genes",
+ "Curated Genes"
],
+ "name" : "Curated Genes (noncoding)",
+ "trackId" : "c_remanei_PRJNA53967_curated_genes_noncoding",
+ "description" : "Non-coding curated gene models, including ncRNA, tRNA, miRNA, snRNA, snoRNA, piRNA, lincRNA and antisense RNA."
+ },
+ {
"assemblyNames" : [
"c_remanei_PRJNA53967"
],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Reagents"
+ ],
+ "trackId" : "c_remanei_PRJNA53967_yacs_fosmids_cosmids",
+ "name" : "YACs, Fosmids, & Cosmids",
+ "description" : "This track shows the locations of the cosmids, fosmids, and YACs used for the physical mapping and sequencing of the C. elegans genome. The clone termini do not necessarily correspond to the termini of submitted GenBank/EMBL entries. In some cases the exact termini of the clones is not known. For example, YACs were sequenced using PCR amplification across gaps in the cosmid maps. When a clone end is not known, it is shown as an arrow extending to the end of the display. Such data is to be treated with caution. The Vancouver fosmids can be ordered directly from GeneService.",
"displays" : [
{
"displayId" : "yacs,_fosmids,_&_cosmids-c_remanei_PRJNA53967-LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 3,
- "color1" : "black",
- "type" : "SvgFeatureRenderer"
+ "color1" : "black"
},
"type" : "LinearBasicDisplay"
}
@@ -49480,28 +48676,32 @@
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "name" : "YACs, Fosmids, & Cosmids",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/YACs, Fosmids, & Cosmids/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "This track shows the locations of the cosmids, fosmids, and YACs used for the physical mapping and sequencing of the C. elegans genome. The clone termini do not necessarily correspond to the termini of submitted GenBank/EMBL entries. In some cases the exact termini of the clones is not known. For example, YACs were sequenced using PCR amplification across gaps in the cosmid maps. When a clone end is not known, it is shown as an arrow extending to the end of the display. Such data is to be treated with caution. The Vancouver fosmids can be ordered directly from GeneService."
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/YACs, Fosmids, & Cosmids/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
+ "name" : "genBlastG CDS predictions",
+ "trackId" : "c_remanei_PRJNA53967_genblastg_cds_predictions",
+ "description" : "Data from 'genBlastG: using BLAST searches to build homologous gene models' (WBPaper00040677).",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
+ ],
"category" : [
"Genes",
"Ab-initio predictions"
],
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ],
- "trackId" : "c_remanei_PRJNA53967_genblastg_cds_predictions",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/genBlastG CDS predictions/{refseq}/trackData.jsonz"
+ }
},
"displays" : [
{
@@ -49513,123 +48713,120 @@
"type" : "LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/genBlastG CDS predictions/{refseq}/trackData.jsonz"
- }
- },
- "name" : "genBlastG CDS predictions",
- "description" : "Data from 'genBlastG: using BLAST searches to build homologous gene models' (WBPaper00040677)."
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ }
},
{
- "description" : "Historical gene predictions.",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Gene Models (historical)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Gene Models (historical)/{refseq}/trackData.jsonz"
}
},
- "type" : "FeatureTrack",
- "name" : "Gene Models (historical)",
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
"displays" : [
{
- "displayId" : "gene_models_(historical)-c_remanei_PRJNA53967-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
+ "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
"labels" : {
"description" : "jexl:get(feature,'type')"
},
- "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'"
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "gene_models_(historical)-c_remanei_PRJNA53967-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
+ "name" : "Gene Models (historical)",
+ "trackId" : "c_remanei_PRJNA53967_gene_models_(historical)",
+ "description" : "Historical gene predictions.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
+ ],
"category" : [
"Genes",
"Curated Genes"
+ ]
+ },
+ {
+ "category" : [
+ "Genes",
+ "Supporting Evidence"
],
"assemblyNames" : [
"c_remanei_PRJNA53967"
],
- "trackId" : "c_remanei_PRJNA53967_gene_models_(historical)"
- },
- {
+ "type" : "FeatureTrack",
"description" : "Native (same species) full length cDNAs and ncRNAs aligned to the genome using BLAT. This track shows the best unique location for each cDNA.",
+ "trackId" : "c_remanei_PRJNA53967_mrnas/ncrnas_(best)",
"name" : "mRNAs/ncRNAs (best)",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/mRNAs_ncRNAs (best)/{refseq}/trackData.jsonz"
- }
- },
- "type" : "FeatureTrack",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "jexl:startsWith(get(feature,'source'),'BLAT_mRNA_')==true?'yellow':'gray'",
"outline" : "black",
- "height" : 6
+ "height" : 6,
+ "color1" : "jexl:startsWith(get(feature,'source'),'BLAT_mRNA_')==true?'yellow':'gray'",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "mrnas/ncrnas_(best)-c_remanei_PRJNA53967-LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
- "trackId" : "c_remanei_PRJNA53967_mrnas/ncrnas_(best)",
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ],
- "category" : [
- "Genes",
- "Supporting Evidence"
- ]
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/mRNAs_ncRNAs (best)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Curated Genes (pseudogenes)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "displayId" : "curated_genes_(pseudogenes)-c_remanei_PRJNA53967-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
+ "color1" : "gray",
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "gray"
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "curated_genes_(pseudogenes)-c_remanei_PRJNA53967-LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
+ "name" : "Curated Genes (pseudogenes)",
"trackId" : "c_remanei_PRJNA53967_curated_genes_pseudogenes",
- "category" : [
- "Genes",
- "Curated Genes"
- ],
+ "description" : "A subset of the full Curated Genes set limited to pseudogenes only. Pseudogenes of tRNA are lighter gray and pseudogenes of rRNA are darker gray than pseudogenes of protein coding genes.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_remanei_PRJNA53967"
],
- "description" : "A subset of the full Curated Genes set limited to pseudogenes only. Pseudogenes of tRNA are lighter gray and pseudogenes of rRNA are darker gray than pseudogenes of protein coding genes.",
- "name" : "Curated Genes (pseudogenes)",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Curated Genes (pseudogenes)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- }
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ]
},
{
+ "name" : "Trans-spliced acceptor",
+ "trackId" : "c_remanei_PRJNA53967_trans-spliced_acceptor",
+ "description" : "This track contains SL1 and SL2 trans-spliced acceptors from a variety of sources: SL1 and SL2 trans-spliced acceptors published by Blumenthal et al, Nature (2002), Trans-Spliced Exon Coupled RNA End Determination (TEC-RED) Hwang et al, PNAS (2004), EST/mRNA sequence data, RNASeq read data from ENA. SL1 acceptors are show in red, SL2 in green. Direction of transcription is indicated by arrow direction.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_remanei_PRJNA53967"
],
@@ -49637,12 +48834,19 @@
"Sequence Features",
"Signals & Motifs"
],
- "trackId" : "c_remanei_PRJNA53967_trans-spliced_acceptor",
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Trans-spliced acceptor/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "trans-spliced_acceptor-c_remanei_PRJNA53967-LinearBasicDisplay",
"renderer" : {
"color1" : "jexl:get(feature,'source')=='SL1'?'red':get(feature,'source')=='SL2'?'green':'black'",
@@ -49650,191 +48854,183 @@
"description" : "jexl:get(feature,'source') || get(feature,'description')"
},
"type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay"
+ }
}
- ],
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Trans-spliced acceptor/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "name" : "Trans-spliced acceptor",
- "description" : "This track contains SL1 and SL2 trans-spliced acceptors from a variety of sources: SL1 and SL2 trans-spliced acceptors published by Blumenthal et al, Nature (2002), Trans-Spliced Exon Coupled RNA End Determination (TEC-RED) Hwang et al, PNAS (2004), EST/mRNA sequence data, RNASeq read data from ENA. SL1 acceptors are show in red, SL2 in green. Direction of transcription is indicated by arrow direction."
+ ]
},
{
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
+ ],
"type" : "FeatureTrack",
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
+ "trackId" : "c_remanei_PRJNA53967_curated_genes_protein_coding",
"name" : "Curated Genes (protein coding)",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "curated_genes_(protein_coding)-c_remanei_PRJNA53967-LinearBasicDisplay",
"renderer" : {
"color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
- "maxHeight" : 5000,
+ "color3" : "#965567",
"type" : "SvgFeatureRenderer",
- "color3" : "#965567"
- },
- "type" : "LinearBasicDisplay"
+ "maxHeight" : 5000
+ }
}
],
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ],
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "trackId" : "c_remanei_PRJNA53967_curated_genes_protein_coding"
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
+ "trackId" : "c_remanei_PRJNA53967_links_and_superlinks",
+ "name" : "Links and Superlinks",
+ "description" : "This track shows the location and coordinates of contigs created during the assembly of the C. elegans genome.",
"assemblyNames" : [
"c_remanei_PRJNA53967"
],
+ "type" : "FeatureTrack",
"category" : [
"Genome Structure",
"Assembly & Curation"
],
- "trackId" : "c_remanei_PRJNA53967_links_and_superlinks",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Links and Superlinks/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
},
"displays" : [
{
- "displayId" : "links_and_superlinks-c_remanei_PRJNA53967-LinearBasicDisplay",
"renderer" : {
- "color1" : "black",
"type" : "SvgFeatureRenderer",
+ "color1" : "black",
"height" : 4
},
+ "displayId" : "links_and_superlinks-c_remanei_PRJNA53967-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Links and Superlinks/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "name" : "Links and Superlinks",
- "description" : "This track shows the location and coordinates of contigs created during the assembly of the C. elegans genome."
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ }
},
{
"trackId" : "c_remanei_PRJNA53967_D_melanogaster_proteins",
+ "name" : "D. melanogaster proteins",
+ "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"assemblyNames" : [
"c_remanei_PRJNA53967"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
"renderer" : {
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
+ "height" : 4,
"showLabels" : false,
- "height" : 4
+ "color1" : "orange"
},
"mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
- "displayId" : "D_melanogaster_proteins-c_remanei_PRJNA53967-LinearBasicDisplay"
- }
- ],
- "name" : "D. melanogaster proteins",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz"
+ "displayId" : "D_melanogaster_proteins-c_remanei_PRJNA53967-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- },
- "type" : "FeatureTrack",
- "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ ]
},
{
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_remanei_PRJNA53967_C_remanei_proteins",
+ "name" : "C. remanei proteins",
"displays" : [
{
- "displayId" : "C_remanei_proteins-c_remanei_PRJNA53967-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
+ "color1" : "orange",
+ "height" : 4,
"showLabels" : false
- }
+ },
+ "displayId" : "C_remanei_proteins-c_remanei_PRJNA53967-LinearBasicDisplay"
}
],
- "trackId" : "c_remanei_PRJNA53967_C_remanei_proteins",
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "C. remanei proteins",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/C. remanei proteins/{refseq}/trackData.jsonz"
}
- },
- "type" : "FeatureTrack"
+ }
},
{
- "trackId" : "c_remanei_PRJNA53967_H_sapiens_proteins",
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/H. sapiens proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "mouseover" : "jexl:get(feature,'clone')",
+ "type" : "LinearBasicDisplay",
+ "displayId" : "H_sapiens_proteins-c_remanei_PRJNA53967-LinearBasicDisplay",
"renderer" : {
- "color1" : "orange",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "height" : 4
+ "showLabels" : false,
+ "height" : 4,
+ "color1" : "orange"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "H_sapiens_proteins-c_remanei_PRJNA53967-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')"
}
],
+ "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"name" : "H. sapiens proteins",
+ "trackId" : "c_remanei_PRJNA53967_H_sapiens_proteins",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/H. sapiens proteins/{refseq}/trackData.jsonz"
- }
- },
- "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
+ ]
},
{
+ "name" : "WormBase nematode mRNAs/ESTs (best)",
"trackId" : "wormbase_nematode_mrnas/ests_(best)-c_remanei_PRJNA53967",
+ "description" : "ESTs and mRNAs from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each cDNA sequence. mRNAs are shown in light blue; ESTs in green.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_remanei_PRJNA53967"
],
@@ -49842,22 +49038,6 @@
"Sequence Similarity",
"Nucleotide"
],
- "displays" : [
- {
- "renderer" : {
- "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA_BEST'?'lightblue':get(feature,'source')=='BLAT_Caen_EST_BEST'?'green':'black'",
- "type" : "SvgFeatureRenderer",
- "labels" : {
- "name" : "jexl:get(feature,'species') || get(feature,'id')"
- },
- "height" : 4
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "wormbase_nematode_mrnas/ests_(best)-c_remanei_PRJNA53967-LinearBasicDisplay"
- }
- ],
- "name" : "WormBase nematode mRNAs/ESTs (best)",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -49865,70 +49045,50 @@
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/WormBase nematode mRNAs_ESTs (best)/{refseq}/trackData.jsonz"
}
},
- "description" : "ESTs and mRNAs from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each cDNA sequence. mRNAs are shown in light blue; ESTs in green."
- },
- {
- "description" : "Matches to WormBase S. ratti proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "S. ratti proteins",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/S. ratti proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "orange",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 4
+ "height" : 4,
+ "labels" : {
+ "name" : "jexl:get(feature,'species') || get(feature,'id')"
+ },
+ "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA_BEST'?'lightblue':get(feature,'source')=='BLAT_Caen_EST_BEST'?'green':'black'",
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
- "displayId" : "S_ratti_proteins-c_remanei_PRJNA53967-LinearBasicDisplay"
+ "displayId" : "wormbase_nematode_mrnas/ests_(best)-c_remanei_PRJNA53967-LinearBasicDisplay"
}
- ],
+ ]
+ },
+ {
+ "name" : "S. ratti proteins",
"trackId" : "c_remanei_PRJNA53967_S_ratti_proteins",
+ "description" : "Matches to WormBase S. ratti proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_remanei_PRJNA53967"
],
"category" : [
"Sequence Similarity",
"Proteins"
- ]
- },
- {
- "name" : "O. volvulus proteins",
+ ],
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/O. volvulus proteins/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/S. ratti proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "description" : "Matches to WormBase O. volvulus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "trackId" : "c_remanei_PRJNA53967_O_volvulus_proteins",
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
"displays" : [
{
- "displayId" : "O_volvulus_proteins-c_remanei_PRJNA53967-LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
+ "color1" : "orange",
"showLabels" : false,
"height" : 4
},
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "S_ratti_proteins-c_remanei_PRJNA53967-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
]
@@ -49936,94 +49096,117 @@
{
"displays" : [
{
- "displayId" : "contig_submissions-c_remanei_PRJNA53967-LinearBasicDisplay",
"renderer" : {
- "height" : 7,
"type" : "SvgFeatureRenderer",
- "color1" : "sienna"
+ "showLabels" : false,
+ "height" : 4,
+ "color1" : "orange"
},
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "O_volvulus_proteins-c_remanei_PRJNA53967-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/O. volvulus proteins/{refseq}/trackData.jsonz"
+ }
},
- "trackId" : "c_remanei_PRJNA53967_contig_submissions",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
"assemblyNames" : [
"c_remanei_PRJNA53967"
],
- "category" : [
- "Genome Structure",
- "Assembly & Curation"
- ],
- "description" : "This track shows the location and coordinates of contigs (mostly cosmids) submitted to GenBank/EMBL.",
- "name" : "Contig submissions",
+ "type" : "FeatureTrack",
+ "description" : "Matches to WormBase O. volvulus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_remanei_PRJNA53967_O_volvulus_proteins",
+ "name" : "O. volvulus proteins"
+ },
+ {
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Contig submissions/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ }
+ },
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "type" : "FeatureTrack"
- },
- {
"displays" : [
{
- "displayId" : "C_elegans_proteins-c_remanei_PRJNA53967-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "contig_submissions-c_remanei_PRJNA53967-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "orange"
+ "height" : 7,
+ "color1" : "sienna",
+ "type" : "SvgFeatureRenderer"
}
}
],
- "trackId" : "c_remanei_PRJNA53967_C_elegans_proteins",
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
+ "description" : "This track shows the location and coordinates of contigs (mostly cosmids) submitted to GenBank/EMBL.",
+ "name" : "Contig submissions",
+ "trackId" : "c_remanei_PRJNA53967_contig_submissions",
+ "category" : [
+ "Genome Structure",
+ "Assembly & Curation"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
+ ]
+ },
+ {
+ "displays" : [
+ {
+ "displayId" : "C_elegans_proteins-c_remanei_PRJNA53967-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
+ "renderer" : {
+ "color1" : "orange",
+ "height" : 4,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
+ }
],
- "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "C. elegans proteins",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/C. elegans proteins/{refseq}/trackData.jsonz"
- }
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/C. elegans proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
},
- "type" : "FeatureTrack"
- },
- {
- "trackId" : "c_remanei_PRJNA53967_B_malayi_proteins",
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ],
+ "trackId" : "c_remanei_PRJNA53967_C_elegans_proteins",
+ "name" : "C. elegans proteins",
+ "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ },
+ {
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "B_malayi_proteins-c_remanei_PRJNA53967-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
"color1" : "orange",
+ "height" : 4,
"showLabels" : false,
"type" : "SvgFeatureRenderer"
- },
- "mouseover" : "jexl:get(feature,'clone')",
- "displayId" : "B_malayi_proteins-c_remanei_PRJNA53967-LinearBasicDisplay"
+ }
}
],
- "name" : "B. malayi proteins",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -50031,253 +49214,254 @@
"locationType" : "UriLocation"
}
},
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "trackId" : "c_remanei_PRJNA53967_B_malayi_proteins",
+ "name" : "B. malayi proteins",
"description" : "Matches to WormBase B. malayi proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
},
{
+ "category" : [
+ "Genome Structure",
+ "Repeats"
+ ],
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
+ ],
+ "type" : "FeatureTrack",
"description" : "Low-complexity regions identified by Dust.",
+ "trackId" : "c_remanei_PRJNA53967_low_complextity_region_(dust)",
"name" : "Low complextity region (Dust)",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 4,
+ "showLabels" : false,
"showDescriptions" : false,
+ "height" : 4,
"color1" : "bisque",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "low_complextity_region_(dust)-c_remanei_PRJNA53967-LinearBasicDisplay"
+ "displayId" : "low_complextity_region_(dust)-c_remanei_PRJNA53967-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_remanei_PRJNA53967_low_complextity_region_(dust)",
- "category" : [
- "Genome Structure",
- "Repeats"
- ],
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ]
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
- "trackId" : "c_remanei_PRJNA53967_rnaseq_asymmetries",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_remanei_PRJNA53967"
],
"category" : [
"Expression"
],
+ "name" : "RNASeq Asymmetries",
+ "trackId" : "c_remanei_PRJNA53967_rnaseq_asymmetries",
+ "description" : "Red boxes indicate regions where there are more than 2 times as many forward sense RNASeq reads aligned to the genome as reverse sense reads. This asymmetrical signal has been found empirically to be a sensitive marker for the ends of transcripts. Green boxes indicate regions where there are more than 2 times as many reverse sense RNASeq reads aligned to the genome as forward sense reads. This asymmetrical signal has been found empirically to be sensitive marker for the ends of transcripts. The height of all boxes indicates the relative score of the feature.",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "rnaseq_asymmetries-c_remanei_PRJNA53967-LinearBasicDisplay",
"renderer" : {
"height" : 24,
- "displayMode" : "collapse",
- "color1" : "jexl:get(feature,'source')=='RNASeq_R_asymmetry'?'red': get(feature,'source')=='RNASeq_F_asymmetry'?'green':'black'",
"showLabels" : false,
+ "color1" : "jexl:get(feature,'source')=='RNASeq_R_asymmetry'?'red': get(feature,'source')=='RNASeq_F_asymmetry'?'green':'black'",
+ "displayMode" : "collapse",
"type" : "SvgFeatureRenderer"
},
"mouseover" : "jexl:'Score: '+get(feature,'score')",
- "displayId" : "rnaseq_asymmetries-c_remanei_PRJNA53967-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "name" : "RNASeq Asymmetries",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/RNASeq Asymmetries/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "description" : "Red boxes indicate regions where there are more than 2 times as many forward sense RNASeq reads aligned to the genome as reverse sense reads. This asymmetrical signal has been found empirically to be a sensitive marker for the ends of transcripts. Green boxes indicate regions where there are more than 2 times as many reverse sense RNASeq reads aligned to the genome as forward sense reads. This asymmetrical signal has been found empirically to be sensitive marker for the ends of transcripts. The height of all boxes indicates the relative score of the feature."
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/RNASeq Asymmetries/{refseq}/trackData.jsonz"
+ }
+ }
},
{
+ "name" : "RNASeq introns",
+ "trackId" : "c_remanei_PRJNA53967_rnaseq_introns",
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
+ ],
+ "category" : [
+ "Expression"
+ ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/RNASeq introns/{refseq}/trackData.jsonz"
+ }
+ },
"displays" : [
{
"displayId" : "rnaseq_introns-c_remanei_PRJNA53967-LinearBasicDisplay",
"renderer" : {
- "color1" : "green",
"type" : "SvgFeatureRenderer",
"showLabels" : false,
"height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)",
- "showDescriptions" : false
+ "showDescriptions" : false,
+ "color1" : "green"
},
"mouseover" : "jexl:get(feature,'score')+' reads'",
"type" : "LinearBasicDisplay"
}
- ],
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ],
+ ]
+ },
+ {
"category" : [
"Expression"
],
- "trackId" : "c_remanei_PRJNA53967_rnaseq_introns",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display.",
"type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/RNASeq introns/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "name" : "RNASeq introns"
- },
- {
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
+ ],
"description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/RNASeq Splice Junctions (common)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
"name" : "RNASeq Splice Junctions (common)",
+ "trackId" : "c_remanei_PRJNA53967_rnaseq_splice_junctions_(common)",
"displays" : [
{
- "displayId" : "rnaseq_splice_junctions_(common)-c_remanei_PRJNA53967-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'score')+' reads'",
+ "displayId" : "rnaseq_splice_junctions_(common)-c_remanei_PRJNA53967-LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer",
"color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
- }
+ "showDescriptions" : false
+ },
+ "mouseover" : "jexl:get(feature,'score')+' reads'"
}
],
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ],
- "category" : [
- "Expression"
- ],
- "trackId" : "c_remanei_PRJNA53967_rnaseq_splice_junctions_(common)"
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/RNASeq Splice Junctions (common)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ }
},
- "type" : "FeatureTrack",
- "name" : "RNASeq Splice Junctions (rare)",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
- "category" : [
- "Expression"
- ],
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ],
- "trackId" : "c_remanei_PRJNA53967_rnaseq_splice_junctions_(rare)",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "rnaseq_splice_junctions_(rare)-c_remanei_PRJNA53967-LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'score')+' reads'",
"renderer" : {
+ "color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
+ "showLabels" : false,
+ "showDescriptions" : false,
"height" : "jexl:4",
"type" : "SvgFeatureRenderer",
- "showDescriptions" : false,
- "showLabels" : false,
- "maxHeight" : 5000,
- "color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))"
- },
- "type" : "LinearBasicDisplay"
+ "maxHeight" : 5000
+ }
}
+ ],
+ "name" : "RNASeq Splice Junctions (rare)",
+ "trackId" : "c_remanei_PRJNA53967_rnaseq_splice_junctions_(rare)",
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
+ ],
+ "category" : [
+ "Expression"
]
},
{
- "displays" : [
- {
- "displayId" : "C_japonica_proteins-c_remanei_PRJNA53967-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
- "renderer" : {
- "height" : 4,
- "color1" : "orange",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
- }
- }
- ],
+ "trackId" : "c_remanei_PRJNA53967_C_japonica_proteins",
+ "name" : "C. japonica proteins",
+ "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"assemblyNames" : [
"c_remanei_PRJNA53967"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "trackId" : "c_remanei_PRJNA53967_C_japonica_proteins",
- "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/C. japonica proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/C. japonica proteins/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "name" : "C. japonica proteins"
- },
- {
- "name" : "S. cerevisiae proteins",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz"
- }
- },
- "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "trackId" : "c_remanei_PRJNA53967_S_cerevisiae_proteins",
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ],
"displays" : [
{
- "displayId" : "S_cerevisiae_proteins-c_remanei_PRJNA53967-LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
+ "type" : "SvgFeatureRenderer",
"color1" : "orange",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "height" : 4
},
+ "displayId" : "C_japonica_proteins-c_remanei_PRJNA53967-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
]
},
{
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "trackId" : "c_remanei_PRJNA53967_S_cerevisiae_proteins",
+ "name" : "S. cerevisiae proteins",
+ "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "orange",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "height" : 4
+ "color1" : "orange",
+ "height" : 4,
+ "showLabels" : false
},
"mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
- "displayId" : "C_brenneri_proteins-c_remanei_PRJNA53967-LinearBasicDisplay"
+ "displayId" : "S_cerevisiae_proteins-c_remanei_PRJNA53967-LinearBasicDisplay"
}
],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ }
+ },
+ {
+ "name" : "C. brenneri proteins",
+ "trackId" : "c_remanei_PRJNA53967_C_brenneri_proteins",
+ "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_remanei_PRJNA53967"
],
@@ -50285,63 +49469,81 @@
"Sequence Similarity",
"Proteins"
],
- "trackId" : "c_remanei_PRJNA53967_C_brenneri_proteins",
- "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/C. brenneri proteins/{refseq}/trackData.jsonz"
- }
+ },
+ "type" : "NCListAdapter"
},
- "name" : "C. brenneri proteins"
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "C_brenneri_proteins-c_remanei_PRJNA53967-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showLabels" : false,
+ "height" : 4,
+ "color1" : "orange"
+ },
+ "mouseover" : "jexl:get(feature,'clone')"
+ }
+ ]
},
{
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ],
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Matches to WormBase T. muris proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"trackId" : "c_remanei_PRJNA53967_T_muris_proteins",
+ "name" : "T. muris proteins",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "T_muris_proteins-c_remanei_PRJNA53967-LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "color1" : "orange",
- "type" : "SvgFeatureRenderer",
+ "height" : 4,
"showLabels" : false,
- "height" : 4
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "T_muris_proteins-c_remanei_PRJNA53967-LinearBasicDisplay"
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/T. muris proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "name" : "T. muris proteins",
- "description" : "Matches to WormBase T. muris proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ }
+ }
},
{
- "name" : "Tandem and Inverted Repeats",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "tandem_and_inverted_repeats-c_remanei_PRJNA53967-LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "bisque",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
+ }
+ }
+ ],
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Tandem and Inverted Repeats/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "NCListAdapter"
},
"type" : "FeatureTrack",
- "description" : "Exact tandem and inverted repetitive elements.",
- "trackId" : "c_remanei_PRJNA53967_tandem_and_inverted_repeats",
"assemblyNames" : [
"c_remanei_PRJNA53967"
],
@@ -50349,208 +49551,186 @@
"Genome Structure",
"Repeats"
],
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "showDescriptions" : false,
- "color1" : "bisque",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
- },
- "displayId" : "tandem_and_inverted_repeats-c_remanei_PRJNA53967-LinearBasicDisplay"
- }
- ]
+ "name" : "Tandem and Inverted Repeats",
+ "trackId" : "c_remanei_PRJNA53967_tandem_and_inverted_repeats",
+ "description" : "Exact tandem and inverted repetitive elements."
},
{
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "rnaseq-c_remanei_PRJNA53967-LinearBasicDisplay",
"renderer" : {
+ "displayMode" : "collapse",
"color1" : "black",
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
"height" : "jexl:get(feature,'score')>100?50:floor(get(feature,'score')/2)>4?floor(get(feature,'score')/2):4",
- "displayMode" : "collapse",
- "showDescriptions" : false
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:'Score: '+get(feature,'score')",
- "type" : "LinearBasicDisplay",
- "displayId" : "rnaseq-c_remanei_PRJNA53967-LinearBasicDisplay"
+ "mouseover" : "jexl:'Score: '+get(feature,'score')"
}
],
- "category" : [
- "Expression"
- ],
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ],
- "trackId" : "c_remanei_PRJNA53967_rnaseq",
- "description" : "These boxes indicate alignments of short read sequences from all available RNASeq projects. The number of reads has been normalised by averaging over the number of libraries. The height of all boxes indicates the relative score of the feature.",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/RNASeq/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/RNASeq/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
},
"type" : "FeatureTrack",
- "name" : "RNASeq"
- },
- {
- "trackId" : "c_remanei_PRJNA53967_other_uniprot_proteins",
"assemblyNames" : [
"c_remanei_PRJNA53967"
],
"category" : [
- "Sequence Similarity",
- "Proteins"
+ "Expression"
],
+ "name" : "RNASeq",
+ "trackId" : "c_remanei_PRJNA53967_rnaseq",
+ "description" : "These boxes indicate alignments of short read sequences from all available RNASeq projects. The number of reads has been normalised by averaging over the number of libraries. The height of all boxes indicates the relative score of the feature."
+ },
+ {
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "other_uniprot_proteins-c_remanei_PRJNA53967-LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "orange",
+ "showLabels" : false,
+ "height" : 4,
"showDescriptions" : false,
- "height" : 4
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "other_uniprot_proteins-c_remanei_PRJNA53967-LinearBasicDisplay"
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "name" : "Other UniProt proteins",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Other UniProt proteins/{refseq}/trackData.jsonz"
- }
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Other UniProt proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
},
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "trackId" : "c_remanei_PRJNA53967_other_uniprot_proteins",
+ "name" : "Other UniProt proteins",
"description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation)."
},
{
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "ests-c_remanei_PRJNA53967-LinearBasicDisplay",
"renderer" : {
+ "maxHeight" : 5000,
"type" : "SvgFeatureRenderer",
- "color1" : "jexl:parent(feature)=='undefined'?'red':get(parent(feature),'has_mate')==1?'limegreen':get(parent(feature),'has_mate')==2?'green':get(parent(feature),'has_mate')==0?'gold':'black'",
- "maxHeight" : 5000
- },
- "displayId" : "ests-c_remanei_PRJNA53967-LinearBasicDisplay"
+ "color1" : "jexl:parent(feature)=='undefined'?'red':get(parent(feature),'has_mate')==1?'limegreen':get(parent(feature),'has_mate')==2?'green':get(parent(feature),'has_mate')==0?'gold':'black'"
+ }
}
],
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ],
- "category" : [
- "Genes",
- "Supporting Evidence"
- ],
- "trackId" : "c_remanei_PRJNA53967_ests",
- "description" : "Native (same-species) Expressed Sequence Tags (ESTs), aligned to the genome using BLAT. This track shows the best unique location for each EST. The paired 5' and 3' ESTs from the same cDNA clone are connected by a dashed line and a colored light green. ESTs with no mate are yellow, and ESTs with a mate that is 'far away' are dark green.",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/ESTs (best)/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ }
},
+ "category" : [
+ "Genes",
+ "Supporting Evidence"
+ ],
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
+ ],
"type" : "FeatureTrack",
+ "description" : "Native (same-species) Expressed Sequence Tags (ESTs), aligned to the genome using BLAT. This track shows the best unique location for each EST. The paired 5' and 3' ESTs from the same cDNA clone are connected by a dashed line and a colored light green. ESTs with no mate are yellow, and ESTs with a mate that is 'far away' are dark green.",
+ "trackId" : "c_remanei_PRJNA53967_ests",
"name" : "ESTs"
},
{
"description" : "IsoSeq from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each IsoSeqsequence.",
"name" : "Non-C. elegans Isoseq collection (best)",
+ "trackId" : "non-c._elegans_isoseq_collection_(best)-c_remanei_PRJNA53967",
+ "category" : [
+ "Sequence Similarity",
+ "Nucleotide"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Non-C. elegans Isoseq collection (best)/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Non-C. elegans Isoseq collection (best)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "non-c._elegans_isoseq_collection_(best)-c_remanei_PRJNA53967-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"color1" : "green",
"height" : 4
},
+ "displayId" : "non-c._elegans_isoseq_collection_(best)-c_remanei_PRJNA53967-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
- ],
- "trackId" : "non-c._elegans_isoseq_collection_(best)-c_remanei_PRJNA53967",
- "category" : [
- "Sequence Similarity",
- "Nucleotide"
- ],
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
]
},
{
- "name" : "C. briggsae proteins",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/C. briggsae proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/C. briggsae proteins/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "trackId" : "c_remanei_PRJNA53967_C_briggsae_proteins",
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ],
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "color1" : "orange",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "height" : 4
+ "color1" : "orange",
+ "height" : 4,
+ "showLabels" : false
},
- "type" : "LinearBasicDisplay",
"displayId" : "C_briggsae_proteins-c_remanei_PRJNA53967-LinearBasicDisplay"
}
+ ],
+ "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "C. briggsae proteins",
+ "trackId" : "c_remanei_PRJNA53967_C_briggsae_proteins",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
]
},
{
- "displays" : [
- {
- "displayId" : "microarray_oligo_probes-c_remanei_PRJNA53967-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "black",
- "type" : "SvgFeatureRenderer",
- "height" : 4
- }
- }
- ],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
+ "name" : "Microarray oligo probes",
"trackId" : "c_remanei_PRJNA53967_microarray_oligo_probes",
+ "description" : "This track contains Affymetrix GeneChip and Washington University GSC microarray probe sets.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_remanei_PRJNA53967"
],
"category" : [
"Reagents"
],
- "description" : "This track contains Affymetrix GeneChip and Washington University GSC microarray probe sets.",
- "name" : "Microarray oligo probes",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -50558,371 +49738,278 @@
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack"
+ "displays" : [
+ {
+ "displayId" : "microarray_oligo_probes-c_remanei_PRJNA53967-LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "black",
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ }
},
{
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/P. pacificus proteins/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/P. pacificus proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "name" : "P. pacificus proteins",
- "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "orange",
+ "showLabels" : false,
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
+ },
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "P_pacificus_proteins-c_remanei_PRJNA53967-LinearBasicDisplay"
+ }
],
+ "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "P. pacificus proteins",
+ "trackId" : "c_remanei_PRJNA53967_P_pacificus_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "trackId" : "c_remanei_PRJNA53967_P_pacificus_proteins",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
+ ]
+ },
+ {
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "displayId" : "P_pacificus_proteins-c_remanei_PRJNA53967-LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
+ "type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
+ "color1" : "bisque",
"showLabels" : false,
- "color1" : "orange",
+ "showDescriptions" : false,
"height" : 4
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "repeat_region_(repeatmasker)-c_remanei_PRJNA53967-LinearBasicDisplay"
}
- ]
- },
- {
- "trackId" : "c_remanei_PRJNA53967_repeat_region_(repeatmasker)",
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
],
+ "description" : "Repetitive regions identified by RepeatMasker.",
+ "name" : "Repeat Region (RepeatMasker)",
+ "trackId" : "c_remanei_PRJNA53967_repeat_region_(repeatmasker)",
"category" : [
"Genome Structure",
"Repeats"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
+ ]
+ },
+ {
"displays" : [
{
- "displayId" : "repeat_region_(repeatmasker)-c_remanei_PRJNA53967-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "showDescriptions" : false,
- "color1" : "bisque",
"type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "showDescriptions" : false,
+ "height" : 4,
+ "showLabels" : false,
+ "color1" : "SlateBlue"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "TTCN_sequence_search_c_remanei_PRJNA53967-LinearBasicDisplay"
}
],
- "name" : "Repeat Region (RepeatMasker)",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "description" : "Repetitive regions identified by RepeatMasker."
- },
- {
- "type" : "FeatureTrack",
"adapter" : {
"search" : "TTC.",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA53967.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ },
"type" : "BgzipFastaAdapter",
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA53967.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
"faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA53967.WS284.genomic.fa.gz.fai"
- },
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA53967.WS284.genomic.fa.gz.gzi",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA53967.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
}
- },
- "type" : "SequenceSearchAdapter"
+ }
},
- "name" : "Cas12e TTCN PAM sites",
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ],
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
"trackId" : "c_remanei_PRJNA53967_TTCN_sequence_search",
+ "name" : "Cas12e TTCN PAM sites"
+ },
+ {
"displays" : [
{
"renderer" : {
- "color1" : "SlateBlue",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
+ "color1" : "Indigo",
+ "showLabels" : false,
"height" : 4,
"showDescriptions" : false
},
- "type" : "LinearBasicDisplay",
- "displayId" : "TTCN_sequence_search_c_remanei_PRJNA53967-LinearBasicDisplay"
+ "displayId" : "TTN_sequence_search_c_remanei_PRJNA53967-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ]
- },
- {
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
- "name" : "Cas12a TTN PAM sites",
- "type" : "FeatureTrack",
+ ],
"adapter" : {
"search" : "TT.",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
- "gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA53967.WS284.genomic.fa.gz.gzi"
- },
"fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA53967.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA53967.WS284.genomic.fa.gz"
},
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA53967.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
- }
+ },
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA53967.WS284.genomic.fa.gz.gzi"
+ },
+ "type" : "BgzipFastaAdapter"
},
"type" : "SequenceSearchAdapter"
},
- "displays" : [
- {
- "renderer" : {
- "color1" : "Indigo",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "height" : 4,
- "showDescriptions" : false
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "TTN_sequence_search_c_remanei_PRJNA53967-LinearBasicDisplay"
- }
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
],
- "trackId" : "c_remanei_PRJNA53967_TTN_sequence_search",
+ "type" : "FeatureTrack",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ]
+ "trackId" : "c_remanei_PRJNA53967_TTN_sequence_search",
+ "name" : "Cas12a TTN PAM sites",
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time."
},
{
"trackId" : "c_remanei_PRJNA53967_NNGRRT_sequence_search",
+ "name" : "SaCas9 NNGRRT PAM sites",
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
"assemblyNames" : [
"c_remanei_PRJNA53967"
],
+ "type" : "FeatureTrack",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "displays" : [
- {
- "renderer" : {
- "height" : 4,
- "showDescriptions" : false,
- "color1" : "DarkViolet",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "NNGRRT_sequence_search_c_remanei_PRJNA53967-LinearBasicDisplay"
- }
- ],
- "name" : "SaCas9 NNGRRT PAM sites",
- "type" : "FeatureTrack",
"adapter" : {
- "search" : "..G[AG][AG]T",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA53967.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
- },
"fastaLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA53967.WS284.genomic.fa.gz"
},
- "gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA53967.WS284.genomic.fa.gz.gzi"
- },
- "type" : "BgzipFastaAdapter"
- },
- "type" : "SequenceSearchAdapter"
- },
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time."
- },
- {
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "SequenceSearchAdapter",
- "search" : ".GG",
- "sequenceAdapter" : {
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA53967.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
- },
"faiLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA53967.WS284.genomic.fa.gz.fai"
},
- "fastaLocation" : {
+ "gziLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA53967.WS284.genomic.fa.gz"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA53967.WS284.genomic.fa.gz.gzi"
},
"type" : "BgzipFastaAdapter"
- }
- },
- "name" : "SpCas9 NGG PAM sites",
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ],
- "trackId" : "c_remanei_PRJNA53967_NGG_sequence_search",
- "displays" : [
- {
- "displayId" : "NGG_sequence_search_c_remanei_PRJNA53967-LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "RebeccaPurple",
- "showDescriptions" : false,
- "height" : 4
- },
- "type" : "LinearBasicDisplay"
- }
- ]
- },
- {
- "displays" : [
- {
- "renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "green",
- "showDescriptions" : false,
- "height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)"
- },
- "mouseover" : "jexl:get(feature,'score')+' reads'",
- "type" : "LinearBasicDisplay",
- "displayId" : "rnaseq_introns-c_remanei_PRJNA53967-LinearBasicDisplay"
- }
- ],
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ],
- "category" : [
- "Expression"
- ],
- "trackId" : "c_remanei_PRJNA53967_rnaseq_introns",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display.",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/RNASeq introns/{refseq}/trackData.jsonz"
- }
- },
- "name" : "RNASeq introns"
- },
- {
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
- "name" : "RNASeq Splice Junctions (common)",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/RNASeq Splice Junctions (common)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
},
- "type" : "NCListAdapter"
+ "search" : "..G[AG][AG]T"
},
"displays" : [
{
- "displayId" : "rnaseq_splice_junctions_(common)-c_remanei_PRJNA53967-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'score')+' reads'",
+ "displayId" : "NNGRRT_sequence_search_c_remanei_PRJNA53967-LinearBasicDisplay",
"renderer" : {
+ "height" : 4,
+ "showDescriptions" : false,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "jexl:get(feature,'score')>1000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/1000))))+'00'+hex(round(255-(140*(get(feature,'score')/1000)))):'#00'+hex(round(255-(140*(get(feature,'score')/1000))))+hex(round(255-(140*(get(feature,'score')/1000))))",
- "showDescriptions" : false
+ "color1" : "DarkViolet",
+ "type" : "SvgFeatureRenderer"
}
}
- ],
- "trackId" : "c_remanei_PRJNA53967_rnaseq_splice_junctions_(common)",
- "assemblyNames" : [
- "c_remanei_PRJNA53967"
- ],
- "category" : [
- "Expression"
]
},
{
- "trackId" : "c_remanei_PRJNA53967_rnaseq_splice_junctions_(rare)",
- "category" : [
- "Expression"
- ],
"assemblyNames" : [
"c_remanei_PRJNA53967"
],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
+ "trackId" : "c_remanei_PRJNA53967_NGG_sequence_search",
+ "name" : "SpCas9 NGG PAM sites",
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
"displays" : [
{
- "displayId" : "rnaseq_splice_junctions_(rare)-c_remanei_PRJNA53967-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "jexl:get(feature,'score')>1000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/1000))))+'00'+hex(round(255-(140*(get(feature,'score')/1000)))):'#00'+hex(round(255-(140*(get(feature,'score')/1000))))+hex(round(255-(140*(get(feature,'score')/1000))))",
- "maxHeight" : 5000,
+ "color1" : "RebeccaPurple",
+ "height" : 4,
"showDescriptions" : false,
- "height" : "jexl:4"
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'score')+' reads'",
- "type" : "LinearBasicDisplay"
+ "displayId" : "NGG_sequence_search_c_remanei_PRJNA53967-LinearBasicDisplay"
}
],
- "name" : "RNASeq Splice Junctions (rare)",
"adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "type" : "SequenceSearchAdapter",
+ "sequenceAdapter" : {
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA53967.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
+ },
+ "fastaLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA53967.WS284.genomic.fa.gz"
+ },
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA53967.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ }
},
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads."
+ "search" : ".GG"
+ }
},
{
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA577507/tracks/Curated_Genes/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "Curated Genes",
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
"category" : [
"Genes",
"Curated Genes"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_remanei_PRJNA577507"
],
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
+ "name" : "Curated Genes",
"trackId" : "c_remanei_PRJNA577507_curated_genes",
"formatDetails" : {
"feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
@@ -50930,21 +50017,42 @@
"displays" : [
{
"displayId" : "curated_genes-c_remanei_PRJNA577507-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
},
- "maxHeight" : 5000,
"color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
+ "type" : "SvgFeatureRenderer",
+ "maxHeight" : 5000,
"color3" : "#965567"
- }
+ },
+ "type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA577507/tracks/Curated_Genes/{refseq}/trackData.jsonz"
+ }
+ }
},
{
- "name" : "Curated Genes (protein coding)",
+ "displays" : [
+ {
+ "renderer" : {
+ "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
+ "color3" : "#965567",
+ "maxHeight" : 5000,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "curated_genes_(protein_coding)-c_remanei_PRJNA577507-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
"adapter" : {
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA577507/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz",
@@ -50952,225 +50060,188 @@
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
- "trackId" : "c_remanei_PRJNA577507_curated_genes_protein_coding",
"assemblyNames" : [
"c_remanei_PRJNA577507"
],
+ "type" : "FeatureTrack",
"category" : [
"Genes",
"Curated Genes"
],
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
- "maxHeight" : 5000,
- "type" : "SvgFeatureRenderer",
- "color3" : "#965567"
- },
- "displayId" : "curated_genes_(protein_coding)-c_remanei_PRJNA577507-LinearBasicDisplay"
- }
- ],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- }
+ "trackId" : "c_remanei_PRJNA577507_curated_genes_protein_coding",
+ "name" : "Curated Genes (protein coding)",
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track."
},
{
- "trackId" : "c_remanei_PRJNA577507_low_complextity_region_(dust)",
"assemblyNames" : [
"c_remanei_PRJNA577507"
],
+ "type" : "FeatureTrack",
"category" : [
"Genome Structure",
"Repeats"
],
+ "trackId" : "c_remanei_PRJNA577507_low_complextity_region_(dust)",
+ "name" : "Low complextity region (Dust)",
+ "description" : "Low-complexity regions identified by Dust.",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "low_complextity_region_(dust)-c_remanei_PRJNA577507-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
"showDescriptions" : false,
+ "height" : 4,
+ "showLabels" : false,
"color1" : "bisque",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "type" : "LinearBasicDisplay"
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "name" : "Low complextity region (Dust)",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA577507/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz"
- }
- },
- "description" : "Low-complexity regions identified by Dust."
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA577507/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "TTCN_sequence_search_c_remanei_PRJNA577507-LinearBasicDisplay",
"renderer" : {
"color1" : "SlateBlue",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
"height" : 4,
- "showDescriptions" : false
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "TTCN_sequence_search_c_remanei_PRJNA577507-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_remanei_PRJNA577507"
- ],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "trackId" : "c_remanei_PRJNA577507_TTCN_sequence_search",
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
- "type" : "FeatureTrack",
"adapter" : {
- "search" : "TTC.",
"sequenceAdapter" : {
"faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA577507.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA577507.WS284.genomic.fa.gz.fai"
},
"fastaLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA577507.WS284.genomic.fa.gz"
},
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA577507.WS284.genomic.fa.gz.gzi"
- },
- "type" : "BgzipFastaAdapter"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA577507.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ }
},
- "type" : "SequenceSearchAdapter"
+ "type" : "SequenceSearchAdapter",
+ "search" : "TTC."
},
- "name" : "Cas12e TTCN PAM sites"
- },
- {
- "trackId" : "c_remanei_PRJNA577507_TTN_sequence_search",
"assemblyNames" : [
"c_remanei_PRJNA577507"
],
+ "type" : "FeatureTrack",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "displays" : [
- {
- "displayId" : "TTN_sequence_search_c_remanei_PRJNA577507-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "Indigo",
- "showDescriptions" : false,
- "height" : 4
- }
- }
- ],
- "name" : "Cas12a TTN PAM sites",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "SequenceSearchAdapter",
- "sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA577507.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
- },
- "fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA577507.WS284.genomic.fa.gz"
- },
- "faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA577507.WS284.genomic.fa.gz.fai"
- }
- },
- "search" : "TT."
- },
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time."
+ "trackId" : "c_remanei_PRJNA577507_TTCN_sequence_search",
+ "name" : "Cas12e TTCN PAM sites",
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time."
},
{
"adapter" : {
+ "search" : "TT.",
"type" : "SequenceSearchAdapter",
- "search" : "..G[AG][AG]T",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
"fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA577507.WS284.genomic.fa.gz"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA577507.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
},
"faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA577507.WS284.genomic.fa.gz.fai"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA577507.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
},
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA577507.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA577507.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
}
}
},
- "type" : "FeatureTrack",
- "name" : "SaCas9 NNGRRT PAM sites",
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
- "assemblyNames" : [
- "c_remanei_PRJNA577507"
- ],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "trackId" : "c_remanei_PRJNA577507_NNGRRT_sequence_search",
"displays" : [
{
- "displayId" : "NNGRRT_sequence_search_c_remanei_PRJNA577507-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "TTN_sequence_search_c_remanei_PRJNA577507-LinearBasicDisplay",
"renderer" : {
+ "color1" : "Indigo",
+ "showLabels" : false,
"showDescriptions" : false,
"height" : 4,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "DarkViolet"
+ "type" : "SvgFeatureRenderer"
}
}
- ]
- },
- {
+ ],
+ "name" : "Cas12a TTN PAM sites",
+ "trackId" : "c_remanei_PRJNA577507_TTN_sequence_search",
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_remanei_PRJNA577507"
],
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ]
+ },
+ {
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
+ "trackId" : "c_remanei_PRJNA577507_NNGRRT_sequence_search",
+ "name" : "SaCas9 NNGRRT PAM sites",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "trackId" : "c_remanei_PRJNA577507_NGG_sequence_search",
+ "assemblyNames" : [
+ "c_remanei_PRJNA577507"
+ ],
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "type" : "SequenceSearchAdapter",
+ "sequenceAdapter" : {
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA577507.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
+ },
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA577507.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
+ },
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA577507.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BgzipFastaAdapter"
+ },
+ "search" : "..G[AG][AG]T"
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
+ "showLabels" : false,
"height" : 4,
"showDescriptions" : false,
- "color1" : "RebeccaPurple",
- "showLabels" : false,
+ "color1" : "DarkViolet",
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "NGG_sequence_search_c_remanei_PRJNA577507-LinearBasicDisplay"
+ "displayId" : "NNGRRT_sequence_search_c_remanei_PRJNA577507-LinearBasicDisplay"
}
- ],
- "type" : "FeatureTrack",
+ ]
+ },
+ {
"adapter" : {
- "type" : "SequenceSearchAdapter",
"search" : ".GG",
"sequenceAdapter" : {
"fastaLocation" : {
@@ -51182,14 +50253,37 @@
"locationType" : "UriLocation"
},
"gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA577507.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA577507.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
},
"type" : "BgzipFastaAdapter"
- }
+ },
+ "type" : "SequenceSearchAdapter"
},
+ "displays" : [
+ {
+ "displayId" : "NGG_sequence_search_c_remanei_PRJNA577507-LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "RebeccaPurple",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ],
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
+ "trackId" : "c_remanei_PRJNA577507_NGG_sequence_search",
"name" : "SpCas9 NGG PAM sites",
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time."
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
+ "assemblyNames" : [
+ "c_remanei_PRJNA577507"
+ ],
+ "type" : "FeatureTrack"
},
{
"adapter" : {
@@ -51199,164 +50293,164 @@
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "name" : "Curated Genes (protein coding)",
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "assemblyNames" : [
- "c_sinica_PRJNA194557"
- ],
- "trackId" : "c_sinica_PRJNA194557_curated_genes_protein_coding",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
"displays" : [
{
"displayId" : "curated_genes_(protein_coding)-c_sinica_PRJNA194557-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
"maxHeight" : 5000,
- "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
"type" : "SvgFeatureRenderer",
- "color3" : "#965567"
- }
+ "color3" : "#965567",
+ "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'"
+ },
+ "type" : "LinearBasicDisplay"
}
+ ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
+ "trackId" : "c_sinica_PRJNA194557_curated_genes_protein_coding",
+ "name" : "Curated Genes (protein coding)",
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
+ "assemblyNames" : [
+ "c_sinica_PRJNA194557"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Genes",
+ "Curated Genes"
]
},
{
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sinica_PRJNA194557/tracks/Curated_Genes/{refseq}/trackData.jsonz"
- }
- },
- "name" : "Curated Genes",
"formatDetails" : {
"feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
},
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "color3" : "#965567",
- "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
- "maxHeight" : 5000,
- "type" : "SvgFeatureRenderer",
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
- }
+ },
+ "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
+ "color3" : "#965567",
+ "maxHeight" : 5000,
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "curated_genes-c_sinica_PRJNA194557-LinearBasicDisplay"
+ "displayId" : "curated_genes-c_sinica_PRJNA194557-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_sinica_PRJNA194557"
- ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sinica_PRJNA194557/tracks/Curated_Genes/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"category" : [
"Genes",
"Curated Genes"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_sinica_PRJNA194557"
+ ],
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
+ "name" : "Curated Genes",
"trackId" : "c_sinica_PRJNA194557_curated_genes"
},
{
"description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "C. brenneri proteins",
+ "trackId" : "c_sinica_PRJNA194557_C_brenneri_proteins",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_sinica_PRJNA194557"
+ ],
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sinica_PRJNA194557/tracks/C. brenneri proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sinica_PRJNA194557/tracks/C. brenneri proteins/{refseq}/trackData.jsonz"
+ }
},
- "type" : "FeatureTrack",
- "name" : "C. brenneri proteins",
"displays" : [
{
- "type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "C_brenneri_proteins-c_sinica_PRJNA194557-LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "orange",
- "height" : 4
+ "height" : 4,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "C_brenneri_proteins-c_sinica_PRJNA194557-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')",
+ "type" : "LinearBasicDisplay"
}
- ],
+ ]
+ },
+ {
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_sinica_PRJNA194557"
],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "trackId" : "c_sinica_PRJNA194557_C_brenneri_proteins"
- },
- {
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
- "type" : "SvgFeatureRenderer",
+ "color1" : "orange",
"showLabels" : false,
- "color1" : "orange"
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "C_elegans_proteins-c_sinica_PRJNA194557-LinearBasicDisplay"
}
],
- "trackId" : "c_sinica_PRJNA194557_C_elegans_proteins",
- "assemblyNames" : [
- "c_sinica_PRJNA194557"
- ],
"category" : [
"Sequence Similarity",
"Proteins"
],
- "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "C. elegans proteins",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sinica_PRJNA194557/tracks/C. elegans proteins/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sinica_PRJNA194557/tracks/C. elegans proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
- }
+ },
+ "name" : "C. elegans proteins",
+ "trackId" : "c_sinica_PRJNA194557_C_elegans_proteins",
+ "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
},
{
- "type" : "FeatureTrack",
+ "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sinica_PRJNA194557/tracks/C. briggsae proteins/{refseq}/trackData.jsonz"
- }
+ },
+ "type" : "NCListAdapter"
},
"name" : "C. briggsae proteins",
- "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "assemblyNames" : [
- "c_sinica_PRJNA194557"
- ],
+ "trackId" : "c_sinica_PRJNA194557_C_briggsae_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "trackId" : "c_sinica_PRJNA194557_C_briggsae_proteins",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_sinica_PRJNA194557"
+ ],
"displays" : [
{
"displayId" : "C_briggsae_proteins-c_sinica_PRJNA194557-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
+ "height" : 4,
"showLabels" : false,
"color1" : "orange",
- "height" : 4
+ "type" : "SvgFeatureRenderer"
},
"mouseover" : "jexl:get(feature,'clone')",
"type" : "LinearBasicDisplay"
@@ -51364,107 +50458,116 @@
]
},
{
- "description" : "Low-complexity regions identified by Dust.",
- "name" : "Low complextity region (Dust)",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sinica_PRJNA194557/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sinica_PRJNA194557/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
}
},
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
"showDescriptions" : false,
"height" : 4,
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "bisque"
+ "color1" : "bisque",
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "low_complextity_region_(dust)-c_sinica_PRJNA194557-LinearBasicDisplay"
+ "displayId" : "low_complextity_region_(dust)-c_sinica_PRJNA194557-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
+ "description" : "Low-complexity regions identified by Dust.",
+ "name" : "Low complextity region (Dust)",
"trackId" : "c_sinica_PRJNA194557_low_complextity_region_(dust)",
- "assemblyNames" : [
- "c_sinica_PRJNA194557"
- ],
"category" : [
"Genome Structure",
"Repeats"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_sinica_PRJNA194557"
]
},
{
+ "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_sinica_PRJNA194557_S_cerevisiae_proteins",
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sinica_PRJNA194557/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
+ "name" : "S. cerevisiae proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "assemblyNames" : [
- "c_sinica_PRJNA194557"
- ],
- "trackId" : "c_sinica_PRJNA194557_S_cerevisiae_proteins",
"displays" : [
{
- "displayId" : "S_cerevisiae_proteins-c_sinica_PRJNA194557-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
"color1" : "orange",
+ "showLabels" : false,
"height" : 4
- }
+ },
+ "displayId" : "S_cerevisiae_proteins-c_sinica_PRJNA194557-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sinica_PRJNA194557/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz"
- }
- },
- "name" : "S. cerevisiae proteins",
- "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ "assemblyNames" : [
+ "c_sinica_PRJNA194557"
+ ],
+ "type" : "FeatureTrack"
},
{
- "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sinica_PRJNA194557/tracks/H. sapiens proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "H. sapiens proteins",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "H_sapiens_proteins-c_sinica_PRJNA194557-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "orange",
- "height" : 4
+ "showLabels" : false,
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')",
- "displayId" : "H_sapiens_proteins-c_sinica_PRJNA194557-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_sinica_PRJNA194557"
- ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sinica_PRJNA194557/tracks/H. sapiens proteins/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_sinica_PRJNA194557"
+ ],
+ "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "H. sapiens proteins",
"trackId" : "c_sinica_PRJNA194557_H_sapiens_proteins"
},
{
"description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_sinica_PRJNA194557_other_uniprot_proteins",
"name" : "Other UniProt proteins",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "assemblyNames" : [
+ "c_sinica_PRJNA194557"
+ ],
+ "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sinica_PRJNA194557/tracks/Other UniProt proteins/{refseq}/trackData.jsonz",
@@ -51472,65 +50575,66 @@
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "other_uniprot_proteins-c_sinica_PRJNA194557-LinearBasicDisplay",
"renderer" : {
- "color1" : "orange",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
"height" : 4,
- "showDescriptions" : false
+ "showLabels" : false,
+ "color1" : "orange"
},
- "displayId" : "other_uniprot_proteins-c_sinica_PRJNA194557-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
- ],
- "trackId" : "c_sinica_PRJNA194557_other_uniprot_proteins",
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "c_sinica_PRJNA194557"
]
},
{
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sinica_PRJNA194557/tracks/C. japonica proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
+ "displayId" : "C_japonica_proteins-c_sinica_PRJNA194557-LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
"height" : 4,
- "color1" : "orange",
"showLabels" : false,
+ "color1" : "orange",
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "C_japonica_proteins-c_sinica_PRJNA194557-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_sinica_PRJNA194557"
- ],
+ "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "C. japonica proteins",
+ "trackId" : "c_sinica_PRJNA194557_C_japonica_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "trackId" : "c_sinica_PRJNA194557_C_japonica_proteins",
- "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sinica_PRJNA194557/tracks/C. japonica proteins/{refseq}/trackData.jsonz"
- }
- },
- "name" : "C. japonica proteins"
+ "assemblyNames" : [
+ "c_sinica_PRJNA194557"
+ ]
},
{
- "name" : "Tandem and Inverted Repeats",
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "tandem_and_inverted_repeats-c_sinica_PRJNA194557-LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "bisque",
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
+ }
+ }
+ ],
"adapter" : {
"rootUrlTemplate" : {
"locationType" : "UriLocation",
@@ -51538,85 +50642,63 @@
},
"type" : "NCListAdapter"
},
- "description" : "Exact tandem and inverted repetitive elements.",
- "trackId" : "c_sinica_PRJNA194557_tandem_and_inverted_repeats",
+ "category" : [
+ "Genome Structure",
+ "Repeats"
+ ],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_sinica_PRJNA194557"
],
+ "description" : "Exact tandem and inverted repetitive elements.",
+ "name" : "Tandem and Inverted Repeats",
+ "trackId" : "c_sinica_PRJNA194557_tandem_and_inverted_repeats"
+ },
+ {
+ "description" : "Repetitive regions identified by RepeatMasker.",
+ "name" : "Repeat Region (RepeatMasker)",
+ "trackId" : "c_sinica_PRJNA194557_repeat_region_(repeatmasker)",
"category" : [
"Genome Structure",
"Repeats"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_sinica_PRJNA194557"
+ ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sinica_PRJNA194557/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz"
+ }
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "bisque",
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "showDescriptions" : false
- },
- "displayId" : "tandem_and_inverted_repeats-c_sinica_PRJNA194557-LinearBasicDisplay"
- }
- ]
- },
- {
- "description" : "Repetitive regions identified by RepeatMasker.",
- "name" : "Repeat Region (RepeatMasker)",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sinica_PRJNA194557/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "displays" : [
- {
- "displayId" : "repeat_region_(repeatmasker)-c_sinica_PRJNA194557-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
"height" : 4,
"showDescriptions" : false,
- "color1" : "bisque",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "repeat_region_(repeatmasker)-c_sinica_PRJNA194557-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ],
- "trackId" : "c_sinica_PRJNA194557_repeat_region_(repeatmasker)",
- "category" : [
- "Genome Structure",
- "Repeats"
- ],
- "assemblyNames" : [
- "c_sinica_PRJNA194557"
]
},
{
- "displays" : [
- {
- "displayId" : "P_pacificus_proteins-c_sinica_PRJNA194557-LinearBasicDisplay",
- "renderer" : {
- "height" : 4,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "orange"
- },
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay"
- }
+ "trackId" : "c_sinica_PRJNA194557_P_pacificus_proteins",
+ "name" : "P. pacificus proteins",
+ "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "assemblyNames" : [
+ "c_sinica_PRJNA194557"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "assemblyNames" : [
- "c_sinica_PRJNA194557"
- ],
- "trackId" : "c_sinica_PRJNA194557_P_pacificus_proteins",
- "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
"locationType" : "UriLocation",
@@ -51624,12 +50706,21 @@
},
"type" : "NCListAdapter"
},
- "name" : "P. pacificus proteins"
+ "displays" : [
+ {
+ "displayId" : "P_pacificus_proteins-c_sinica_PRJNA194557-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
+ "renderer" : {
+ "color1" : "orange",
+ "showLabels" : false,
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
- "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "C. remanei proteins",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sinica_PRJNA194557/tracks/C. remanei proteins/{refseq}/trackData.jsonz",
@@ -51643,17 +50734,20 @@
"renderer" : {
"type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "orange",
- "height" : 4
+ "height" : 4,
+ "color1" : "orange"
},
"mouseover" : "jexl:get(feature,'clone')",
"type" : "LinearBasicDisplay"
}
],
"trackId" : "c_sinica_PRJNA194557_C_remanei_proteins",
+ "name" : "C. remanei proteins",
+ "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"assemblyNames" : [
"c_sinica_PRJNA194557"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
@@ -51662,39 +50756,50 @@
{
"displays" : [
{
- "displayId" : "D_melanogaster_proteins-c_sinica_PRJNA194557-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "orange"
+ "height" : 4,
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "D_melanogaster_proteins-c_sinica_PRJNA194557-LinearBasicDisplay"
}
],
- "trackId" : "c_sinica_PRJNA194557_D_melanogaster_proteins",
- "assemblyNames" : [
- "c_sinica_PRJNA194557"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "D. melanogaster proteins",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sinica_PRJNA194557/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
- }
+ },
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "assemblyNames" : [
+ "c_sinica_PRJNA194557"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_sinica_PRJNA194557_D_melanogaster_proteins",
+ "name" : "D. melanogaster proteins"
},
{
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
- "name" : "Cas12e TTCN PAM sites",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "TTCN_sequence_search_c_sinica_PRJNA194557-LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "SlateBlue",
+ "showLabels" : false,
+ "height" : 4,
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
+ }
+ }
+ ],
"adapter" : {
"search" : "TTC.",
"sequenceAdapter" : {
@@ -51702,6 +50807,7 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sinica.PRJNA194557.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
},
+ "type" : "BgzipFastaAdapter",
"fastaLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sinica.PRJNA194557.WS284.genomic.fa.gz"
@@ -51709,543 +50815,518 @@
"faiLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sinica.PRJNA194557.WS284.genomic.fa.gz.fai"
- },
- "type" : "BgzipFastaAdapter"
+ }
},
"type" : "SequenceSearchAdapter"
},
- "type" : "FeatureTrack",
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "SlateBlue",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 4,
- "showDescriptions" : false
- },
- "displayId" : "TTCN_sequence_search_c_sinica_PRJNA194557-LinearBasicDisplay"
- }
+ "assemblyNames" : [
+ "c_sinica_PRJNA194557"
],
- "trackId" : "c_sinica_PRJNA194557_TTCN_sequence_search",
+ "type" : "FeatureTrack",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "assemblyNames" : [
- "c_sinica_PRJNA194557"
- ]
+ "trackId" : "c_sinica_PRJNA194557_TTCN_sequence_search",
+ "name" : "Cas12e TTCN PAM sites",
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time."
},
{
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_sinica_PRJNA194557"
+ ],
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
+ "name" : "Cas12a TTN PAM sites",
+ "trackId" : "c_sinica_PRJNA194557_TTN_sequence_search",
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
"displays" : [
{
- "displayId" : "TTN_sequence_search_c_sinica_PRJNA194557-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
+ "showLabels" : false,
"showDescriptions" : false,
"height" : 4,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "Indigo"
+ "color1" : "Indigo",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "TTN_sequence_search_c_sinica_PRJNA194557-LinearBasicDisplay"
}
],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "assemblyNames" : [
- "c_sinica_PRJNA194557"
- ],
- "trackId" : "c_sinica_PRJNA194557_TTN_sequence_search",
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
- "gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sinica.PRJNA194557.WS284.genomic.fa.gz.gzi"
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sinica.PRJNA194557.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
},
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sinica.PRJNA194557.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sinica.PRJNA194557.WS284.genomic.fa.gz.fai",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sinica.PRJNA194557.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "BgzipFastaAdapter"
},
+ "type" : "SequenceSearchAdapter",
"search" : "TT."
- },
- "name" : "Cas12a TTN PAM sites"
+ }
},
{
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
+ "trackId" : "c_sinica_PRJNA194557_NNGRRT_sequence_search",
"name" : "SaCas9 NNGRRT PAM sites",
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
+ "assemblyNames" : [
+ "c_sinica_PRJNA194557"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
"adapter" : {
- "type" : "SequenceSearchAdapter",
"search" : "..G[AG][AG]T",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sinica.PRJNA194557.WS284.genomic.fa.gz.gzi"
- },
"fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sinica.PRJNA194557.WS284.genomic.fa.gz"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sinica.PRJNA194557.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
},
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sinica.PRJNA194557.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sinica.PRJNA194557.WS284.genomic.fa.gz.gzi"
+ },
"type" : "BgzipFastaAdapter"
}
},
- "type" : "FeatureTrack",
"displays" : [
{
"displayId" : "NNGRRT_sequence_search_c_sinica_PRJNA194557-LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 4,
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "DarkViolet"
+ "color1" : "DarkViolet",
+ "height" : 4,
+ "showDescriptions" : false,
+ "showLabels" : false
},
"type" : "LinearBasicDisplay"
}
- ],
- "trackId" : "c_sinica_PRJNA194557_NNGRRT_sequence_search",
- "assemblyNames" : [
- "c_sinica_PRJNA194557"
- ],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
]
},
{
- "trackId" : "c_sinica_PRJNA194557_NGG_sequence_search",
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "assemblyNames" : [
- "c_sinica_PRJNA194557"
- ],
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "RebeccaPurple",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 4,
- "showDescriptions" : false
- },
- "displayId" : "NGG_sequence_search_c_sinica_PRJNA194557-LinearBasicDisplay"
- }
- ],
- "name" : "SpCas9 NGG PAM sites",
"adapter" : {
"sequenceAdapter" : {
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sinica.PRJNA194557.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
},
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sinica.PRJNA194557.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
+ },
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sinica.PRJNA194557.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
- },
- "faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sinica.PRJNA194557.WS284.genomic.fa.gz.fai"
- },
- "type" : "BgzipFastaAdapter"
+ }
},
- "search" : ".GG",
- "type" : "SequenceSearchAdapter"
+ "type" : "SequenceSearchAdapter",
+ "search" : ".GG"
},
+ "displays" : [
+ {
+ "renderer" : {
+ "color1" : "RebeccaPurple",
+ "showDescriptions" : false,
+ "height" : 4,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "NGG_sequence_search_c_sinica_PRJNA194557-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
+ "name" : "SpCas9 NGG PAM sites",
+ "trackId" : "c_sinica_PRJNA194557_NGG_sequence_search",
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
"type" : "FeatureTrack",
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time."
+ "assemblyNames" : [
+ "c_sinica_PRJNA194557"
+ ],
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ]
},
{
- "trackId" : "c_sulstoni_PRJEB12601_curated_genes",
+ "assemblyNames" : [
+ "c_sulstoni_PRJEB12601"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"Genes",
"Curated Genes"
],
- "assemblyNames" : [
- "c_sulstoni_PRJEB12601"
- ],
+ "trackId" : "c_sulstoni_PRJEB12601_curated_genes",
+ "name" : "Curated Genes",
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
+ "formatDetails" : {
+ "feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
+ },
"displays" : [
{
"displayId" : "curated_genes-c_sulstoni_PRJEB12601-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
"color3" : "#965567",
"maxHeight" : 5000,
+ "type" : "SvgFeatureRenderer",
"color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
- },
- "type" : "SvgFeatureRenderer"
- }
+ }
+ },
+ "type" : "LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
- },
- "name" : "Curated Genes",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sulstoni_PRJEB12601/tracks/Curated_Genes/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes."
+ }
+ }
},
{
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_sulstoni_PRJEB12601"
+ ],
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
+ "name" : "Curated Genes (protein coding)",
+ "trackId" : "c_sulstoni_PRJEB12601_curated_genes_protein_coding",
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
"displays" : [
{
- "displayId" : "curated_genes_(protein_coding)-c_sulstoni_PRJEB12601-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
"maxHeight" : 5000,
"type" : "SvgFeatureRenderer",
- "color3" : "#965567"
- }
+ "color3" : "#965567",
+ "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'"
+ },
+ "displayId" : "curated_genes_(protein_coding)-c_sulstoni_PRJEB12601-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_sulstoni_PRJEB12601"
- ],
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "trackId" : "c_sulstoni_PRJEB12601_curated_genes_protein_coding",
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sulstoni_PRJEB12601/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "Curated Genes (protein coding)"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sulstoni_PRJEB12601/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz"
+ }
+ }
},
{
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sulstoni_PRJEB12601/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz"
+ }
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 4,
- "type" : "SvgFeatureRenderer",
+ "color1" : "bisque",
"showLabels" : false,
- "color1" : "bisque"
+ "height" : 4,
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "low_complextity_region_(dust)-c_sulstoni_PRJEB12601-LinearBasicDisplay"
}
],
+ "description" : "Low-complexity regions identified by Dust.",
+ "name" : "Low complextity region (Dust)",
+ "trackId" : "c_sulstoni_PRJEB12601_low_complextity_region_(dust)",
"category" : [
"Genome Structure",
"Repeats"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_sulstoni_PRJEB12601"
- ],
- "trackId" : "c_sulstoni_PRJEB12601_low_complextity_region_(dust)",
- "description" : "Low-complexity regions identified by Dust.",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sulstoni_PRJEB12601/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "Low complextity region (Dust)"
+ ]
},
{
- "trackId" : "c_sulstoni_PRJEB12601_TTCN_sequence_search",
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
"assemblyNames" : [
"c_sulstoni_PRJEB12601"
],
"displays" : [
{
- "displayId" : "TTCN_sequence_search_c_sulstoni_PRJEB12601-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "TTCN_sequence_search_c_sulstoni_PRJEB12601-LinearBasicDisplay",
"renderer" : {
- "color1" : "SlateBlue",
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
+ "showDescriptions" : false,
"height" : 4,
- "showDescriptions" : false
+ "showLabels" : false,
+ "color1" : "SlateBlue"
}
}
],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
+ "trackId" : "c_sulstoni_PRJEB12601_TTCN_sequence_search",
"name" : "Cas12e TTCN PAM sites",
"adapter" : {
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
- "faiLocation" : {
+ "gziLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz.fai"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz.gzi"
},
+ "type" : "BgzipFastaAdapter",
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
+ "faiLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz.fai"
}
},
- "search" : "TTC.",
- "type" : "SequenceSearchAdapter"
+ "search" : "TTC."
},
- "type" : "FeatureTrack",
"description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time."
},
{
- "assemblyNames" : [
- "c_sulstoni_PRJEB12601"
- ],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "trackId" : "c_sulstoni_PRJEB12601_TTN_sequence_search",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "TTN_sequence_search_c_sulstoni_PRJEB12601-LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "Indigo",
"showDescriptions" : false,
- "height" : 4
- },
- "displayId" : "TTN_sequence_search_c_sulstoni_PRJEB12601-LinearBasicDisplay"
+ "height" : 4,
+ "showLabels" : false,
+ "color1" : "Indigo"
+ }
}
],
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz",
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
},
"faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz.fai"
- },
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz.gzi",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
- "type" : "BgzipFastaAdapter"
+ "fastaLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz"
+ }
},
+ "type" : "SequenceSearchAdapter",
"search" : "TT."
},
- "name" : "Cas12a TTN PAM sites",
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time."
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
+ "assemblyNames" : [
+ "c_sulstoni_PRJEB12601"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
+ "trackId" : "c_sulstoni_PRJEB12601_TTN_sequence_search",
+ "name" : "Cas12a TTN PAM sites"
},
{
"adapter" : {
+ "search" : "..G[AG][AG]T",
"type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz.gzi",
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
"faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz.fai"
- },
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz.gzi"
+ },
"type" : "BgzipFastaAdapter"
- },
- "search" : "..G[AG][AG]T"
+ }
},
- "type" : "FeatureTrack",
- "name" : "SaCas9 NNGRRT PAM sites",
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
- "assemblyNames" : [
- "c_sulstoni_PRJEB12601"
- ],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "trackId" : "c_sulstoni_PRJEB12601_NNGRRT_sequence_search",
"displays" : [
{
- "displayId" : "NNGRRT_sequence_search_c_sulstoni_PRJEB12601-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "NNGRRT_sequence_search_c_sulstoni_PRJEB12601-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "showDescriptions" : false,
- "color1" : "DarkViolet",
"type" : "SvgFeatureRenderer",
+ "color1" : "DarkViolet",
+ "showDescriptions" : false,
+ "height" : 4,
"showLabels" : false
}
}
+ ],
+ "name" : "SaCas9 NNGRRT PAM sites",
+ "trackId" : "c_sulstoni_PRJEB12601_NNGRRT_sequence_search",
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_sulstoni_PRJEB12601"
+ ],
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
]
},
{
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
+ "assemblyNames" : [
+ "c_sulstoni_PRJEB12601"
+ ],
+ "type" : "FeatureTrack",
"description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
+ "trackId" : "c_sulstoni_PRJEB12601_NGG_sequence_search",
"name" : "SpCas9 NGG PAM sites",
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "renderer" : {
+ "height" : 4,
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "color1" : "RebeccaPurple",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "NGG_sequence_search_c_sulstoni_PRJEB12601-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
- "type" : "SequenceSearchAdapter",
+ "search" : ".GG",
"sequenceAdapter" : {
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
},
"faiLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz.fai"
},
"fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz"
- },
- "type" : "BgzipFastaAdapter"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
+ }
},
- "search" : ".GG"
+ "type" : "SequenceSearchAdapter"
+ }
+ },
+ {
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tribulationis_PRJEB12608/tracks/Curated_Genes/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
+ "formatDetails" : {
+ "feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
},
"displays" : [
{
- "displayId" : "NGG_sequence_search_c_sulstoni_PRJEB12601-LinearBasicDisplay",
+ "displayId" : "curated_genes-c_tribulationis_PRJEB12608-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "showDescriptions" : false,
- "color1" : "RebeccaPurple",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "maxHeight" : 5000,
+ "type" : "SvgFeatureRenderer",
+ "color3" : "#965567",
+ "labels" : {
+ "name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
+ },
+ "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'"
},
"type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_sulstoni_PRJEB12601_NGG_sequence_search",
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "assemblyNames" : [
- "c_sulstoni_PRJEB12601"
- ]
- },
- {
"trackId" : "c_tribulationis_PRJEB12608_curated_genes",
+ "name" : "Curated Genes",
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
"assemblyNames" : [
"c_tribulationis_PRJEB12608"
],
+ "type" : "FeatureTrack",
"category" : [
"Genes",
"Curated Genes"
- ],
+ ]
+ },
+ {
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
"displays" : [
{
- "displayId" : "curated_genes-c_tribulationis_PRJEB12608-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
"type" : "SvgFeatureRenderer",
- "labels" : {
- "name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
- },
- "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
"maxHeight" : 5000,
"color3" : "#965567"
- }
+ },
+ "displayId" : "curated_genes_(protein_coding)-c_tribulationis_PRJEB12608-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
- },
- "name" : "Curated Genes",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tribulationis_PRJEB12608/tracks/Curated_Genes/{refseq}/trackData.jsonz"
- }
- },
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes."
- },
- {
- "name" : "Curated Genes (protein coding)",
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tribulationis_PRJEB12608/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tribulationis_PRJEB12608/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
- "trackId" : "c_tribulationis_PRJEB12608_curated_genes_protein_coding",
"category" : [
"Genes",
"Curated Genes"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_tribulationis_PRJEB12608"
],
- "displays" : [
- {
- "displayId" : "curated_genes_(protein_coding)-c_tribulationis_PRJEB12608-LinearBasicDisplay",
- "renderer" : {
- "color3" : "#965567",
- "type" : "SvgFeatureRenderer",
- "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
- "maxHeight" : 5000
- },
- "type" : "LinearBasicDisplay"
- }
- ],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- }
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
+ "name" : "Curated Genes (protein coding)",
+ "trackId" : "c_tribulationis_PRJEB12608_curated_genes_protein_coding"
},
{
- "displays" : [
- {
- "displayId" : "low_complextity_region_(dust)-c_tribulationis_PRJEB12608-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "bisque",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "height" : 4,
- "showDescriptions" : false
- }
- }
- ],
- "trackId" : "c_tribulationis_PRJEB12608_low_complextity_region_(dust)",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_tribulationis_PRJEB12608"
],
@@ -52253,132 +51334,100 @@
"Genome Structure",
"Repeats"
],
- "description" : "Low-complexity regions identified by Dust.",
"name" : "Low complextity region (Dust)",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tribulationis_PRJEB12608/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack"
- },
- {
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "assemblyNames" : [
- "c_tribulationis_PRJEB12608"
- ],
- "trackId" : "c_tribulationis_PRJEB12608_TTCN_sequence_search",
+ "trackId" : "c_tribulationis_PRJEB12608_low_complextity_region_(dust)",
+ "description" : "Low-complexity regions identified by Dust.",
"displays" : [
{
- "displayId" : "TTCN_sequence_search_c_tribulationis_PRJEB12608-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
"height" : 4,
- "type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
"showLabels" : false,
- "color1" : "SlateBlue"
+ "color1" : "bisque",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "low_complextity_region_(dust)-c_tribulationis_PRJEB12608-LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "SequenceSearchAdapter",
- "search" : "TTC.",
- "sequenceAdapter" : {
- "faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tribulationis.PRJEB12608.WS284.genomic.fa.gz.fai"
- },
- "fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tribulationis.PRJEB12608.WS284.genomic.fa.gz"
- },
- "gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tribulationis.PRJEB12608.WS284.genomic.fa.gz.gzi"
- },
- "type" : "BgzipFastaAdapter"
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tribulationis_PRJEB12608/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz"
}
- },
- "name" : "Cas12e TTCN PAM sites",
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time."
+ }
},
{
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
- "name" : "Cas12a TTN PAM sites",
+ "trackId" : "c_tribulationis_PRJEB12608_TTCN_sequence_search",
+ "name" : "Cas12e TTCN PAM sites",
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
+ "assemblyNames" : [
+ "c_tribulationis_PRJEB12608"
+ ],
"type" : "FeatureTrack",
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
"adapter" : {
- "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
"type" : "BgzipFastaAdapter",
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tribulationis.PRJEB12608.WS284.genomic.fa.gz",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tribulationis.PRJEB12608.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
},
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tribulationis.PRJEB12608.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tribulationis.PRJEB12608.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
+ "fastaLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tribulationis.PRJEB12608.WS284.genomic.fa.gz"
}
},
- "search" : "TT."
+ "type" : "SequenceSearchAdapter",
+ "search" : "TTC."
},
"displays" : [
{
- "displayId" : "TTN_sequence_search_c_tribulationis_PRJEB12608-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
+ "displayId" : "TTCN_sequence_search_c_tribulationis_PRJEB12608-LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "Indigo",
+ "showLabels" : false,
+ "height" : 4,
"showDescriptions" : false,
- "height" : 4
- },
- "type" : "LinearBasicDisplay"
+ "color1" : "SlateBlue"
+ }
}
+ ]
+ },
+ {
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_tribulationis_PRJEB12608"
],
- "trackId" : "c_tribulationis_PRJEB12608_TTN_sequence_search",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "assemblyNames" : [
- "c_tribulationis_PRJEB12608"
- ]
- },
- {
+ "name" : "Cas12a TTN PAM sites",
+ "trackId" : "c_tribulationis_PRJEB12608_TTN_sequence_search",
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
"displays" : [
{
+ "displayId" : "TTN_sequence_search_c_tribulationis_PRJEB12608-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
+ "color1" : "Indigo",
"showLabels" : false,
- "color1" : "DarkViolet",
+ "height" : 4,
"showDescriptions" : false,
- "height" : 4
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "NNGRRT_sequence_search_c_tribulationis_PRJEB12608-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_tribulationis_PRJEB12608_NNGRRT_sequence_search",
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "assemblyNames" : [
- "c_tribulationis_PRJEB12608"
- ],
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
- "name" : "SaCas9 NNGRRT PAM sites",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
@@ -52386,6 +51435,7 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tribulationis.PRJEB12608.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
},
+ "type" : "BgzipFastaAdapter",
"fastaLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tribulationis.PRJEB12608.WS284.genomic.fa.gz"
@@ -52393,43 +51443,60 @@
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tribulationis.PRJEB12608.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
- },
- "type" : "BgzipFastaAdapter"
+ }
},
- "search" : "..G[AG][AG]T"
+ "search" : "TT."
}
},
{
- "trackId" : "c_tribulationis_PRJEB12608_NGG_sequence_search",
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "assemblyNames" : [
- "c_tribulationis_PRJEB12608"
- ],
+ "adapter" : {
+ "search" : "..G[AG][AG]T",
+ "type" : "SequenceSearchAdapter",
+ "sequenceAdapter" : {
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tribulationis.PRJEB12608.WS284.genomic.fa.gz.gzi"
+ },
+ "type" : "BgzipFastaAdapter",
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tribulationis.PRJEB12608.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
+ },
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tribulationis.PRJEB12608.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
+ }
+ }
+ },
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"showDescriptions" : false,
"height" : 4,
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "RebeccaPurple"
+ "color1" : "DarkViolet"
},
- "displayId" : "NGG_sequence_search_c_tribulationis_PRJEB12608-LinearBasicDisplay"
+ "displayId" : "NNGRRT_sequence_search_c_tribulationis_PRJEB12608-LinearBasicDisplay"
}
],
- "name" : "SpCas9 NGG PAM sites",
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
+ "name" : "SaCas9 NNGRRT PAM sites",
+ "trackId" : "c_tribulationis_PRJEB12608_NNGRRT_sequence_search",
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_tribulationis_PRJEB12608"
+ ]
+ },
+ {
"adapter" : {
"type" : "SequenceSearchAdapter",
- "search" : ".GG",
"sequenceAdapter" : {
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tribulationis.PRJEB12608.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
- },
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tribulationis.PRJEB12608.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
@@ -52438,100 +51505,136 @@
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tribulationis.PRJEB12608.WS284.genomic.fa.gz"
},
- "type" : "BgzipFastaAdapter"
- }
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tribulationis.PRJEB12608.WS284.genomic.fa.gz.gzi"
+ }
+ },
+ "search" : ".GG"
},
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 4,
+ "color1" : "RebeccaPurple"
+ },
+ "displayId" : "NGG_sequence_search_c_tribulationis_PRJEB12608-LinearBasicDisplay"
+ }
+ ],
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
+ "name" : "SpCas9 NGG PAM sites",
+ "trackId" : "c_tribulationis_PRJEB12608_NGG_sequence_search",
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
"type" : "FeatureTrack",
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time."
+ "assemblyNames" : [
+ "c_tribulationis_PRJEB12608"
+ ]
},
{
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
+ "name" : "Curated Genes",
"trackId" : "c_tropicalis_PRJNA53597_curated_genes",
- "assemblyNames" : [
- "c_tropicalis_PRJNA53597"
- ],
"category" : [
"Genes",
"Curated Genes"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_tropicalis_PRJNA53597"
+ ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/tracks/Curated_Genes/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
+ "formatDetails" : {
+ "feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "curated_genes-c_tropicalis_PRJNA53597-LinearBasicDisplay",
"renderer" : {
- "color3" : "#965567",
- "maxHeight" : 5000,
"color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
},
+ "color3" : "#965567",
+ "maxHeight" : 5000,
"type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay"
+ }
}
- ],
- "formatDetails" : {
- "feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
- },
- "name" : "Curated Genes",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/tracks/Curated_Genes/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes."
+ ]
},
{
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "curated_genes_(protein_coding)-c_tropicalis_PRJNA53597-LinearBasicDisplay",
"renderer" : {
- "color3" : "#965567",
- "type" : "SvgFeatureRenderer",
+ "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
"maxHeight" : 5000,
- "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'"
- },
- "displayId" : "curated_genes_(protein_coding)-c_tropicalis_PRJNA53597-LinearBasicDisplay"
+ "type" : "SvgFeatureRenderer",
+ "color3" : "#965567"
+ }
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
- "trackId" : "c_tropicalis_PRJNA53597_curated_genes_protein_coding",
- "assemblyNames" : [
- "c_tropicalis_PRJNA53597"
- ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"category" : [
"Genes",
"Curated Genes"
],
+ "assemblyNames" : [
+ "c_tropicalis_PRJNA53597"
+ ],
+ "type" : "FeatureTrack",
"description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
- "name" : "Curated Genes (protein coding)",
+ "trackId" : "c_tropicalis_PRJNA53597_curated_genes_protein_coding",
+ "name" : "Curated Genes (protein coding)"
+ },
+ {
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
},
- "type" : "FeatureTrack"
- },
- {
"displays" : [
{
- "displayId" : "D_melanogaster_proteins-c_tropicalis_PRJNA53597-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
+ "height" : 4,
"color1" : "orange",
- "height" : 4
+ "type" : "SvgFeatureRenderer"
},
"mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay"
+ "displayId" : "D_melanogaster_proteins-c_tropicalis_PRJNA53597-LinearBasicDisplay"
}
],
+ "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"trackId" : "c_tropicalis_PRJNA53597_D_melanogaster_proteins",
+ "name" : "D. melanogaster proteins",
"category" : [
"Sequence Similarity",
"Proteins"
@@ -52539,86 +51642,88 @@
"assemblyNames" : [
"c_tropicalis_PRJNA53597"
],
- "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "D. melanogaster proteins",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- }
+ "type" : "FeatureTrack"
},
{
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "assemblyNames" : [
+ "c_tropicalis_PRJNA53597"
+ ],
+ "type" : "FeatureTrack",
"description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_tropicalis_PRJNA53597_H_sapiens_proteins",
"name" : "H. sapiens proteins",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/tracks/H. sapiens proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
"displays" : [
{
- "displayId" : "H_sapiens_proteins-c_tropicalis_PRJNA53597-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "color1" : "orange",
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "height" : 4
+ "height" : 4,
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "H_sapiens_proteins-c_tropicalis_PRJNA53597-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_tropicalis_PRJNA53597_H_sapiens_proteins",
- "assemblyNames" : [
- "c_tropicalis_PRJNA53597"
- ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/tracks/H. sapiens proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ }
+ },
+ {
"category" : [
"Sequence Similarity",
"Proteins"
- ]
- },
- {
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_tropicalis_PRJNA53597"
+ ],
+ "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "C. elegans proteins",
+ "trackId" : "c_tropicalis_PRJNA53597_C_elegans_proteins",
"displays" : [
{
"displayId" : "C_elegans_proteins-c_tropicalis_PRJNA53597-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "color1" : "orange",
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "height" : 4
+ "height" : 4,
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')"
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "c_tropicalis_PRJNA53597_C_elegans_proteins",
- "assemblyNames" : [
- "c_tropicalis_PRJNA53597"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "C. elegans proteins",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/tracks/C. elegans proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/tracks/C. elegans proteins/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
}
},
{
- "name" : "P. pacificus proteins",
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "height" : 4,
+ "showLabels" : false,
+ "color1" : "orange"
+ },
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "P_pacificus_proteins-c_tropicalis_PRJNA53597-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/tracks/P. pacificus proteins/{refseq}/trackData.jsonz",
@@ -52626,8 +51731,6 @@
},
"type" : "NCListAdapter"
},
- "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "trackId" : "c_tropicalis_PRJNA53597_P_pacificus_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
@@ -52635,35 +51738,15 @@
"assemblyNames" : [
"c_tropicalis_PRJNA53597"
],
- "displays" : [
- {
- "mouseover" : "jexl:get(feature,'clone')",
- "renderer" : {
- "color1" : "orange",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 4
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "P_pacificus_proteins-c_tropicalis_PRJNA53597-LinearBasicDisplay"
- }
- ]
+ "type" : "FeatureTrack",
+ "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_tropicalis_PRJNA53597_P_pacificus_proteins",
+ "name" : "P. pacificus proteins"
},
{
- "displays" : [
- {
- "displayId" : "low_complextity_region_(dust)-c_tropicalis_PRJNA53597-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "bisque",
- "showDescriptions" : false,
- "height" : 4
- }
- }
- ],
+ "description" : "Low-complexity regions identified by Dust.",
"trackId" : "c_tropicalis_PRJNA53597_low_complextity_region_(dust)",
+ "name" : "Low complextity region (Dust)",
"category" : [
"Genome Structure",
"Repeats"
@@ -52671,16 +51754,27 @@
"assemblyNames" : [
"c_tropicalis_PRJNA53597"
],
- "description" : "Low-complexity regions identified by Dust.",
- "name" : "Low complextity region (Dust)",
+ "type" : "FeatureTrack",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "NCListAdapter"
},
- "type" : "FeatureTrack"
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "height" : 4,
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "color1" : "bisque"
+ },
+ "displayId" : "low_complextity_region_(dust)-c_tropicalis_PRJNA53597-LinearBasicDisplay"
+ }
+ ]
},
{
"category" : [
@@ -52690,77 +51784,65 @@
"assemblyNames" : [
"c_tropicalis_PRJNA53597"
],
+ "type" : "FeatureTrack",
+ "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"trackId" : "c_tropicalis_PRJNA53597_C_briggsae_proteins",
+ "name" : "C. briggsae proteins",
"displays" : [
{
"type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
"color1" : "orange",
+ "height" : 4,
"showLabels" : false,
"type" : "SvgFeatureRenderer"
},
+ "mouseover" : "jexl:get(feature,'clone')",
"displayId" : "C_briggsae_proteins-c_tropicalis_PRJNA53597-LinearBasicDisplay"
}
],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/tracks/C. briggsae proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/tracks/C. briggsae proteins/{refseq}/trackData.jsonz"
}
- },
- "type" : "FeatureTrack",
- "name" : "C. briggsae proteins",
- "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ }
},
{
- "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "C. japonica proteins",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/tracks/C. japonica proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
"color1" : "orange",
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "height" : 4
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "C_japonica_proteins-c_tropicalis_PRJNA53597-LinearBasicDisplay"
}
],
- "trackId" : "c_tropicalis_PRJNA53597_C_japonica_proteins",
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/tracks/C. japonica proteins/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
+ "assemblyNames" : [
+ "c_tropicalis_PRJNA53597"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "assemblyNames" : [
- "c_tropicalis_PRJNA53597"
- ]
+ "trackId" : "c_tropicalis_PRJNA53597_C_japonica_proteins",
+ "name" : "C. japonica proteins",
+ "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
},
{
- "displays" : [
- {
- "displayId" : "tandem_and_inverted_repeats-c_tropicalis_PRJNA53597-LinearBasicDisplay",
- "renderer" : {
- "showDescriptions" : false,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "bisque"
- },
- "type" : "LinearBasicDisplay"
- }
- ],
"category" : [
"Genome Structure",
"Repeats"
@@ -52768,50 +51850,62 @@
"assemblyNames" : [
"c_tropicalis_PRJNA53597"
],
- "trackId" : "c_tropicalis_PRJNA53597_tandem_and_inverted_repeats",
+ "type" : "FeatureTrack",
"description" : "Exact tandem and inverted repetitive elements.",
+ "trackId" : "c_tropicalis_PRJNA53597_tandem_and_inverted_repeats",
+ "name" : "Tandem and Inverted Repeats",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "tandem_and_inverted_repeats-c_tropicalis_PRJNA53597-LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "bisque",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
+ }
+ }
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/tracks/Tandem and Inverted Repeats/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
}
- },
- "type" : "FeatureTrack",
- "name" : "Tandem and Inverted Repeats"
+ }
},
{
- "displays" : [
- {
- "displayId" : "S_cerevisiae_proteins-c_tropicalis_PRJNA53597-LinearBasicDisplay",
- "renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "orange",
- "height" : 4
- },
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay"
- }
+ "name" : "S. cerevisiae proteins",
+ "trackId" : "c_tropicalis_PRJNA53597_S_cerevisiae_proteins",
+ "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_tropicalis_PRJNA53597"
],
"category" : [
"Sequence Similarity",
"Proteins"
],
- "assemblyNames" : [
- "c_tropicalis_PRJNA53597"
- ],
- "trackId" : "c_tropicalis_PRJNA53597_S_cerevisiae_proteins",
- "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
},
- "name" : "S. cerevisiae proteins"
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "S_cerevisiae_proteins-c_tropicalis_PRJNA53597-LinearBasicDisplay",
+ "renderer" : {
+ "height" : 4,
+ "showLabels" : false,
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
+ },
+ "mouseover" : "jexl:get(feature,'clone')"
+ }
+ ]
},
{
"adapter" : {
@@ -52821,111 +51915,88 @@
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "name" : "Other UniProt proteins",
- "description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "c_tropicalis_PRJNA53597"
- ],
- "trackId" : "c_tropicalis_PRJNA53597_other_uniprot_proteins",
"displays" : [
{
- "displayId" : "other_uniprot_proteins-c_tropicalis_PRJNA53597-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "other_uniprot_proteins-c_tropicalis_PRJNA53597-LinearBasicDisplay",
"renderer" : {
+ "showDescriptions" : false,
+ "height" : 4,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "orange",
- "showDescriptions" : false,
- "height" : 4
+ "type" : "SvgFeatureRenderer"
}
}
+ ],
+ "name" : "Other UniProt proteins",
+ "trackId" : "c_tropicalis_PRJNA53597_other_uniprot_proteins",
+ "description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_tropicalis_PRJNA53597"
+ ],
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
]
},
{
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "bisque",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 4,
- "showDescriptions" : false
- },
- "displayId" : "repeat_region_(repeatmasker)-c_tropicalis_PRJNA53597-LinearBasicDisplay"
- }
+ "trackId" : "c_tropicalis_PRJNA53597_repeat_region_(repeatmasker)",
+ "name" : "Repeat Region (RepeatMasker)",
+ "description" : "Repetitive regions identified by RepeatMasker.",
+ "assemblyNames" : [
+ "c_tropicalis_PRJNA53597"
],
+ "type" : "FeatureTrack",
"category" : [
"Genome Structure",
"Repeats"
],
- "assemblyNames" : [
- "c_tropicalis_PRJNA53597"
- ],
- "trackId" : "c_tropicalis_PRJNA53597_repeat_region_(repeatmasker)",
- "description" : "Repetitive regions identified by RepeatMasker.",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "name" : "Repeat Region (RepeatMasker)"
- },
- {
"displays" : [
{
- "displayId" : "C_remanei_proteins-c_tropicalis_PRJNA53597-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "repeat_region_(repeatmasker)-c_tropicalis_PRJNA53597-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
+ "color1" : "bisque",
"showLabels" : false,
- "color1" : "orange",
- "height" : 4
- }
+ "height" : 4,
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
}
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "c_tropicalis_PRJNA53597"
- ],
- "trackId" : "c_tropicalis_PRJNA53597_C_remanei_proteins",
- "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "type" : "FeatureTrack",
+ ]
+ },
+ {
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/tracks/C. remanei proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ }
},
- "name" : "C. remanei proteins"
- },
- {
"displays" : [
{
- "displayId" : "C_brenneri_proteins-c_tropicalis_PRJNA53597-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 4,
"color1" : "orange",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "showLabels" : false,
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')"
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "C_remanei_proteins-c_tropicalis_PRJNA53597-LinearBasicDisplay"
}
],
+ "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "c_tropicalis_PRJNA53597_C_remanei_proteins",
+ "name" : "C. remanei proteins",
"category" : [
"Sequence Similarity",
"Proteins"
@@ -52933,20 +52004,43 @@
"assemblyNames" : [
"c_tropicalis_PRJNA53597"
],
- "trackId" : "c_tropicalis_PRJNA53597_C_brenneri_proteins",
- "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack"
+ },
+ {
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/tracks/C. brenneri proteins/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/tracks/C. brenneri proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
}
},
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showLabels" : false,
+ "height" : 4,
+ "color1" : "orange"
+ },
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "C_brenneri_proteins-c_tropicalis_PRJNA53597-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
+ "trackId" : "c_tropicalis_PRJNA53597_C_brenneri_proteins",
+ "name" : "C. brenneri proteins",
+ "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "assemblyNames" : [
+ "c_tropicalis_PRJNA53597"
+ ],
"type" : "FeatureTrack",
- "name" : "C. brenneri proteins"
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ]
},
{
- "trackId" : "c_tropicalis_PRJNA53597_TTCN_sequence_search",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_tropicalis_PRJNA53597"
],
@@ -52954,112 +52048,136 @@
"Externally Sourced Resources",
"CRISPR predictions"
],
+ "name" : "Cas12e TTCN PAM sites",
+ "trackId" : "c_tropicalis_PRJNA53597_TTCN_sequence_search",
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
"displays" : [
{
- "displayId" : "TTCN_sequence_search_c_tropicalis_PRJNA53597-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "SlateBlue",
+ "height" : 4,
"showDescriptions" : false,
- "height" : 4
- }
+ "showLabels" : false,
+ "color1" : "SlateBlue"
+ },
+ "displayId" : "TTCN_sequence_search_c_tropicalis_PRJNA53597-LinearBasicDisplay"
}
],
- "name" : "Cas12e TTCN PAM sites",
"adapter" : {
- "search" : "TTC.",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tropicalis.PRJNA53597.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
+ "fastaLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tropicalis.PRJNA53597.WS284.genomic.fa.gz"
},
"faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tropicalis.PRJNA53597.WS284.genomic.fa.gz.fai"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tropicalis.PRJNA53597.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
},
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tropicalis.PRJNA53597.WS284.genomic.fa.gz",
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tropicalis.PRJNA53597.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
}
},
- "type" : "SequenceSearchAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time."
+ "type" : "SequenceSearchAdapter",
+ "search" : "TTC."
+ }
},
{
+ "adapter" : {
+ "search" : "TT.",
+ "type" : "SequenceSearchAdapter",
+ "sequenceAdapter" : {
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tropicalis.PRJNA53597.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
+ },
+ "fastaLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tropicalis.PRJNA53597.WS284.genomic.fa.gz"
+ },
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tropicalis.PRJNA53597.WS284.genomic.fa.gz.gzi"
+ },
+ "type" : "BgzipFastaAdapter"
+ }
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "Indigo",
+ "showLabels" : false,
+ "height" : 4,
"showDescriptions" : false,
- "height" : 4
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "TTN_sequence_search_c_tropicalis_PRJNA53597-LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_tropicalis_PRJNA53597"
- ],
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
+ "trackId" : "c_tropicalis_PRJNA53597_TTN_sequence_search",
+ "name" : "Cas12a TTN PAM sites",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "trackId" : "c_tropicalis_PRJNA53597_TTN_sequence_search",
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
+ "assemblyNames" : [
+ "c_tropicalis_PRJNA53597"
+ ],
+ "type" : "FeatureTrack"
+ },
+ {
"adapter" : {
+ "search" : "..G[AG][AG]T",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
- "faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tropicalis.PRJNA53597.WS284.genomic.fa.gz.fai"
- },
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tropicalis.PRJNA53597.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tropicalis.PRJNA53597.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
+ },
"gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tropicalis.PRJNA53597.WS284.genomic.fa.gz.gzi"
- }
- },
- "search" : "TT.",
- "type" : "SequenceSearchAdapter"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tropicalis.PRJNA53597.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BgzipFastaAdapter"
+ }
},
- "type" : "FeatureTrack",
- "name" : "Cas12a TTN PAM sites"
- },
- {
- "trackId" : "c_tropicalis_PRJNA53597_NNGRRT_sequence_search",
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "assemblyNames" : [
- "c_tropicalis_PRJNA53597"
- ],
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "DarkViolet",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
"height" : 4,
- "showDescriptions" : false
+ "showLabels" : false,
+ "color1" : "DarkViolet"
},
"displayId" : "NNGRRT_sequence_search_c_tropicalis_PRJNA53597-LinearBasicDisplay"
}
],
"name" : "SaCas9 NNGRRT PAM sites",
+ "trackId" : "c_tropicalis_PRJNA53597_NNGRRT_sequence_search",
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_tropicalis_PRJNA53597"
+ ],
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ]
+ },
+ {
"adapter" : {
"sequenceAdapter" : {
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tropicalis.PRJNA53597.WS284.genomic.fa.gz.gzi"
@@ -53069,64 +52187,54 @@
"locationType" : "UriLocation"
},
"fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tropicalis.PRJNA53597.WS284.genomic.fa.gz"
- },
- "type" : "BgzipFastaAdapter"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tropicalis.PRJNA53597.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
+ }
},
- "search" : "..G[AG][AG]T",
- "type" : "SequenceSearchAdapter"
+ "type" : "SequenceSearchAdapter",
+ "search" : ".GG"
},
- "type" : "FeatureTrack",
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time."
- },
- {
- "trackId" : "c_tropicalis_PRJNA53597_NGG_sequence_search",
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "assemblyNames" : [
- "c_tropicalis_PRJNA53597"
- ],
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "RebeccaPurple",
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
"height" : 4,
- "showDescriptions" : false
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
},
"displayId" : "NGG_sequence_search_c_tropicalis_PRJNA53597-LinearBasicDisplay"
}
],
"name" : "SpCas9 NGG PAM sites",
+ "trackId" : "c_tropicalis_PRJNA53597_NGG_sequence_search",
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "SequenceSearchAdapter",
- "sequenceAdapter" : {
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tropicalis.PRJNA53597.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
- },
- "fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tropicalis.PRJNA53597.WS284.genomic.fa.gz"
- },
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tropicalis.PRJNA53597.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
- },
- "type" : "BgzipFastaAdapter"
- },
- "search" : ".GG"
- },
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time."
+ "assemblyNames" : [
+ "c_tropicalis_PRJNA53597"
+ ],
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ]
},
{
- "name" : "Curated Genes (protein coding)",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
+ "displays" : [
+ {
+ "displayId" : "curated_genes_(protein_coding)-c_uteleia_PRJEB12600-LinearBasicDisplay",
+ "renderer" : {
+ "color3" : "#965567",
+ "maxHeight" : 5000,
+ "type" : "SvgFeatureRenderer",
+ "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'"
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_uteleia_PRJEB12600/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz",
@@ -53134,194 +52242,229 @@
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
- "trackId" : "c_uteleia_PRJEB12600_curated_genes_protein_coding",
"assemblyNames" : [
"c_uteleia_PRJEB12600"
],
+ "type" : "FeatureTrack",
"category" : [
"Genes",
"Curated Genes"
],
- "displays" : [
- {
- "renderer" : {
- "color3" : "#965567",
- "type" : "SvgFeatureRenderer",
- "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
- "maxHeight" : 5000
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "curated_genes_(protein_coding)-c_uteleia_PRJEB12600-LinearBasicDisplay"
- }
- ],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- }
+ "trackId" : "c_uteleia_PRJEB12600_curated_genes_protein_coding",
+ "name" : "Curated Genes (protein coding)",
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track."
},
{
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_uteleia_PRJEB12600/tracks/Curated_Genes/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_uteleia_PRJEB12600"
+ ],
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
"name" : "Curated Genes",
+ "trackId" : "c_uteleia_PRJEB12600_curated_genes",
"formatDetails" : {
"feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
},
"displays" : [
{
"displayId" : "curated_genes-c_uteleia_PRJEB12600-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "color3" : "#965567",
- "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
- "maxHeight" : 5000,
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
},
+ "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
+ "color3" : "#965567",
+ "maxHeight" : 5000,
"type" : "SvgFeatureRenderer"
- }
+ },
+ "type" : "LinearBasicDisplay"
}
],
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "assemblyNames" : [
- "c_uteleia_PRJEB12600"
- ],
- "trackId" : "c_uteleia_PRJEB12600_curated_genes"
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_uteleia_PRJEB12600/tracks/Curated_Genes/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
+ "description" : "Low-complexity regions identified by Dust.",
+ "name" : "Low complextity region (Dust)",
"trackId" : "c_uteleia_PRJEB12600_low_complextity_region_(dust)",
"category" : [
"Genome Structure",
"Repeats"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_uteleia_PRJEB12600"
],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_uteleia_PRJEB12600/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
- "displayId" : "low_complextity_region_(dust)-c_uteleia_PRJEB12600-LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 4,
- "type" : "SvgFeatureRenderer",
+ "color1" : "bisque",
"showLabels" : false,
- "color1" : "bisque"
+ "height" : 4,
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
},
+ "displayId" : "low_complextity_region_(dust)-c_uteleia_PRJEB12600-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
- ],
- "name" : "Low complextity region (Dust)",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_uteleia_PRJEB12600/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Low-complexity regions identified by Dust."
+ ]
},
{
+ "name" : "Cas12e TTCN PAM sites",
+ "trackId" : "c_uteleia_PRJEB12600_TTCN_sequence_search",
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_uteleia_PRJEB12600"
+ ],
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
"adapter" : {
- "type" : "SequenceSearchAdapter",
"search" : "TTC.",
"sequenceAdapter" : {
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_uteleia.PRJEB12600.WS284.genomic.fa.gz.gzi"
+ },
+ "type" : "BgzipFastaAdapter",
"fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_uteleia.PRJEB12600.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_uteleia.PRJEB12600.WS284.genomic.fa.gz"
},
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_uteleia.PRJEB12600.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
- },
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_uteleia.PRJEB12600.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
- },
- "type" : "BgzipFastaAdapter"
- }
+ }
+ },
+ "type" : "SequenceSearchAdapter"
},
- "name" : "Cas12e TTCN PAM sites",
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
- "assemblyNames" : [
- "c_uteleia_PRJEB12600"
- ],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "trackId" : "c_uteleia_PRJEB12600_TTCN_sequence_search",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 4,
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "SlateBlue"
+ "height" : 4,
+ "showDescriptions" : false,
+ "color1" : "SlateBlue",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "TTCN_sequence_search_c_uteleia_PRJEB12600-LinearBasicDisplay"
}
]
},
{
"adapter" : {
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
"type" : "BgzipFastaAdapter",
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_uteleia.PRJEB12600.WS284.genomic.fa.gz",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_uteleia.PRJEB12600.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
},
"faiLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_uteleia.PRJEB12600.WS284.genomic.fa.gz.fai"
},
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_uteleia.PRJEB12600.WS284.genomic.fa.gz.gzi",
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_uteleia.PRJEB12600.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
}
},
- "search" : "TT.",
- "type" : "SequenceSearchAdapter"
+ "search" : "TT."
},
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "renderer" : {
+ "color1" : "Indigo",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "TTN_sequence_search_c_uteleia_PRJEB12600-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
+ "trackId" : "c_uteleia_PRJEB12600_TTN_sequence_search",
"name" : "Cas12a TTN PAM sites",
"description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
"assemblyNames" : [
"c_uteleia_PRJEB12600"
],
+ "type" : "FeatureTrack",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
- ],
- "trackId" : "c_uteleia_PRJEB12600_TTN_sequence_search",
+ ]
+ },
+ {
+ "adapter" : {
+ "type" : "SequenceSearchAdapter",
+ "sequenceAdapter" : {
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_uteleia.PRJEB12600.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
+ },
+ "fastaLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_uteleia.PRJEB12600.WS284.genomic.fa.gz"
+ },
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_uteleia.PRJEB12600.WS284.genomic.fa.gz.gzi"
+ },
+ "type" : "BgzipFastaAdapter"
+ },
+ "search" : "..G[AG][AG]T"
+ },
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "Indigo",
"showDescriptions" : false,
- "height" : 4
+ "height" : 4,
+ "showLabels" : false,
+ "color1" : "DarkViolet"
},
- "displayId" : "TTN_sequence_search_c_uteleia_PRJEB12600-LinearBasicDisplay"
+ "displayId" : "NNGRRT_sequence_search_c_uteleia_PRJEB12600-LinearBasicDisplay"
}
+ ],
+ "name" : "SaCas9 NNGRRT PAM sites",
+ "trackId" : "c_uteleia_PRJEB12600_NNGRRT_sequence_search",
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_uteleia_PRJEB12600"
+ ],
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
]
},
{
+ "name" : "SpCas9 NGG PAM sites",
+ "trackId" : "c_uteleia_PRJEB12600_NGG_sequence_search",
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_uteleia_PRJEB12600"
],
@@ -53329,410 +52472,365 @@
"Externally Sourced Resources",
"CRISPR predictions"
],
- "trackId" : "c_uteleia_PRJEB12600_NNGRRT_sequence_search",
- "displays" : [
- {
- "renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "DarkViolet",
- "showDescriptions" : false,
- "height" : 4
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "NNGRRT_sequence_search_c_uteleia_PRJEB12600-LinearBasicDisplay"
- }
- ],
- "type" : "FeatureTrack",
"adapter" : {
- "search" : "..G[AG][AG]T",
"sequenceAdapter" : {
- "gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_uteleia.PRJEB12600.WS284.genomic.fa.gz.gzi"
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_uteleia.PRJEB12600.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
},
"fastaLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_uteleia.PRJEB12600.WS284.genomic.fa.gz"
},
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_uteleia.PRJEB12600.WS284.genomic.fa.gz.fai",
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_uteleia.PRJEB12600.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
- },
- "type" : "BgzipFastaAdapter"
+ }
},
- "type" : "SequenceSearchAdapter"
+ "type" : "SequenceSearchAdapter",
+ "search" : ".GG"
},
- "name" : "SaCas9 NNGRRT PAM sites",
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time."
- },
- {
- "trackId" : "c_uteleia_PRJEB12600_NGG_sequence_search",
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "assemblyNames" : [
- "c_uteleia_PRJEB12600"
- ],
"displays" : [
{
- "displayId" : "NGG_sequence_search_c_uteleia_PRJEB12600-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "RebeccaPurple",
"showDescriptions" : false,
- "height" : 4
+ "height" : 4,
+ "showLabels" : false,
+ "color1" : "RebeccaPurple"
},
+ "displayId" : "NGG_sequence_search_c_uteleia_PRJEB12600-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
- ],
- "name" : "SpCas9 NGG PAM sites",
- "type" : "FeatureTrack",
- "adapter" : {
- "search" : ".GG",
- "sequenceAdapter" : {
- "gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_uteleia.PRJEB12600.WS284.genomic.fa.gz.gzi"
- },
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_uteleia.PRJEB12600.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
- },
- "faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_uteleia.PRJEB12600.WS284.genomic.fa.gz.fai"
- },
- "type" : "BgzipFastaAdapter"
- },
- "type" : "SequenceSearchAdapter"
- },
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time."
+ ]
},
{
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_waitukubuli_PRJEB12602"
+ ],
"category" : [
"Genes",
"Curated Genes"
],
- "assemblyNames" : [
- "c_waitukubuli_PRJEB12602"
- ],
+ "name" : "Curated Genes",
"trackId" : "c_waitukubuli_PRJEB12602_curated_genes",
- "formatDetails" : {
- "feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
- },
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
+ "color3" : "#965567",
+ "type" : "SvgFeatureRenderer",
+ "maxHeight" : 5000,
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
},
- "type" : "SvgFeatureRenderer",
- "maxHeight" : 5000,
- "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
- "color3" : "#965567"
+ "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'"
},
- "type" : "LinearBasicDisplay",
"displayId" : "curated_genes-c_waitukubuli_PRJEB12602-LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
+ "formatDetails" : {
+ "feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
+ },
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_waitukubuli_PRJEB12602/tracks/Curated_Genes/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "name" : "Curated Genes",
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes."
+ }
+ }
},
{
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_waitukubuli_PRJEB12602/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "name" : "Curated Genes (protein coding)",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ }
},
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "color3" : "#965567",
- "type" : "SvgFeatureRenderer",
"color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
- "maxHeight" : 5000
+ "color3" : "#965567",
+ "maxHeight" : 5000,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "curated_genes_(protein_coding)-c_waitukubuli_PRJEB12602-LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "c_waitukubuli_PRJEB12602"
- ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
+ "name" : "Curated Genes (protein coding)",
+ "trackId" : "c_waitukubuli_PRJEB12602_curated_genes_protein_coding",
"category" : [
"Genes",
"Curated Genes"
],
- "trackId" : "c_waitukubuli_PRJEB12602_curated_genes_protein_coding"
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_waitukubuli_PRJEB12602"
+ ]
},
{
- "description" : "Low-complexity regions identified by Dust.",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_waitukubuli_PRJEB12602/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "Low complextity region (Dust)",
"displays" : [
{
- "displayId" : "low_complextity_region_(dust)-c_waitukubuli_PRJEB12602-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "showDescriptions" : false,
"color1" : "bisque",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- }
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "low_complextity_region_(dust)-c_waitukubuli_PRJEB12602-LinearBasicDisplay"
}
],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_waitukubuli_PRJEB12602/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"category" : [
"Genome Structure",
"Repeats"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_waitukubuli_PRJEB12602"
],
+ "description" : "Low-complexity regions identified by Dust.",
+ "name" : "Low complextity region (Dust)",
"trackId" : "c_waitukubuli_PRJEB12602_low_complextity_region_(dust)"
},
{
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_waitukubuli_PRJEB12602"
+ ],
"description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
"name" : "Cas12e TTCN PAM sites",
- "type" : "FeatureTrack",
+ "trackId" : "c_waitukubuli_PRJEB12602_TTCN_sequence_search",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "TTCN_sequence_search_c_waitukubuli_PRJEB12602-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "SlateBlue",
+ "height" : 4,
+ "showDescriptions" : false,
+ "showLabels" : false
+ }
+ }
+ ],
"adapter" : {
- "type" : "SequenceSearchAdapter",
"search" : "TTC.",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
},
"fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
},
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
- },
- "type" : "BgzipFastaAdapter"
- }
- },
- "displays" : [
- {
- "displayId" : "TTCN_sequence_search_c_waitukubuli_PRJEB12602-LinearBasicDisplay",
- "renderer" : {
- "color1" : "SlateBlue",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 4,
- "showDescriptions" : false
- },
- "type" : "LinearBasicDisplay"
+ }
}
- ],
- "trackId" : "c_waitukubuli_PRJEB12602_TTCN_sequence_search",
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "assemblyNames" : [
- "c_waitukubuli_PRJEB12602"
- ]
+ }
},
{
- "trackId" : "c_waitukubuli_PRJEB12602_TTN_sequence_search",
"assemblyNames" : [
"c_waitukubuli_PRJEB12602"
],
+ "type" : "FeatureTrack",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
+ "trackId" : "c_waitukubuli_PRJEB12602_TTN_sequence_search",
+ "name" : "Cas12a TTN PAM sites",
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "TTN_sequence_search_c_waitukubuli_PRJEB12602-LinearBasicDisplay",
"renderer" : {
"showDescriptions" : false,
"height" : 4,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "Indigo"
+ "color1" : "Indigo",
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "TTN_sequence_search_c_waitukubuli_PRJEB12602-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "name" : "Cas12a TTN PAM sites",
- "type" : "FeatureTrack",
"adapter" : {
+ "search" : "TT.",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz.gzi",
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
- "fastaLocation" : {
+ "faiLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz.fai"
},
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz.fai",
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
- },
- "type" : "BgzipFastaAdapter"
- },
- "search" : "TT.",
- "type" : "SequenceSearchAdapter"
- },
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time."
+ }
+ }
+ }
},
{
- "type" : "FeatureTrack",
"adapter" : {
+ "search" : "..G[AG][AG]T",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
- "gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz.gzi"
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
},
"faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz.fai"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
},
- "fastaLocation" : {
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz.gzi"
}
- },
- "search" : "..G[AG][AG]T",
- "type" : "SequenceSearchAdapter"
+ }
},
- "name" : "SaCas9 NNGRRT PAM sites",
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "assemblyNames" : [
- "c_waitukubuli_PRJEB12602"
- ],
- "trackId" : "c_waitukubuli_PRJEB12602_NNGRRT_sequence_search",
"displays" : [
{
- "displayId" : "NNGRRT_sequence_search_c_waitukubuli_PRJEB12602-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
"height" : 4,
- "type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
"showLabels" : false,
- "color1" : "DarkViolet"
+ "color1" : "DarkViolet",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "NNGRRT_sequence_search_c_waitukubuli_PRJEB12602-LinearBasicDisplay"
}
+ ],
+ "name" : "SaCas9 NNGRRT PAM sites",
+ "trackId" : "c_waitukubuli_PRJEB12602_NNGRRT_sequence_search",
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "c_waitukubuli_PRJEB12602"
+ ],
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
]
},
{
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
- "type" : "FeatureTrack",
"adapter" : {
"search" : ".GG",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
- },
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz.gzi",
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
- }
+ },
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz.gzi"
+ },
+ "type" : "BgzipFastaAdapter"
},
"type" : "SequenceSearchAdapter"
},
- "name" : "SpCas9 NGG PAM sites",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "RebeccaPurple",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"height" : 4,
- "showDescriptions" : false
+ "showDescriptions" : false,
+ "color1" : "RebeccaPurple",
+ "type" : "SvgFeatureRenderer"
},
"displayId" : "NGG_sequence_search_c_waitukubuli_PRJEB12602-LinearBasicDisplay"
}
],
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
+ "name" : "SpCas9 NGG PAM sites",
+ "trackId" : "c_waitukubuli_PRJEB12602_NGG_sequence_search",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_waitukubuli_PRJEB12602"
- ],
- "trackId" : "c_waitukubuli_PRJEB12602_NGG_sequence_search"
+ ]
},
{
+ "assemblyNames" : [
+ "c_zanzibari_PRJEB12596"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"Genes",
"Curated Genes"
],
- "assemblyNames" : [
- "c_zanzibari_PRJEB12596"
- ],
"trackId" : "c_zanzibari_PRJEB12596_curated_genes_protein_coding",
+ "name" : "Curated Genes (protein coding)",
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "curated_genes_(protein_coding)-c_zanzibari_PRJEB12596-LinearBasicDisplay",
"renderer" : {
+ "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
"type" : "SvgFeatureRenderer",
"maxHeight" : 5000,
- "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
"color3" : "#965567"
},
- "displayId" : "curated_genes_(protein_coding)-c_zanzibari_PRJEB12596-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_zanzibari_PRJEB12596/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz"
}
- },
- "name" : "Curated Genes (protein coding)",
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track."
+ }
},
{
+ "name" : "Curated Genes",
+ "trackId" : "c_zanzibari_PRJEB12596_curated_genes",
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_zanzibari_PRJEB12596"
],
@@ -53740,218 +52838,204 @@
"Genes",
"Curated Genes"
],
- "trackId" : "c_zanzibari_PRJEB12596_curated_genes",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_zanzibari_PRJEB12596/tracks/Curated_Genes/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"formatDetails" : {
"feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
},
"displays" : [
{
"displayId" : "curated_genes-c_zanzibari_PRJEB12596-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "maxHeight" : 5000,
+ "type" : "SvgFeatureRenderer",
"color3" : "#965567",
+ "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
- },
- "type" : "SvgFeatureRenderer",
- "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
- "maxHeight" : 5000
- }
+ }
+ },
+ "type" : "LinearBasicDisplay"
}
- ],
+ ]
+ },
+ {
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_zanzibari_PRJEB12596/tracks/Curated_Genes/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_zanzibari_PRJEB12596/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ }
},
- "type" : "FeatureTrack",
- "name" : "Curated Genes",
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes."
- },
- {
- "category" : [
- "Genome Structure",
- "Repeats"
- ],
- "assemblyNames" : [
- "c_zanzibari_PRJEB12596"
- ],
- "trackId" : "c_zanzibari_PRJEB12596_low_complextity_region_(dust)",
"displays" : [
{
- "displayId" : "low_complextity_region_(dust)-c_zanzibari_PRJEB12596-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "showDescriptions" : false,
"color1" : "bisque",
"showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 4,
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "low_complextity_region_(dust)-c_zanzibari_PRJEB12596-LinearBasicDisplay"
}
],
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_zanzibari_PRJEB12596/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
+ "description" : "Low-complexity regions identified by Dust.",
"name" : "Low complextity region (Dust)",
- "description" : "Low-complexity regions identified by Dust."
- },
- {
+ "trackId" : "c_zanzibari_PRJEB12596_low_complextity_region_(dust)",
"category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
+ "Genome Structure",
+ "Repeats"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"c_zanzibari_PRJEB12596"
- ],
+ ]
+ },
+ {
"trackId" : "c_zanzibari_PRJEB12596_TTCN_sequence_search",
- "displays" : [
- {
- "renderer" : {
- "showDescriptions" : false,
- "height" : 4,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "SlateBlue"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "TTCN_sequence_search_c_zanzibari_PRJEB12596-LinearBasicDisplay"
- }
- ],
+ "name" : "Cas12e TTCN PAM sites",
"adapter" : {
"type" : "SequenceSearchAdapter",
- "search" : "TTC.",
"sequenceAdapter" : {
"type" : "BgzipFastaAdapter",
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz.gzi"
},
"faiLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz.fai"
},
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz.gzi",
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
}
- }
+ },
+ "search" : "TTC."
},
- "type" : "FeatureTrack",
- "name" : "Cas12e TTCN PAM sites",
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time."
- },
- {
- "trackId" : "c_zanzibari_PRJEB12596_TTN_sequence_search",
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
"assemblyNames" : [
"c_zanzibari_PRJEB12596"
],
"displays" : [
{
+ "displayId" : "TTCN_sequence_search_c_zanzibari_PRJEB12596-LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 4,
"type" : "SvgFeatureRenderer",
+ "color1" : "SlateBlue",
"showLabels" : false,
- "color1" : "Indigo"
+ "showDescriptions" : false,
+ "height" : 4
},
- "type" : "LinearBasicDisplay",
- "displayId" : "TTN_sequence_search_c_zanzibari_PRJEB12596-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "name" : "Cas12a TTN PAM sites",
"type" : "FeatureTrack",
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ]
+ },
+ {
"adapter" : {
- "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
- },
"fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz"
},
"faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz.fai"
+ },
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz.gzi"
}
},
+ "type" : "SequenceSearchAdapter",
"search" : "TT."
},
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time."
+ "displays" : [
+ {
+ "displayId" : "TTN_sequence_search_c_zanzibari_PRJEB12596-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "Indigo",
+ "showDescriptions" : false,
+ "height" : 4,
+ "showLabels" : false
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ],
+ "trackId" : "c_zanzibari_PRJEB12596_TTN_sequence_search",
+ "name" : "Cas12a TTN PAM sites",
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
+ "assemblyNames" : [
+ "c_zanzibari_PRJEB12596"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ]
},
{
+ "trackId" : "c_zanzibari_PRJEB12596_NNGRRT_sequence_search",
"name" : "SaCas9 NNGRRT PAM sites",
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
+ "assemblyNames" : [
+ "c_zanzibari_PRJEB12596"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
"adapter" : {
- "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
"type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz.gzi"
+ },
"fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz"
},
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
- },
- "gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz.gzi"
}
},
+ "type" : "SequenceSearchAdapter",
"search" : "..G[AG][AG]T"
},
- "type" : "FeatureTrack",
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
- "trackId" : "c_zanzibari_PRJEB12596_NNGRRT_sequence_search",
- "assemblyNames" : [
- "c_zanzibari_PRJEB12596"
- ],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "DarkViolet",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
"height" : 4,
- "showDescriptions" : false
+ "showLabels" : false,
+ "color1" : "DarkViolet",
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "NNGRRT_sequence_search_c_zanzibari_PRJEB12596-LinearBasicDisplay"
+ "displayId" : "NNGRRT_sequence_search_c_zanzibari_PRJEB12596-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
]
},
{
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "RebeccaPurple",
- "showDescriptions" : false,
- "height" : 4
- },
- "displayId" : "NGG_sequence_search_c_zanzibari_PRJEB12596-LinearBasicDisplay"
- }
- ],
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
+ "trackId" : "c_zanzibari_PRJEB12596_NGG_sequence_search",
+ "name" : "SpCas9 NGG PAM sites",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
@@ -53959,492 +53043,500 @@
"assemblyNames" : [
"c_zanzibari_PRJEB12596"
],
- "trackId" : "c_zanzibari_PRJEB12596_NGG_sequence_search",
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
+ "type" : "FeatureTrack",
"adapter" : {
- "type" : "SequenceSearchAdapter",
"search" : ".GG",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ },
"faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz.fai"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
},
"fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz"
- },
- "gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz.gzi"
- },
- "type" : "BgzipFastaAdapter"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
+ }
}
},
- "type" : "FeatureTrack",
- "name" : "SpCas9 NGG PAM sites"
- },
- {
- "trackId" : "o_tipulae_PRJEB15512_curated_genes_protein_coding",
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "assemblyNames" : [
- "o_tipulae_PRJEB15512"
- ],
"displays" : [
{
- "displayId" : "curated_genes_(protein_coding)-o_tipulae_PRJEB15512-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "NGG_sequence_search_c_zanzibari_PRJEB12596-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "maxHeight" : 5000,
- "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
- "color3" : "#965567"
+ "showLabels" : false,
+ "height" : 4,
+ "showDescriptions" : false,
+ "color1" : "RebeccaPurple",
+ "type" : "SvgFeatureRenderer"
}
}
- ],
+ ]
+ },
+ {
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
- "name" : "Curated Genes (protein coding)",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
+ "color3" : "#965567",
+ "type" : "SvgFeatureRenderer",
+ "maxHeight" : 5000
+ },
+ "displayId" : "curated_genes_(protein_coding)-o_tipulae_PRJEB15512-LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_tipulae_PRJEB15512/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_tipulae_PRJEB15512/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track."
- },
- {
- "trackId" : "o_tipulae_PRJEB15512_curated_genes",
- "assemblyNames" : [
- "o_tipulae_PRJEB15512"
- ],
"category" : [
"Genes",
"Curated Genes"
],
+ "assemblyNames" : [
+ "o_tipulae_PRJEB15512"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
+ "trackId" : "o_tipulae_PRJEB15512_curated_genes_protein_coding",
+ "name" : "Curated Genes (protein coding)"
+ },
+ {
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_tipulae_PRJEB15512/tracks/Curated_Genes/{refseq}/trackData.jsonz"
+ }
+ },
"displays" : [
{
- "displayId" : "curated_genes-o_tipulae_PRJEB15512-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
"color3" : "#965567",
- "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
"maxHeight" : 5000,
+ "type" : "SvgFeatureRenderer",
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
},
- "type" : "SvgFeatureRenderer"
+ "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "curated_genes-o_tipulae_PRJEB15512-LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
},
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
+ "trackId" : "o_tipulae_PRJEB15512_curated_genes",
"name" : "Curated Genes",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_tipulae_PRJEB15512/tracks/Curated_Genes/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes."
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
+ "assemblyNames" : [
+ "o_tipulae_PRJEB15512"
+ ],
+ "type" : "FeatureTrack"
},
{
- "description" : "Low-complexity regions identified by Dust.",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_tipulae_PRJEB15512/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_tipulae_PRJEB15512/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "name" : "Low complextity region (Dust)",
"displays" : [
{
"displayId" : "low_complextity_region_(dust)-o_tipulae_PRJEB15512-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "bisque",
+ "height" : 4,
"showDescriptions" : false,
- "height" : 4
- }
+ "color1" : "bisque",
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
}
],
+ "trackId" : "o_tipulae_PRJEB15512_low_complextity_region_(dust)",
+ "name" : "Low complextity region (Dust)",
+ "description" : "Low-complexity regions identified by Dust.",
"assemblyNames" : [
"o_tipulae_PRJEB15512"
],
+ "type" : "FeatureTrack",
"category" : [
"Genome Structure",
"Repeats"
- ],
- "trackId" : "o_tipulae_PRJEB15512_low_complextity_region_(dust)"
+ ]
},
{
- "adapter" : {
- "type" : "SequenceSearchAdapter",
- "search" : "TTC.",
- "sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
- "faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz.fai"
- },
- "fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz"
- },
- "gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz.gzi"
- }
- }
- },
- "type" : "FeatureTrack",
- "name" : "Cas12e TTCN PAM sites",
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
- "assemblyNames" : [
- "o_tipulae_PRJEB15512"
- ],
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
+ "assemblyNames" : [
+ "o_tipulae_PRJEB15512"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
"trackId" : "o_tipulae_PRJEB15512_TTCN_sequence_search",
+ "name" : "Cas12e TTCN PAM sites",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "TTCN_sequence_search_o_tipulae_PRJEB15512-LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "SlateBlue",
"showDescriptions" : false,
"height" : 4,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "SlateBlue"
- },
- "displayId" : "TTCN_sequence_search_o_tipulae_PRJEB15512-LinearBasicDisplay"
+ "showLabels" : false
+ }
}
- ]
+ ],
+ "adapter" : {
+ "sequenceAdapter" : {
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ },
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
+ },
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
+ }
+ },
+ "type" : "SequenceSearchAdapter",
+ "search" : "TTC."
+ }
},
{
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "o_tipulae_PRJEB15512"
+ ],
"description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
+ "name" : "Cas12a TTN PAM sites",
+ "trackId" : "o_tipulae_PRJEB15512_TTN_sequence_search",
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 4,
+ "color1" : "Indigo"
+ },
+ "displayId" : "TTN_sequence_search_o_tipulae_PRJEB15512-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
- "search" : "TT.",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
"faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz.fai"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
},
"gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
},
"type" : "BgzipFastaAdapter"
},
- "type" : "SequenceSearchAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "Cas12a TTN PAM sites",
+ "search" : "TT."
+ }
+ },
+ {
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "Indigo",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
+ "color1" : "DarkViolet",
+ "showDescriptions" : false,
"height" : 4,
- "showDescriptions" : false
+ "showLabels" : false
},
- "type" : "LinearBasicDisplay",
- "displayId" : "TTN_sequence_search_o_tipulae_PRJEB15512-LinearBasicDisplay"
+ "displayId" : "NNGRRT_sequence_search_o_tipulae_PRJEB15512-LinearBasicDisplay"
}
],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "assemblyNames" : [
- "o_tipulae_PRJEB15512"
- ],
- "trackId" : "o_tipulae_PRJEB15512_TTN_sequence_search"
- },
- {
"adapter" : {
- "type" : "SequenceSearchAdapter",
"search" : "..G[AG][AG]T",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
"faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz.fai"
},
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz.gzi"
- },
- "type" : "BgzipFastaAdapter"
+ }
}
},
+ "assemblyNames" : [
+ "o_tipulae_PRJEB15512"
+ ],
"type" : "FeatureTrack",
- "name" : "SaCas9 NNGRRT PAM sites",
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "assemblyNames" : [
- "o_tipulae_PRJEB15512"
- ],
"trackId" : "o_tipulae_PRJEB15512_NNGRRT_sequence_search",
+ "name" : "SaCas9 NNGRRT PAM sites",
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time."
+ },
+ {
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "color1" : "RebeccaPurple",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "DarkViolet",
+ "height" : 4,
"showDescriptions" : false,
- "height" : 4
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "NNGRRT_sequence_search_o_tipulae_PRJEB15512-LinearBasicDisplay"
- }
- ]
- },
- {
- "displays" : [
- {
"displayId" : "NGG_sequence_search_o_tipulae_PRJEB15512-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "showDescriptions" : false,
- "height" : 4,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "RebeccaPurple"
- }
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "o_tipulae_PRJEB15512_NGG_sequence_search",
- "assemblyNames" : [
- "o_tipulae_PRJEB15512"
- ],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
- "name" : "SpCas9 NGG PAM sites",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
- "gziLocation" : {
+ "fastaLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz"
},
"faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz.fai"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
},
- "fastaLocation" : {
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz.gzi"
}
},
- "search" : ".GG",
- "type" : "SequenceSearchAdapter"
- }
- },
- {
- "trackId" : "o_volvulus_PRJEB513_protein_motifs",
+ "search" : ".GG"
+ },
"category" : [
- "Sequence Features",
- "Translated Features"
+ "Externally Sourced Resources",
+ "CRISPR predictions"
],
"assemblyNames" : [
- "o_volvulus_PRJEB513"
+ "o_tipulae_PRJEB15512"
],
+ "type" : "FeatureTrack",
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
+ "trackId" : "o_tipulae_PRJEB15512_NGG_sequence_search",
+ "name" : "SpCas9 NGG PAM sites"
+ },
+ {
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Protein motifs/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
+ "height" : 7,
"color1" : "jexl:parent(feature)=='undefined'?'purple':get(parent(feature),'predictiontype')=='tmhmm'?'magenta':get(parent(feature),'predictiontype')=='seg'?'lightseagreen':get(parent(feature),'predictiontype')=='signalp'?'aquamarine':get(parent(feature),'predictiontype')=='ncoils'?'chartreuse':\nget(parent(feature),'predictiontype')=='pfam'?'lightsalmon':'purple'",
- "height" : 7
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "protein_motifs-o_volvulus_PRJEB513-LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
+ "trackId" : "o_volvulus_PRJEB513_protein_motifs",
"name" : "Protein motifs",
+ "description" : "This track shows the extent of predicted protein motifs. Note these spans correspond to amino acid coordinates interpolated onto the physical map. Included are signal peptide (signalp), coiled coil (ncoils) and transmembrane (tmhmm) domains, regions of low complexity (seg), and Pfam annotated motif homologies.",
+ "assemblyNames" : [
+ "o_volvulus_PRJEB513"
+ ],
"type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Protein motifs/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "description" : "This track shows the extent of predicted protein motifs. Note these spans correspond to amino acid coordinates interpolated onto the physical map. Included are signal peptide (signalp), coiled coil (ncoils) and transmembrane (tmhmm) domains, regions of low complexity (seg), and Pfam annotated motif homologies."
+ "category" : [
+ "Sequence Features",
+ "Translated Features"
+ ]
},
{
- "description" : "Historical gene predictions.",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Gene Models (historical)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "Gene Models (historical)",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
"displays" : [
{
- "displayId" : "gene_models_(historical)-o_volvulus_PRJEB513-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "gene_models_(historical)-o_volvulus_PRJEB513-LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
"labels" : {
"description" : "jexl:get(feature,'type')"
- },
- "type" : "SvgFeatureRenderer"
+ }
}
}
],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Gene Models (historical)/{refseq}/trackData.jsonz"
+ }
+ },
+ "assemblyNames" : [
+ "o_volvulus_PRJEB513"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"Genes",
"Curated Genes"
],
- "assemblyNames" : [
- "o_volvulus_PRJEB513"
- ],
- "trackId" : "o_volvulus_PRJEB513_gene_models_(historical)"
+ "trackId" : "o_volvulus_PRJEB513_gene_models_(historical)",
+ "name" : "Gene Models (historical)",
+ "description" : "Historical gene predictions."
},
{
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz"
+ }
+ },
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
"displays" : [
{
- "displayId" : "curated_genes_(protein_coding)-o_volvulus_PRJEB513-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "curated_genes_(protein_coding)-o_volvulus_PRJEB513-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"maxHeight" : 5000,
- "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
- "color3" : "#965567"
+ "type" : "SvgFeatureRenderer",
+ "color3" : "#965567",
+ "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'"
}
}
],
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
+ "name" : "Curated Genes (protein coding)",
+ "trackId" : "o_volvulus_PRJEB513_curated_genes_protein_coding",
"category" : [
"Genes",
"Curated Genes"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"o_volvulus_PRJEB513"
- ],
- "trackId" : "o_volvulus_PRJEB513_curated_genes_protein_coding",
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "name" : "Curated Genes (protein coding)"
+ ]
},
{
- "name" : "Curated Genes (noncoding)",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Curated Genes (noncoding)/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Curated Genes (noncoding)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "description" : "Non-coding curated gene models, including ncRNA, tRNA, miRNA, snRNA, snoRNA, piRNA, lincRNA and antisense RNA.",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "curated_genes_(noncoding)-o_volvulus_PRJEB513-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "gray",
+ "height" : 6
+ }
+ }
+ ],
+ "name" : "Curated Genes (noncoding)",
"trackId" : "o_volvulus_PRJEB513_curated_genes_noncoding",
+ "description" : "Non-coding curated gene models, including ncRNA, tRNA, miRNA, snRNA, snoRNA, piRNA, lincRNA and antisense RNA.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"o_volvulus_PRJEB513"
],
"category" : [
"Genes",
"Curated Genes"
- ],
+ ]
+ },
+ {
"displays" : [
{
- "displayId" : "curated_genes_(noncoding)-o_volvulus_PRJEB513-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "gray",
- "type" : "SvgFeatureRenderer",
- "height" : 6
- }
+ "height" : 6,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "curated_genes_(pseudogenes)-o_volvulus_PRJEB513-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- }
- },
- {
- "description" : "A subset of the full Curated Genes set limited to pseudogenes only. Pseudogenes of tRNA are lighter gray and pseudogenes of rRNA are darker gray than pseudogenes of protein coding genes.",
+ },
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Curated Genes (pseudogenes)/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Curated Genes (pseudogenes)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
"type" : "FeatureTrack",
- "name" : "Curated Genes (pseudogenes)",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
- "displays" : [
- {
- "renderer" : {
- "height" : 6,
- "color1" : "gray",
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "curated_genes_(pseudogenes)-o_volvulus_PRJEB513-LinearBasicDisplay"
- }
+ "assemblyNames" : [
+ "o_volvulus_PRJEB513"
],
"category" : [
"Genes",
"Curated Genes"
],
- "assemblyNames" : [
- "o_volvulus_PRJEB513"
- ],
- "trackId" : "o_volvulus_PRJEB513_curated_genes_pseudogenes"
+ "name" : "Curated Genes (pseudogenes)",
+ "trackId" : "o_volvulus_PRJEB513_curated_genes_pseudogenes",
+ "description" : "A subset of the full Curated Genes set limited to pseudogenes only. Pseudogenes of tRNA are lighter gray and pseudogenes of rRNA are darker gray than pseudogenes of protein coding genes."
},
{
- "name" : "Trans-spliced acceptor",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Trans-spliced acceptor/{refseq}/trackData.jsonz",
@@ -54452,161 +53544,152 @@
},
"type" : "NCListAdapter"
},
- "description" : "This track contains SL1 and SL2 trans-spliced acceptors from a variety of sources: SL1 and SL2 trans-spliced acceptors published by Blumenthal et al, Nature (2002), Trans-Spliced Exon Coupled RNA End Determination (TEC-RED) Hwang et al, PNAS (2004), EST/mRNA sequence data, RNASeq read data from ENA. SL1 acceptors are show in red, SL2 in green. Direction of transcription is indicated by arrow direction.",
- "trackId" : "o_volvulus_PRJEB513_trans-spliced_acceptor",
- "assemblyNames" : [
- "o_volvulus_PRJEB513"
- ],
- "category" : [
- "Sequence Features",
- "Signals & Motifs"
- ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"displays" : [
{
- "displayId" : "trans-spliced_acceptor-o_volvulus_PRJEB513-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"color1" : "jexl:get(feature,'source')=='SL1'?'red':get(feature,'source')=='SL2'?'green':'black'",
"labels" : {
"description" : "jexl:get(feature,'source') || get(feature,'description')"
- },
- "type" : "SvgFeatureRenderer"
+ }
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "trans-spliced_acceptor-o_volvulus_PRJEB513-LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- }
+ "trackId" : "o_volvulus_PRJEB513_trans-spliced_acceptor",
+ "name" : "Trans-spliced acceptor",
+ "description" : "This track contains SL1 and SL2 trans-spliced acceptors from a variety of sources: SL1 and SL2 trans-spliced acceptors published by Blumenthal et al, Nature (2002), Trans-Spliced Exon Coupled RNA End Determination (TEC-RED) Hwang et al, PNAS (2004), EST/mRNA sequence data, RNASeq read data from ENA. SL1 acceptors are show in red, SL2 in green. Direction of transcription is indicated by arrow direction.",
+ "assemblyNames" : [
+ "o_volvulus_PRJEB513"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Sequence Features",
+ "Signals & Motifs"
+ ]
},
{
- "description" : "This track shows the locations of the cosmids, fosmids, and YACs used for the physical mapping and sequencing of the C. elegans genome. The clone termini do not necessarily correspond to the termini of submitted GenBank/EMBL entries. In some cases the exact termini of the clones is not known. For example, YACs were sequenced using PCR amplification across gaps in the cosmid maps. When a clone end is not known, it is shown as an arrow extending to the end of the display. Such data is to be treated with caution. The Vancouver fosmids can be ordered directly from GeneService.",
- "name" : "YACs, Fosmids, & Cosmids",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/YACs, Fosmids, & Cosmids/{refseq}/trackData.jsonz"
- }
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "yacs,_fosmids,_&_cosmids-o_volvulus_PRJEB513-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"color1" : "black",
- "height" : 3
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "yacs,_fosmids,_&_cosmids-o_volvulus_PRJEB513-LinearBasicDisplay"
+ "height" : 3,
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/YACs, Fosmids, & Cosmids/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
},
- "trackId" : "o_volvulus_PRJEB513_yacs_fosmids_cosmids",
+ "category" : [
+ "Reagents"
+ ],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"o_volvulus_PRJEB513"
],
- "category" : [
- "Reagents"
- ]
+ "description" : "This track shows the locations of the cosmids, fosmids, and YACs used for the physical mapping and sequencing of the C. elegans genome. The clone termini do not necessarily correspond to the termini of submitted GenBank/EMBL entries. In some cases the exact termini of the clones is not known. For example, YACs were sequenced using PCR amplification across gaps in the cosmid maps. When a clone end is not known, it is shown as an arrow extending to the end of the display. Such data is to be treated with caution. The Vancouver fosmids can be ordered directly from GeneService.",
+ "name" : "YACs, Fosmids, & Cosmids",
+ "trackId" : "o_volvulus_PRJEB513_yacs_fosmids_cosmids"
},
{
"name" : "mRNAs/ncRNAs (best)",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/mRNAs_ncRNAs (best)/{refseq}/trackData.jsonz"
- }
- },
- "type" : "FeatureTrack",
- "description" : "Native (same species) full length cDNAs and ncRNAs aligned to the genome using BLAT. This track shows the best unique location for each cDNA.",
"trackId" : "o_volvulus_PRJEB513_mrnas/ncrnas_(best)",
+ "description" : "Native (same species) full length cDNAs and ncRNAs aligned to the genome using BLAT. This track shows the best unique location for each cDNA.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "o_volvulus_PRJEB513"
+ ],
"category" : [
"Genes",
"Supporting Evidence"
],
- "assemblyNames" : [
- "o_volvulus_PRJEB513"
- ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/mRNAs_ncRNAs (best)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "mrnas/ncrnas_(best)-o_volvulus_PRJEB513-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
- "outline" : "black",
"color1" : "jexl:startsWith(get(feature,'source'),'BLAT_mRNA_')==true?'yellow':'gray'",
+ "outline" : "black",
+ "height" : 6,
"type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay"
+ }
}
- ],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- }
+ ]
},
{
+ "trackId" : "o_volvulus_PRJEB513_curated_genes",
+ "name" : "Curated Genes",
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
+ "assemblyNames" : [
+ "o_volvulus_PRJEB513"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Curated_Genes/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"formatDetails" : {
"feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
},
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "curated_genes-o_volvulus_PRJEB513-LinearBasicDisplay",
"renderer" : {
"maxHeight" : 5000,
- "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
"type" : "SvgFeatureRenderer",
+ "color3" : "#965567",
+ "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
- },
- "color3" : "#965567"
+ }
},
- "displayId" : "curated_genes-o_volvulus_PRJEB513-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
- ],
- "category" : [
- "Genes",
- "Curated Genes"
- ],
+ ]
+ },
+ {
+ "trackId" : "o_volvulus_PRJEB513_C_briggsae_proteins",
+ "name" : "C. briggsae proteins",
+ "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"assemblyNames" : [
"o_volvulus_PRJEB513"
],
- "trackId" : "o_volvulus_PRJEB513_curated_genes",
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
"type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Curated_Genes/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "name" : "Curated Genes"
- },
- {
- "trackId" : "o_volvulus_PRJEB513_C_briggsae_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "assemblyNames" : [
- "o_volvulus_PRJEB513"
- ],
- "displays" : [
- {
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "orange",
- "height" : 4
- },
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
- "displayId" : "C_briggsae_proteins-o_volvulus_PRJEB513-LinearBasicDisplay"
- }
- ],
- "name" : "C. briggsae proteins",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -54614,241 +53697,255 @@
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/C. briggsae proteins/{refseq}/trackData.jsonz"
}
},
- "type" : "FeatureTrack",
- "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ "displays" : [
+ {
+ "displayId" : "C_briggsae_proteins-o_volvulus_PRJEB513-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "orange",
+ "showLabels" : false,
+ "height" : 4
+ },
+ "mouseover" : "jexl:get(feature,'clone')",
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
- "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "C. japonica proteins",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/C. japonica proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/C. japonica proteins/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "C_japonica_proteins-o_volvulus_PRJEB513-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "C_japonica_proteins-o_volvulus_PRJEB513-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
"color1" : "orange",
+ "height" : 4,
"showLabels" : false,
"type" : "SvgFeatureRenderer"
},
"mouseover" : "jexl:get(feature,'clone')"
}
],
+ "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "C. japonica proteins",
"trackId" : "o_volvulus_PRJEB513_C_japonica_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"o_volvulus_PRJEB513"
]
},
{
- "displays" : [
- {
- "mouseover" : "jexl:'Score: '+get(feature,'score')",
- "renderer" : {
- "height" : 24,
- "displayMode" : "collapse",
- "color1" : "jexl:get(feature,'source')=='RNASeq_R_asymmetry'?'red': get(feature,'source')=='RNASeq_F_asymmetry'?'green':'black'",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "rnaseq_asymmetries-o_volvulus_PRJEB513-LinearBasicDisplay"
- }
- ],
- "trackId" : "o_volvulus_PRJEB513_rnaseq_asymmetries",
- "assemblyNames" : [
- "o_volvulus_PRJEB513"
- ],
- "category" : [
- "Expression"
- ],
- "description" : "Red boxes indicate regions where there are more than 2 times as many forward sense RNASeq reads aligned to the genome as reverse sense reads. This asymmetrical signal has been found empirically to be a sensitive marker for the ends of transcripts. Green boxes indicate regions where there are more than 2 times as many reverse sense RNASeq reads aligned to the genome as forward sense reads. This asymmetrical signal has been found empirically to be sensitive marker for the ends of transcripts. The height of all boxes indicates the relative score of the feature.",
- "name" : "RNASeq Asymmetries",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/RNASeq Asymmetries/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
},
"type" : "NCListAdapter"
- }
- },
- {
+ },
"displays" : [
{
- "displayId" : "trinity-assembled_rnaseq-o_volvulus_PRJEB513-LinearBasicDisplay",
"renderer" : {
- "height" : 5,
- "showLabels" : false,
+ "displayMode" : "collapse",
"type" : "SvgFeatureRenderer",
- "color1" : "mediumpurple"
+ "color1" : "jexl:get(feature,'source')=='RNASeq_R_asymmetry'?'red': get(feature,'source')=='RNASeq_F_asymmetry'?'green':'black'",
+ "height" : 24,
+ "showLabels" : false
},
+ "mouseover" : "jexl:'Score: '+get(feature,'score')",
+ "displayId" : "rnaseq_asymmetries-o_volvulus_PRJEB513-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
- "trackId" : "o_volvulus_PRJEB513_trinity-assembled_rnaseq",
+ "description" : "Red boxes indicate regions where there are more than 2 times as many forward sense RNASeq reads aligned to the genome as reverse sense reads. This asymmetrical signal has been found empirically to be a sensitive marker for the ends of transcripts. Green boxes indicate regions where there are more than 2 times as many reverse sense RNASeq reads aligned to the genome as forward sense reads. This asymmetrical signal has been found empirically to be sensitive marker for the ends of transcripts. The height of all boxes indicates the relative score of the feature.",
+ "trackId" : "o_volvulus_PRJEB513_rnaseq_asymmetries",
+ "name" : "RNASeq Asymmetries",
+ "category" : [
+ "Expression"
+ ],
"assemblyNames" : [
"o_volvulus_PRJEB513"
],
+ "type" : "FeatureTrack"
+ },
+ {
+ "description" : "Native (same species) RNAseq data was assembled with Trinity and then aligned to the genome with BLAT",
+ "name" : "Trinity-assembled RNAseq",
+ "trackId" : "o_volvulus_PRJEB513_trinity-assembled_rnaseq",
"category" : [
"Genes",
"Supporting Evidence"
],
- "description" : "Native (same species) RNAseq data was assembled with Trinity and then aligned to the genome with BLAT",
- "name" : "Trinity-assembled RNAseq",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "o_volvulus_PRJEB513"
+ ],
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Trinity-assembled RNAseq/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- }
- },
- {
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/C. brenneri proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "name" : "C. brenneri proteins",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "height" : 5,
+ "showLabels" : false,
+ "color1" : "mediumpurple",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "trinity-assembled_rnaseq-o_volvulus_PRJEB513-LinearBasicDisplay"
+ }
+ ]
+ },
+ {
"description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "assemblyNames" : [
- "o_volvulus_PRJEB513"
- ],
+ "name" : "C. brenneri proteins",
+ "trackId" : "o_volvulus_PRJEB513_C_brenneri_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "trackId" : "o_volvulus_PRJEB513_C_brenneri_proteins",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "o_volvulus_PRJEB513"
+ ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/C. brenneri proteins/{refseq}/trackData.jsonz"
+ }
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "C_brenneri_proteins-o_volvulus_PRJEB513-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "orange",
+ "showLabels" : false,
"height" : 4
},
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')"
}
]
},
{
- "category" : [
- "Genes",
- "Supporting Evidence"
- ],
- "assemblyNames" : [
- "o_volvulus_PRJEB513"
- ],
- "trackId" : "o_volvulus_PRJEB513_ests",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/ESTs (best)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
"displays" : [
{
"renderer" : {
- "maxHeight" : 5000,
"color1" : "jexl:parent(feature)=='undefined'?'red':get(parent(feature),'has_mate')==1?'limegreen':get(parent(feature),'has_mate')==2?'green':get(parent(feature),'has_mate')==0?'gold':'black'",
+ "maxHeight" : 5000,
"type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "ests-o_volvulus_PRJEB513-LinearBasicDisplay"
+ "displayId" : "ests-o_volvulus_PRJEB513-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/ESTs (best)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
+ "description" : "Native (same-species) Expressed Sequence Tags (ESTs), aligned to the genome using BLAT. This track shows the best unique location for each EST. The paired 5' and 3' ESTs from the same cDNA clone are connected by a dashed line and a colored light green. ESTs with no mate are yellow, and ESTs with a mate that is 'far away' are dark green.",
+ "trackId" : "o_volvulus_PRJEB513_ests",
"name" : "ESTs",
- "description" : "Native (same-species) Expressed Sequence Tags (ESTs), aligned to the genome using BLAT. This track shows the best unique location for each EST. The paired 5' and 3' ESTs from the same cDNA clone are connected by a dashed line and a colored light green. ESTs with no mate are yellow, and ESTs with a mate that is 'far away' are dark green."
+ "category" : [
+ "Genes",
+ "Supporting Evidence"
+ ],
+ "assemblyNames" : [
+ "o_volvulus_PRJEB513"
+ ],
+ "type" : "FeatureTrack"
},
{
- "trackId" : "o_volvulus_PRJEB513_B_malayi_proteins",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "o_volvulus_PRJEB513"
+ ],
"category" : [
"Sequence Similarity",
"Proteins"
],
- "assemblyNames" : [
- "o_volvulus_PRJEB513"
- ],
+ "name" : "B. malayi proteins",
+ "trackId" : "o_volvulus_PRJEB513_B_malayi_proteins",
+ "description" : "Matches to WormBase B. malayi proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"displays" : [
{
"type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
"color1" : "orange",
- "type" : "SvgFeatureRenderer",
+ "height" : 4,
"showLabels" : false,
- "height" : 4
+ "type" : "SvgFeatureRenderer"
},
+ "mouseover" : "jexl:get(feature,'clone')",
"displayId" : "B_malayi_proteins-o_volvulus_PRJEB513-LinearBasicDisplay"
}
],
- "name" : "B. malayi proteins",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/B. malayi proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- }
- },
- "description" : "Matches to WormBase B. malayi proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
- },
- {
- "description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Other UniProt proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
- },
- "name" : "Other UniProt proteins",
+ }
+ },
+ {
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "other_uniprot_proteins-o_volvulus_PRJEB513-LinearBasicDisplay",
"renderer" : {
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
+ "color1" : "orange",
"showLabels" : false,
- "height" : 4,
- "showDescriptions" : false
+ "showDescriptions" : false,
+ "height" : 4
},
- "displayId" : "other_uniprot_proteins-o_volvulus_PRJEB513-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Other UniProt proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"assemblyNames" : [
"o_volvulus_PRJEB513"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "trackId" : "o_volvulus_PRJEB513_other_uniprot_proteins"
+ "trackId" : "o_volvulus_PRJEB513_other_uniprot_proteins",
+ "name" : "Other UniProt proteins",
+ "description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation)."
},
{
+ "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "o_volvulus_PRJEB513_P_pacificus_proteins",
+ "name" : "P. pacificus proteins",
"category" : [
"Sequence Similarity",
"Proteins"
@@ -54856,224 +53953,264 @@
"assemblyNames" : [
"o_volvulus_PRJEB513"
],
- "trackId" : "o_volvulus_PRJEB513_P_pacificus_proteins",
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/P. pacificus proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
- "displayId" : "P_pacificus_proteins-o_volvulus_PRJEB513-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "color1" : "orange",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "height" : 4
+ "height" : 4,
+ "showLabels" : false,
+ "color1" : "orange"
},
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay"
+ "displayId" : "P_pacificus_proteins-o_volvulus_PRJEB513-LinearBasicDisplay"
}
- ],
- "type" : "FeatureTrack",
+ ]
+ },
+ {
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/P. pacificus proteins/{refseq}/trackData.jsonz"
- }
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/RNASeq/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
},
- "name" : "P. pacificus proteins",
- "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
- },
- {
- "category" : [
- "Expression"
- ],
- "assemblyNames" : [
- "o_volvulus_PRJEB513"
- ],
- "trackId" : "o_volvulus_PRJEB513_rnaseq",
"displays" : [
{
"displayId" : "rnaseq-o_volvulus_PRJEB513-LinearBasicDisplay",
+ "mouseover" : "jexl:'Score: '+get(feature,'score')",
"renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "black",
+ "showLabels" : false,
"showDescriptions" : false,
- "displayMode" : "collapse",
- "height" : "jexl:get(feature,'score')>100?50:floor(get(feature,'score')/2)>4?floor(get(feature,'score')/2):4"
+ "height" : "jexl:get(feature,'score')>100?50:floor(get(feature,'score')/2)>4?floor(get(feature,'score')/2):4",
+ "type" : "SvgFeatureRenderer",
+ "displayMode" : "collapse"
},
- "mouseover" : "jexl:'Score: '+get(feature,'score')",
"type" : "LinearBasicDisplay"
}
],
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/RNASeq/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
"name" : "RNASeq",
- "description" : "These boxes indicate alignments of short read sequences from all available RNASeq projects. The number of reads has been normalised by averaging over the number of libraries. The height of all boxes indicates the relative score of the feature."
+ "trackId" : "o_volvulus_PRJEB513_rnaseq",
+ "description" : "These boxes indicate alignments of short read sequences from all available RNASeq projects. The number of reads has been normalised by averaging over the number of libraries. The height of all boxes indicates the relative score of the feature.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "o_volvulus_PRJEB513"
+ ],
+ "category" : [
+ "Expression"
+ ]
},
{
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
+ "assemblyNames" : [
+ "o_volvulus_PRJEB513"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Genome Structure",
+ "Assembly & Curation"
+ ],
+ "trackId" : "o_volvulus_PRJEB513_genbank_submissions",
+ "name" : "Genbank submissions",
+ "description" : "The C. elegans genome was submitted to the GenBank and EMBL databases in in the form of a set of minimally-overlapping segments. This track shows the position of these accessioned entries.",
"displays" : [
{
- "displayId" : "genbank_submissions-o_volvulus_PRJEB513-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'genbank')",
"renderer" : {
"height" : 4,
"color1" : "sienna",
"type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'genbank')"
+ "displayId" : "genbank_submissions-o_volvulus_PRJEB513-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Genbank submissions/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ }
+ },
+ {
+ "description" : "ESTs and mRNAs from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each cDNA sequence. mRNAs are shown in light blue; ESTs in green.",
+ "name" : "WormBase nematode mRNAs/ESTs (best)",
+ "trackId" : "wormbase_nematode_mrnas/ests_(best)-o_volvulus_PRJEB513",
"category" : [
- "Genome Structure",
- "Assembly & Curation"
+ "Sequence Similarity",
+ "Nucleotide"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"o_volvulus_PRJEB513"
],
- "trackId" : "o_volvulus_PRJEB513_genbank_submissions",
- "description" : "The C. elegans genome was submitted to the GenBank and EMBL databases in in the form of a set of minimally-overlapping segments. This track shows the position of these accessioned entries.",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Genbank submissions/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/WormBase nematode mRNAs_ESTs (best)/{refseq}/trackData.jsonz"
+ }
},
- "name" : "Genbank submissions"
- },
- {
"displays" : [
{
"displayId" : "wormbase_nematode_mrnas/ests_(best)-o_volvulus_PRJEB513-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 4,
"labels" : {
"name" : "jexl:get(feature,'species') || get(feature,'id')"
},
- "type" : "SvgFeatureRenderer",
"color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA_BEST'?'lightblue':get(feature,'source')=='BLAT_Caen_EST_BEST'?'green':'black'"
- }
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ]
+ },
+ {
+ "displays" : [
+ {
+ "displayId" : "S_cerevisiae_proteins-o_volvulus_PRJEB513-LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "orange",
+ "height" : 4,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
+ },
+ "mouseover" : "jexl:get(feature,'clone')",
+ "type" : "LinearBasicDisplay"
}
],
- "category" : [
- "Sequence Similarity",
- "Nucleotide"
- ],
- "assemblyNames" : [
- "o_volvulus_PRJEB513"
- ],
- "trackId" : "wormbase_nematode_mrnas/ests_(best)-o_volvulus_PRJEB513",
- "description" : "ESTs and mRNAs from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each cDNA sequence. mRNAs are shown in light blue; ESTs in green.",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/WormBase nematode mRNAs_ESTs (best)/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "name" : "WormBase nematode mRNAs/ESTs (best)"
- },
- {
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz"
- }
- },
- "type" : "FeatureTrack",
- "name" : "S. cerevisiae proteins",
- "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "assemblyNames" : [
- "o_volvulus_PRJEB513"
- ],
"category" : [
"Sequence Similarity",
"Proteins"
],
- "trackId" : "o_volvulus_PRJEB513_S_cerevisiae_proteins",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "o_volvulus_PRJEB513"
+ ],
+ "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "S. cerevisiae proteins",
+ "trackId" : "o_volvulus_PRJEB513_S_cerevisiae_proteins"
+ },
+ {
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 4,
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "orange"
+ "color1" : "orange",
+ "height" : 4,
+ "showLabels" : false
},
"mouseover" : "jexl:get(feature,'clone')",
- "displayId" : "S_cerevisiae_proteins-o_volvulus_PRJEB513-LinearBasicDisplay"
+ "displayId" : "O_volvulus_proteins-o_volvulus_PRJEB513-LinearBasicDisplay"
}
- ]
- },
- {
- "type" : "FeatureTrack",
+ ],
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/O. volvulus proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/O. volvulus proteins/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "name" : "O. volvulus proteins",
- "description" : "Matches to WormBase O. volvulus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
"assemblyNames" : [
"o_volvulus_PRJEB513"
],
+ "type" : "FeatureTrack",
+ "description" : "Matches to WormBase O. volvulus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "o_volvulus_PRJEB513_O_volvulus_proteins",
+ "name" : "O. volvulus proteins"
+ },
+ {
+ "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "o_volvulus_PRJEB513_C_remanei_proteins",
+ "name" : "C. remanei proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "trackId" : "o_volvulus_PRJEB513_O_volvulus_proteins",
+ "assemblyNames" : [
+ "o_volvulus_PRJEB513"
+ ],
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/C. remanei proteins/{refseq}/trackData.jsonz"
+ }
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "C_remanei_proteins-o_volvulus_PRJEB513-LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
+ "type" : "SvgFeatureRenderer",
"color1" : "orange",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "height" : 4
},
- "displayId" : "O_volvulus_proteins-o_volvulus_PRJEB513-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
]
},
{
- "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "description" : "Exact tandem and inverted repetitive elements.",
+ "trackId" : "o_volvulus_PRJEB513_tandem_and_inverted_repeats",
+ "name" : "Tandem and Inverted Repeats",
+ "category" : [
+ "Genome Structure",
+ "Repeats"
+ ],
+ "assemblyNames" : [
+ "o_volvulus_PRJEB513"
+ ],
+ "type" : "FeatureTrack",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/C. remanei proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Tandem and Inverted Repeats/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "name" : "C. remanei proteins",
"displays" : [
{
- "displayId" : "C_remanei_proteins-o_volvulus_PRJEB513-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "color1" : "bisque",
+ "showDescriptions" : false,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "orange",
- "height" : 4
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')"
+ "displayId" : "tandem_and_inverted_repeats-o_volvulus_PRJEB513-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ],
+ ]
+ },
+ {
+ "type" : "FeatureTrack",
"assemblyNames" : [
"o_volvulus_PRJEB513"
],
@@ -55081,154 +54218,117 @@
"Sequence Similarity",
"Proteins"
],
- "trackId" : "o_volvulus_PRJEB513_C_remanei_proteins"
- },
- {
+ "name" : "T. muris proteins",
+ "trackId" : "o_volvulus_PRJEB513_T_muris_proteins",
+ "description" : "Matches to WormBase T. muris proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"displays" : [
{
- "displayId" : "tandem_and_inverted_repeats-o_volvulus_PRJEB513-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "T_muris_proteins-o_volvulus_PRJEB513-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
+ "color1" : "orange",
+ "height" : 4,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "bisque",
- "showDescriptions" : false
+ "type" : "SvgFeatureRenderer"
}
}
],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/T. muris proteins/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ }
+ },
+ {
+ "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "o_volvulus_PRJEB513_H_sapiens_proteins",
+ "name" : "H. sapiens proteins",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
"assemblyNames" : [
"o_volvulus_PRJEB513"
],
- "category" : [
- "Genome Structure",
- "Repeats"
- ],
- "trackId" : "o_volvulus_PRJEB513_tandem_and_inverted_repeats",
- "description" : "Exact tandem and inverted repetitive elements.",
"type" : "FeatureTrack",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Tandem and Inverted Repeats/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/H. sapiens proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ }
},
- "name" : "Tandem and Inverted Repeats"
- },
- {
"displays" : [
{
- "displayId" : "T_muris_proteins-o_volvulus_PRJEB513-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
+ "displayId" : "H_sapiens_proteins-o_volvulus_PRJEB513-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "height" : 4
+ "color1" : "orange",
+ "height" : 4,
+ "showLabels" : false
},
- "mouseover" : "jexl:get(feature,'clone')"
+ "type" : "LinearBasicDisplay"
}
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
+ ]
+ },
+ {
+ "trackId" : "o_volvulus_PRJEB513_nanopore_matches",
+ "name" : "Nanopore matches",
+ "description" : "This Nanopore transcript data is from the paper 'The full-length transcriptome of C. elegans using direct RNA sequencing' Roach et al. https://doi.org/10.1101/598763. Where several transcripts are nearly identical, they are represented by a single transcript and the number of transcripts is recorded in the read coverage. Sequencing is from 3' to 5' and randomly terminates, so the 5' end of transcripts is often incomplete.",
"assemblyNames" : [
"o_volvulus_PRJEB513"
],
- "trackId" : "o_volvulus_PRJEB513_T_muris_proteins",
- "description" : "Matches to WormBase T. muris proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"type" : "FeatureTrack",
+ "category" : [
+ "Genes",
+ "Supporting Evidence"
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/T. muris proteins/{refseq}/trackData.jsonz"
- }
- },
- "name" : "T. muris proteins"
- },
- {
- "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/H. sapiens proteins/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Nanopore matches/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ }
},
- "type" : "FeatureTrack",
- "name" : "H. sapiens proteins",
"displays" : [
{
- "mouseover" : "jexl:get(feature,'clone')",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "orange",
"showLabels" : false,
+ "height" : 4,
+ "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA'?'lightblue':'green'",
"type" : "SvgFeatureRenderer",
- "height" : 4
+ "maxHeight" : 5000
},
- "type" : "LinearBasicDisplay",
- "displayId" : "H_sapiens_proteins-o_volvulus_PRJEB513-LinearBasicDisplay"
+ "displayId" : "nanopore_matches-o_volvulus_PRJEB513-LinearBasicDisplay"
}
- ],
- "assemblyNames" : [
- "o_volvulus_PRJEB513"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "trackId" : "o_volvulus_PRJEB513_H_sapiens_proteins"
+ ]
},
{
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "C_elegans_proteins-o_volvulus_PRJEB513-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
"type" : "SvgFeatureRenderer",
+ "height" : 4,
"showLabels" : false,
- "maxHeight" : 5000,
- "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA'?'lightblue':'green'"
+ "color1" : "orange"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "nanopore_matches-o_volvulus_PRJEB513-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')"
}
],
- "trackId" : "o_volvulus_PRJEB513_nanopore_matches",
- "category" : [
- "Genes",
- "Supporting Evidence"
- ],
- "assemblyNames" : [
- "o_volvulus_PRJEB513"
- ],
- "description" : "This Nanopore transcript data is from the paper 'The full-length transcriptome of C. elegans using direct RNA sequencing' Roach et al. https://doi.org/10.1101/598763. Where several transcripts are nearly identical, they are represented by a single transcript and the number of transcripts is recorded in the read coverage. Sequencing is from 3' to 5' and randomly terminates, so the 5' end of transcripts is often incomplete.",
- "name" : "Nanopore matches",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Nanopore matches/{refseq}/trackData.jsonz"
- }
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/C. elegans proteins/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
},
- "type" : "FeatureTrack"
- },
- {
- "displays" : [
- {
- "mouseover" : "jexl:get(feature,'clone')",
- "renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "orange",
- "height" : 4
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "C_elegans_proteins-o_volvulus_PRJEB513-LinearBasicDisplay"
- }
- ],
- "trackId" : "o_volvulus_PRJEB513_C_elegans_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
@@ -55236,184 +54336,190 @@
"assemblyNames" : [
"o_volvulus_PRJEB513"
],
- "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "C. elegans proteins",
"type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/C. elegans proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- }
+ "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "o_volvulus_PRJEB513_C_elegans_proteins",
+ "name" : "C. elegans proteins"
},
{
- "trackId" : "non-c._elegans_isoseq_collection_(best)-o_volvulus_PRJEB513",
- "category" : [
- "Sequence Similarity",
- "Nucleotide"
- ],
- "assemblyNames" : [
- "o_volvulus_PRJEB513"
- ],
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "color1" : "green",
- "height" : 4
+ "height" : 4,
+ "color1" : "green"
},
"displayId" : "non-c._elegans_isoseq_collection_(best)-o_volvulus_PRJEB513-LinearBasicDisplay"
}
],
- "name" : "Non-C. elegans Isoseq collection (best)",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Non-C. elegans Isoseq collection (best)/{refseq}/trackData.jsonz"
- }
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Non-C. elegans Isoseq collection (best)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
},
"type" : "FeatureTrack",
- "description" : "IsoSeq from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each IsoSeqsequence."
- },
- {
- "trackId" : "o_volvulus_PRJEB513_S_ratti_proteins",
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
"assemblyNames" : [
"o_volvulus_PRJEB513"
],
- "displays" : [
- {
- "displayId" : "S_ratti_proteins-o_volvulus_PRJEB513-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "orange",
- "height" : 4
- },
- "mouseover" : "jexl:get(feature,'clone')"
- }
+ "category" : [
+ "Sequence Similarity",
+ "Nucleotide"
],
- "name" : "S. ratti proteins",
- "type" : "FeatureTrack",
+ "name" : "Non-C. elegans Isoseq collection (best)",
+ "trackId" : "non-c._elegans_isoseq_collection_(best)-o_volvulus_PRJEB513",
+ "description" : "IsoSeq from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each IsoSeqsequence."
+ },
+ {
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/S. ratti proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/S. ratti proteins/{refseq}/trackData.jsonz"
}
},
- "description" : "Matches to WormBase S. ratti proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
- },
- {
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
"displays" : [
{
- "displayId" : "contig_submissions-o_volvulus_PRJEB513-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "sienna",
- "height" : 7
+ "color1" : "orange",
+ "showLabels" : false,
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "S_ratti_proteins-o_volvulus_PRJEB513-LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "o_volvulus_PRJEB513"
- ],
+ "description" : "Matches to WormBase S. ratti proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "S. ratti proteins",
+ "trackId" : "o_volvulus_PRJEB513_S_ratti_proteins",
"category" : [
- "Genome Structure",
- "Assembly & Curation"
+ "Sequence Similarity",
+ "Proteins"
],
- "trackId" : "o_volvulus_PRJEB513_contig_submissions",
- "description" : "This track shows the location and coordinates of contigs (mostly cosmids) submitted to GenBank/EMBL.",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Contig submissions/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
"type" : "FeatureTrack",
- "name" : "Contig submissions"
+ "assemblyNames" : [
+ "o_volvulus_PRJEB513"
+ ]
},
{
+ "trackId" : "o_volvulus_PRJEB513_contig_submissions",
+ "name" : "Contig submissions",
+ "description" : "This track shows the location and coordinates of contigs (mostly cosmids) submitted to GenBank/EMBL.",
"assemblyNames" : [
"o_volvulus_PRJEB513"
],
+ "type" : "FeatureTrack",
"category" : [
"Genome Structure",
"Assembly & Curation"
],
- "trackId" : "o_volvulus_PRJEB513_links_and_superlinks",
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Contig submissions/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "black",
- "height" : 4
+ "height" : 7,
+ "color1" : "sienna",
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "links_and_superlinks-o_volvulus_PRJEB513-LinearBasicDisplay"
+ "displayId" : "contig_submissions-o_volvulus_PRJEB513-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ],
+ ]
+ },
+ {
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Links and Superlinks/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "height" : 4,
+ "color1" : "black",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "links_and_superlinks-o_volvulus_PRJEB513-LinearBasicDisplay"
}
+ ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "type" : "FeatureTrack",
+ "trackId" : "o_volvulus_PRJEB513_links_and_superlinks",
"name" : "Links and Superlinks",
- "description" : "This track shows the location and coordinates of contigs created during the assembly of the C. elegans genome."
+ "description" : "This track shows the location and coordinates of contigs created during the assembly of the C. elegans genome.",
+ "assemblyNames" : [
+ "o_volvulus_PRJEB513"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Genome Structure",
+ "Assembly & Curation"
+ ]
},
{
"name" : "RNASeq introns",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/RNASeq introns/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display.",
"trackId" : "o_volvulus_PRJEB513_rnaseq_introns",
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"o_volvulus_PRJEB513"
],
"category" : [
"Expression"
],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/RNASeq introns/{refseq}/trackData.jsonz"
+ }
+ },
"displays" : [
{
+ "displayId" : "rnaseq_introns-o_volvulus_PRJEB513-LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'score')+' reads'",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showLabels" : false,
"height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)",
"showDescriptions" : false,
- "color1" : "green",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "color1" : "green"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "rnaseq_introns-o_volvulus_PRJEB513-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
]
},
{
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "displayId" : "rnaseq_splice_junctions_(common)-o_volvulus_PRJEB513-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'score')+' reads'",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
+ "showLabels" : false,
+ "showDescriptions" : false
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/RNASeq Splice Junctions (common)/{refseq}/trackData.jsonz",
@@ -55421,65 +54527,73 @@
},
"type" : "NCListAdapter"
},
- "name" : "RNASeq Splice Junctions (common)",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"o_volvulus_PRJEB513"
],
"category" : [
"Expression"
],
+ "name" : "RNASeq Splice Junctions (common)",
"trackId" : "o_volvulus_PRJEB513_rnaseq_splice_junctions_(common)",
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads."
+ },
+ {
+ "name" : "RNASeq Splice Junctions (rare)",
+ "trackId" : "o_volvulus_PRJEB513_rnaseq_splice_junctions_(rare)",
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "o_volvulus_PRJEB513"
+ ],
+ "category" : [
+ "Expression"
+ ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "rnaseq_splice_junctions_(rare)-o_volvulus_PRJEB513-LinearBasicDisplay",
"renderer" : {
+ "showLabels" : false,
"showDescriptions" : false,
+ "height" : "jexl:4",
"color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
"type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "maxHeight" : 5000
},
"mouseover" : "jexl:get(feature,'score')+' reads'",
- "displayId" : "rnaseq_splice_junctions_(common)-o_volvulus_PRJEB513-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
]
},
{
- "category" : [
- "Expression"
- ],
- "assemblyNames" : [
- "o_volvulus_PRJEB513"
- ],
- "trackId" : "o_volvulus_PRJEB513_rnaseq_splice_junctions_(rare)",
"displays" : [
{
- "displayId" : "rnaseq_splice_junctions_(rare)-o_volvulus_PRJEB513-LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'score')+' reads'",
+ "type" : "LinearBasicDisplay",
+ "displayId" : "D_melanogaster_proteins-o_volvulus_PRJEB513-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
+ "height" : 4,
"showLabels" : false,
- "color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
- "maxHeight" : 5000,
- "showDescriptions" : false,
- "height" : "jexl:4"
+ "color1" : "orange"
},
- "type" : "LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')"
}
],
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
"type" : "FeatureTrack",
- "name" : "RNASeq Splice Junctions (rare)",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads."
- },
- {
- "trackId" : "o_volvulus_PRJEB513_D_melanogaster_proteins",
"assemblyNames" : [
"o_volvulus_PRJEB513"
],
@@ -55487,132 +54601,110 @@
"Sequence Similarity",
"Proteins"
],
+ "name" : "D. melanogaster proteins",
+ "trackId" : "o_volvulus_PRJEB513_D_melanogaster_proteins",
+ "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ },
+ {
+ "category" : [
+ "Genome Structure",
+ "Repeats"
+ ],
+ "assemblyNames" : [
+ "o_volvulus_PRJEB513"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Repetitive regions identified by RepeatMasker.",
+ "trackId" : "o_volvulus_PRJEB513_repeat_region_(repeatmasker)",
+ "name" : "Repeat Region (RepeatMasker)",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "repeat_region_(repeatmasker)-o_volvulus_PRJEB513-LinearBasicDisplay",
"renderer" : {
+ "showDescriptions" : false,
+ "height" : 4,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "orange",
- "height" : 4
- },
- "mouseover" : "jexl:get(feature,'clone')",
- "displayId" : "D_melanogaster_proteins-o_volvulus_PRJEB513-LinearBasicDisplay"
+ "color1" : "bisque",
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "name" : "D. melanogaster proteins",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
}
- },
- "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ }
},
{
- "description" : "Repetitive regions identified by RepeatMasker.",
- "name" : "Repeat Region (RepeatMasker)",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "low_complextity_region_(dust)-o_volvulus_PRJEB513-LinearBasicDisplay",
"renderer" : {
- "color1" : "bisque",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
+ "showDescriptions" : false,
"height" : 4,
- "showDescriptions" : false
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "repeat_region_(repeatmasker)-o_volvulus_PRJEB513-LinearBasicDisplay"
+ "showLabels" : false,
+ "color1" : "bisque",
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "trackId" : "o_volvulus_PRJEB513_repeat_region_(repeatmasker)",
- "assemblyNames" : [
- "o_volvulus_PRJEB513"
- ],
+ "description" : "Low-complexity regions identified by Dust.",
+ "name" : "Low complextity region (Dust)",
+ "trackId" : "o_volvulus_PRJEB513_low_complextity_region_(dust)",
"category" : [
"Genome Structure",
"Repeats"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "o_volvulus_PRJEB513"
]
},
{
- "description" : "Low-complexity regions identified by Dust.",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "Low complextity region (Dust)",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "TTCN_sequence_search_o_volvulus_PRJEB513-LinearBasicDisplay",
"renderer" : {
+ "color1" : "SlateBlue",
"height" : 4,
"showDescriptions" : false,
- "color1" : "bisque",
"showLabels" : false,
"type" : "SvgFeatureRenderer"
- },
- "displayId" : "low_complextity_region_(dust)-o_volvulus_PRJEB513-LinearBasicDisplay"
+ }
}
],
- "category" : [
- "Genome Structure",
- "Repeats"
- ],
- "assemblyNames" : [
- "o_volvulus_PRJEB513"
- ],
- "trackId" : "o_volvulus_PRJEB513_low_complextity_region_(dust)"
- },
- {
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
"adapter" : {
"type" : "SequenceSearchAdapter",
- "search" : "TTC.",
"sequenceAdapter" : {
- "gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_volvulus.PRJEB513.WS284.genomic.fa.gz.gzi"
- },
"fastaLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_volvulus.PRJEB513.WS284.genomic.fa.gz"
},
"faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_volvulus.PRJEB513.WS284.genomic.fa.gz.fai"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_volvulus.PRJEB513.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
+ },
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_volvulus.PRJEB513.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
},
"type" : "BgzipFastaAdapter"
- }
+ },
+ "search" : "TTC."
},
"type" : "FeatureTrack",
- "name" : "Cas12e TTCN PAM sites",
- "displays" : [
- {
- "displayId" : "TTCN_sequence_search_o_volvulus_PRJEB513-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "SlateBlue",
- "showDescriptions" : false,
- "height" : 4
- }
- }
- ],
"assemblyNames" : [
"o_volvulus_PRJEB513"
],
@@ -55620,44 +54712,44 @@
"Externally Sourced Resources",
"CRISPR predictions"
],
- "trackId" : "o_volvulus_PRJEB513_TTCN_sequence_search"
+ "name" : "Cas12e TTCN PAM sites",
+ "trackId" : "o_volvulus_PRJEB513_TTCN_sequence_search",
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time."
},
{
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "Indigo",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 4
+ },
+ "displayId" : "TTN_sequence_search_o_volvulus_PRJEB513-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"search" : "TT.",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_volvulus.PRJEB513.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
+ "faiLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_volvulus.PRJEB513.WS284.genomic.fa.gz.fai"
},
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_volvulus.PRJEB513.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_volvulus.PRJEB513.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_volvulus.PRJEB513.WS284.genomic.fa.gz.gzi"
},
"type" : "BgzipFastaAdapter"
- },
- "type" : "SequenceSearchAdapter"
- },
- "name" : "Cas12a TTN PAM sites",
- "displays" : [
- {
- "displayId" : "TTN_sequence_search_o_volvulus_PRJEB513-LinearBasicDisplay",
- "renderer" : {
- "height" : 4,
- "showDescriptions" : false,
- "color1" : "Indigo",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "type" : "LinearBasicDisplay"
}
- ],
+ },
+ "type" : "FeatureTrack",
"assemblyNames" : [
"o_volvulus_PRJEB513"
],
@@ -55665,15 +54757,15 @@
"Externally Sourced Resources",
"CRISPR predictions"
],
- "trackId" : "o_volvulus_PRJEB513_TTN_sequence_search"
+ "name" : "Cas12a TTN PAM sites",
+ "trackId" : "o_volvulus_PRJEB513_TTN_sequence_search",
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time."
},
{
- "name" : "SaCas9 NNGRRT PAM sites",
"adapter" : {
- "type" : "SequenceSearchAdapter",
"search" : "..G[AG][AG]T",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
"faiLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_volvulus.PRJEB513.WS284.genomic.fa.gz.fai"
@@ -55682,218 +54774,119 @@
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_volvulus.PRJEB513.WS284.genomic.fa.gz"
},
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_volvulus.PRJEB513.WS284.genomic.fa.gz.gzi"
}
}
},
- "type" : "FeatureTrack",
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
- "trackId" : "o_volvulus_PRJEB513_NNGRRT_sequence_search",
- "assemblyNames" : [
- "o_volvulus_PRJEB513"
- ],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
"displays" : [
{
- "displayId" : "NNGRRT_sequence_search_o_volvulus_PRJEB513-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
+ "color1" : "DarkViolet",
"height" : 4,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "DarkViolet"
- }
- }
- ]
- },
- {
- "displays" : [
- {
- "displayId" : "NGG_sequence_search_o_volvulus_PRJEB513-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
"showDescriptions" : false,
- "height" : 4,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "RebeccaPurple"
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "NNGRRT_sequence_search_o_volvulus_PRJEB513-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
+ "trackId" : "o_volvulus_PRJEB513_NNGRRT_sequence_search",
+ "name" : "SaCas9 NNGRRT PAM sites",
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
"assemblyNames" : [
"o_volvulus_PRJEB513"
],
- "trackId" : "o_volvulus_PRJEB513_NGG_sequence_search",
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
"type" : "FeatureTrack",
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ]
+ },
+ {
"adapter" : {
"type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_volvulus.PRJEB513.WS284.genomic.fa.gz.gzi",
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_volvulus.PRJEB513.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_volvulus.PRJEB513.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_volvulus.PRJEB513.WS284.genomic.fa.gz.fai",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_volvulus.PRJEB513.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
},
"type" : "BgzipFastaAdapter"
},
"search" : ".GG"
},
- "name" : "SpCas9 NGG PAM sites"
- },
- {
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display.",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/RNASeq introns/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "name" : "RNASeq introns",
"displays" : [
{
- "displayId" : "rnaseq_introns-o_volvulus_PRJEB513-LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'score')+' reads'",
+ "type" : "LinearBasicDisplay",
+ "displayId" : "NGG_sequence_search_o_volvulus_PRJEB513-LinearBasicDisplay",
"renderer" : {
- "height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)",
- "showDescriptions" : false,
- "color1" : "green",
+ "type" : "SvgFeatureRenderer",
+ "color1" : "RebeccaPurple",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay"
+ "height" : 4,
+ "showDescriptions" : false
+ }
}
],
- "assemblyNames" : [
- "o_volvulus_PRJEB513"
- ],
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
+ "name" : "SpCas9 NGG PAM sites",
+ "trackId" : "o_volvulus_PRJEB513_NGG_sequence_search",
"category" : [
- "Expression"
+ "Externally Sourced Resources",
+ "CRISPR predictions"
],
- "trackId" : "o_volvulus_PRJEB513_rnaseq_introns"
- },
- {
- "name" : "RNASeq Splice Junctions (common)",
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/RNASeq Splice Junctions (common)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
- "trackId" : "o_volvulus_PRJEB513_rnaseq_splice_junctions_(common)",
"assemblyNames" : [
"o_volvulus_PRJEB513"
- ],
- "category" : [
- "Expression"
- ],
- "displays" : [
- {
- "displayId" : "rnaseq_splice_junctions_(common)-o_volvulus_PRJEB513-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'score')+' reads'",
- "renderer" : {
- "showDescriptions" : false,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "jexl:get(feature,'score')>1000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/1000))))+'00'+hex(round(255-(140*(get(feature,'score')/1000)))):'#00'+hex(round(255-(140*(get(feature,'score')/1000))))+hex(round(255-(140*(get(feature,'score')/1000))))"
- }
- }
]
},
{
- "trackId" : "o_volvulus_PRJEB513_rnaseq_splice_junctions_(rare)",
- "category" : [
- "Expression"
- ],
+ "trackId" : "p_pacificus_PRJNA12644_curated_genes_protein_coding",
+ "name" : "Curated Genes (protein coding)",
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
"assemblyNames" : [
- "o_volvulus_PRJEB513"
+ "p_pacificus_PRJNA12644"
],
- "displays" : [
- {
- "displayId" : "rnaseq_splice_junctions_(rare)-o_volvulus_PRJEB513-LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'score')+' reads'",
- "renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "maxHeight" : 5000,
- "color1" : "jexl:get(feature,'score')>1000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/1000))))+'00'+hex(round(255-(140*(get(feature,'score')/1000)))):'#00'+hex(round(255-(140*(get(feature,'score')/1000))))+hex(round(255-(140*(get(feature,'score')/1000))))",
- "showDescriptions" : false,
- "height" : "jexl:4"
- },
- "type" : "LinearBasicDisplay"
- }
+ "type" : "FeatureTrack",
+ "category" : [
+ "Genes",
+ "Curated Genes"
],
- "name" : "RNASeq Splice Junctions (rare)",
"adapter" : {
"rootUrlTemplate" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads."
- },
- {
- "assemblyNames" : [
- "p_pacificus_PRJNA12644"
- ],
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "trackId" : "p_pacificus_PRJNA12644_curated_genes_protein_coding",
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
"displays" : [
{
- "displayId" : "curated_genes_(protein_coding)-p_pacificus_PRJNA12644-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "curated_genes_(protein_coding)-p_pacificus_PRJNA12644-LinearBasicDisplay",
"renderer" : {
- "maxHeight" : 5000,
"color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
+ "color3" : "#965567",
"type" : "SvgFeatureRenderer",
- "color3" : "#965567"
+ "maxHeight" : 5000
}
}
- ],
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "name" : "Curated Genes (protein coding)",
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track."
+ ]
},
{
- "name" : "Gene Models (historical)",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/Gene Models (historical)/{refseq}/trackData.jsonz",
@@ -55901,78 +54894,87 @@
},
"type" : "NCListAdapter"
},
- "description" : "Historical gene predictions.",
- "trackId" : "p_pacificus_PRJNA12644_gene_models_(historical)",
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "assemblyNames" : [
- "p_pacificus_PRJNA12644"
- ],
"displays" : [
{
- "displayId" : "gene_models_(historical)-p_pacificus_PRJNA12644-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "gene_models_(historical)-p_pacificus_PRJNA12644-LinearBasicDisplay",
"renderer" : {
- "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
- "type" : "SvgFeatureRenderer",
"labels" : {
"description" : "jexl:get(feature,'type')"
- }
+ },
+ "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
+ "type" : "SvgFeatureRenderer"
}
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- }
- },
- {
- "name" : "Curated Genes",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/Curated_Genes/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
},
+ "description" : "Historical gene predictions.",
+ "name" : "Gene Models (historical)",
+ "trackId" : "p_pacificus_PRJNA12644_gene_models_(historical)",
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
"type" : "FeatureTrack",
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
- "trackId" : "p_pacificus_PRJNA12644_curated_genes",
"assemblyNames" : [
"p_pacificus_PRJNA12644"
- ],
+ ]
+ },
+ {
"category" : [
"Genes",
"Curated Genes"
],
+ "assemblyNames" : [
+ "p_pacificus_PRJNA12644"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
+ "trackId" : "p_pacificus_PRJNA12644_curated_genes",
+ "name" : "Curated Genes",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
},
- "maxHeight" : 5000,
"color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
- "color3" : "#965567"
+ "color3" : "#965567",
+ "maxHeight" : 5000,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "curated_genes-p_pacificus_PRJNA12644-LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
+ },
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/Curated_Genes/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
}
},
{
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/YACs, Fosmids, & Cosmids/{refseq}/trackData.jsonz"
+ }
+ },
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 3,
- "color1" : "black",
- "type" : "SvgFeatureRenderer"
+ "color1" : "black"
},
"displayId" : "yacs,_fosmids,_&_cosmids-p_pacificus_PRJNA12644-LinearBasicDisplay"
}
@@ -55980,173 +54982,188 @@
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
+ "name" : "YACs, Fosmids, & Cosmids",
"trackId" : "p_pacificus_PRJNA12644_yacs_fosmids_cosmids",
+ "description" : "This track shows the locations of the cosmids, fosmids, and YACs used for the physical mapping and sequencing of the C. elegans genome. The clone termini do not necessarily correspond to the termini of submitted GenBank/EMBL entries. In some cases the exact termini of the clones is not known. For example, YACs were sequenced using PCR amplification across gaps in the cosmid maps. When a clone end is not known, it is shown as an arrow extending to the end of the display. Such data is to be treated with caution. The Vancouver fosmids can be ordered directly from GeneService.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "p_pacificus_PRJNA12644"
+ ],
"category" : [
"Reagents"
- ],
+ ]
+ },
+ {
+ "name" : "Protein motifs",
+ "trackId" : "p_pacificus_PRJNA12644_protein_motifs",
+ "description" : "This track shows the extent of predicted protein motifs. Note these spans correspond to amino acid coordinates interpolated onto the physical map. Included are signal peptide (signalp), coiled coil (ncoils) and transmembrane (tmhmm) domains, regions of low complexity (seg), and Pfam annotated motif homologies.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"p_pacificus_PRJNA12644"
],
- "description" : "This track shows the locations of the cosmids, fosmids, and YACs used for the physical mapping and sequencing of the C. elegans genome. The clone termini do not necessarily correspond to the termini of submitted GenBank/EMBL entries. In some cases the exact termini of the clones is not known. For example, YACs were sequenced using PCR amplification across gaps in the cosmid maps. When a clone end is not known, it is shown as an arrow extending to the end of the display. Such data is to be treated with caution. The Vancouver fosmids can be ordered directly from GeneService.",
- "name" : "YACs, Fosmids, & Cosmids",
- "type" : "FeatureTrack",
+ "category" : [
+ "Sequence Features",
+ "Translated Features"
+ ],
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/YACs, Fosmids, & Cosmids/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/Protein motifs/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
},
"type" : "NCListAdapter"
- }
- },
- {
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
"displays" : [
{
"displayId" : "protein_motifs-p_pacificus_PRJNA12644-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
+ "height" : 7,
"color1" : "jexl:parent(feature)=='undefined'?'purple':get(parent(feature),'predictiontype')=='tmhmm'?'magenta':get(parent(feature),'predictiontype')=='seg'?'lightseagreen':get(parent(feature),'predictiontype')=='signalp'?'aquamarine':get(parent(feature),'predictiontype')=='ncoils'?'chartreuse':\nget(parent(feature),'predictiontype')=='pfam'?'lightsalmon':'purple'",
- "height" : 7
+ "type" : "SvgFeatureRenderer"
},
"type" : "LinearBasicDisplay"
}
],
- "category" : [
- "Sequence Features",
- "Translated Features"
- ],
- "assemblyNames" : [
- "p_pacificus_PRJNA12644"
- ],
- "trackId" : "p_pacificus_PRJNA12644_protein_motifs",
- "description" : "This track shows the extent of predicted protein motifs. Note these spans correspond to amino acid coordinates interpolated onto the physical map. Included are signal peptide (signalp), coiled coil (ncoils) and transmembrane (tmhmm) domains, regions of low complexity (seg), and Pfam annotated motif homologies.",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/Protein motifs/{refseq}/trackData.jsonz"
- }
- },
- "name" : "Protein motifs"
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ }
},
{
- "name" : "Curated Genes (pseudogenes)",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "height" : 6,
+ "color1" : "gray",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "curated_genes_(pseudogenes)-p_pacificus_PRJNA12644-LinearBasicDisplay"
+ }
+ ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/Curated Genes (pseudogenes)/{refseq}/trackData.jsonz"
- }
+ },
+ "type" : "NCListAdapter"
},
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
+ "assemblyNames" : [
+ "p_pacificus_PRJNA12644"
+ ],
"type" : "FeatureTrack",
"description" : "A subset of the full Curated Genes set limited to pseudogenes only. Pseudogenes of tRNA are lighter gray and pseudogenes of rRNA are darker gray than pseudogenes of protein coding genes.",
"trackId" : "p_pacificus_PRJNA12644_curated_genes_pseudogenes",
+ "name" : "Curated Genes (pseudogenes)"
+ },
+ {
"assemblyNames" : [
"p_pacificus_PRJNA12644"
],
+ "type" : "FeatureTrack",
"category" : [
"Genes",
- "Curated Genes"
+ "Supporting Evidence"
],
+ "trackId" : "p_pacificus_PRJNA12644_mrnas/ncrnas_(best)",
+ "name" : "mRNAs/ncRNAs (best)",
+ "description" : "Native (same species) full length cDNAs and ncRNAs aligned to the genome using BLAT. This track shows the best unique location for each cDNA.",
"displays" : [
{
- "displayId" : "curated_genes_(pseudogenes)-p_pacificus_PRJNA12644-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "gray",
- "height" : 6
+ "height" : 6,
+ "outline" : "black",
+ "color1" : "jexl:startsWith(get(feature,'source'),'BLAT_mRNA_')==true?'yellow':'gray'",
+ "type" : "SvgFeatureRenderer"
},
+ "displayId" : "mrnas/ncrnas_(best)-p_pacificus_PRJNA12644-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/mRNAs_ncRNAs (best)/{refseq}/trackData.jsonz"
+ }
}
},
{
- "description" : "Native (same species) full length cDNAs and ncRNAs aligned to the genome using BLAT. This track shows the best unique location for each cDNA.",
- "name" : "mRNAs/ncRNAs (best)",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/mRNAs_ncRNAs (best)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/Links and Superlinks/{refseq}/trackData.jsonz"
}
},
- "type" : "FeatureTrack",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "outline" : "black",
- "color1" : "jexl:startsWith(get(feature,'source'),'BLAT_mRNA_')==true?'yellow':'gray'",
"type" : "SvgFeatureRenderer",
- "height" : 6
+ "color1" : "black",
+ "height" : 4
},
- "displayId" : "mrnas/ncrnas_(best)-p_pacificus_PRJNA12644-LinearBasicDisplay"
+ "displayId" : "links_and_superlinks-p_pacificus_PRJNA12644-LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
- "trackId" : "p_pacificus_PRJNA12644_mrnas/ncrnas_(best)",
- "category" : [
- "Genes",
- "Supporting Evidence"
- ],
+ "trackId" : "p_pacificus_PRJNA12644_links_and_superlinks",
+ "name" : "Links and Superlinks",
+ "description" : "This track shows the location and coordinates of contigs created during the assembly of the C. elegans genome.",
"assemblyNames" : [
"p_pacificus_PRJNA12644"
- ]
- },
- {
- "trackId" : "p_pacificus_PRJNA12644_links_and_superlinks",
+ ],
+ "type" : "FeatureTrack",
"category" : [
"Genome Structure",
"Assembly & Curation"
- ],
- "assemblyNames" : [
- "p_pacificus_PRJNA12644"
- ],
+ ]
+ },
+ {
"displays" : [
{
- "displayId" : "links_and_superlinks-p_pacificus_PRJNA12644-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
- "color1" : "black",
- "type" : "SvgFeatureRenderer"
+ "type" : "SvgFeatureRenderer",
+ "color1" : "orange",
+ "showLabels" : false,
+ "height" : 4
},
+ "displayId" : "C_elegans_proteins-p_pacificus_PRJNA12644-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
- "name" : "Links and Superlinks",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/Links and Superlinks/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/C. elegans proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "description" : "This track shows the location and coordinates of contigs created during the assembly of the C. elegans genome."
- },
- {
- "name" : "C. elegans proteins",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/C. elegans proteins/{refseq}/trackData.jsonz"
- }
- },
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "assemblyNames" : [
+ "p_pacificus_PRJNA12644"
+ ],
"type" : "FeatureTrack",
"description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"trackId" : "p_pacificus_PRJNA12644_C_elegans_proteins",
+ "name" : "C. elegans proteins"
+ },
+ {
"category" : [
"Sequence Similarity",
"Proteins"
@@ -56154,194 +55171,183 @@
"assemblyNames" : [
"p_pacificus_PRJNA12644"
],
+ "type" : "FeatureTrack",
+ "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "p_pacificus_PRJNA12644_D_melanogaster_proteins",
+ "name" : "D. melanogaster proteins",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "orange",
+ "showLabels" : false,
"height" : 4
},
"mouseover" : "jexl:get(feature,'clone')",
- "displayId" : "C_elegans_proteins-p_pacificus_PRJNA12644-LinearBasicDisplay"
+ "displayId" : "D_melanogaster_proteins-p_pacificus_PRJNA12644-LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"p_pacificus_PRJNA12644"
],
- "trackId" : "p_pacificus_PRJNA12644_D_melanogaster_proteins",
+ "category" : [
+ "Genome Structure",
+ "Repeats"
+ ],
+ "name" : "Repeat Region (RepeatMasker)",
+ "trackId" : "p_pacificus_PRJNA12644_repeat_region_(repeatmasker)",
+ "description" : "Repetitive regions identified by RepeatMasker.",
"displays" : [
{
- "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "repeat_region_(repeatmasker)-p_pacificus_PRJNA12644-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "color1" : "orange",
+ "type" : "SvgFeatureRenderer",
+ "color1" : "bisque",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "height" : 4,
+ "showDescriptions" : false
},
- "type" : "LinearBasicDisplay",
- "displayId" : "D_melanogaster_proteins-p_pacificus_PRJNA12644-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "D. melanogaster proteins",
- "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ }
},
{
- "description" : "Repetitive regions identified by RepeatMasker.",
- "name" : "Repeat Region (RepeatMasker)",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "repeat_region_(repeatmasker)-p_pacificus_PRJNA12644-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "showDescriptions" : false,
- "height" : 4,
- "type" : "SvgFeatureRenderer",
+ "color1" : "orange",
"showLabels" : false,
- "color1" : "bisque"
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "S_cerevisiae_proteins-p_pacificus_PRJNA12644-LinearBasicDisplay"
}
],
- "trackId" : "p_pacificus_PRJNA12644_repeat_region_(repeatmasker)",
+ "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "S. cerevisiae proteins",
+ "trackId" : "p_pacificus_PRJNA12644_S_cerevisiae_proteins",
"category" : [
- "Genome Structure",
- "Repeats"
+ "Sequence Similarity",
+ "Proteins"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"p_pacificus_PRJNA12644"
]
},
{
- "displays" : [
- {
- "displayId" : "S_cerevisiae_proteins-p_pacificus_PRJNA12644-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
- "renderer" : {
- "height" : 4,
- "color1" : "orange",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- }
- }
- ],
- "trackId" : "p_pacificus_PRJNA12644_S_cerevisiae_proteins",
"assemblyNames" : [
"p_pacificus_PRJNA12644"
],
+ "type" : "FeatureTrack",
"category" : [
- "Sequence Similarity",
- "Proteins"
+ "Genome Structure",
+ "Assembly & Curation"
],
- "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "S. cerevisiae proteins",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz"
- }
- }
- },
- {
"trackId" : "p_pacificus_PRJNA12644_contig_submissions",
- "category" : [
- "Genome Structure",
- "Assembly & Curation"
- ],
- "assemblyNames" : [
- "p_pacificus_PRJNA12644"
- ],
+ "name" : "Contig submissions",
+ "description" : "This track shows the location and coordinates of contigs (mostly cosmids) submitted to GenBank/EMBL.",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
"height" : 7,
- "type" : "SvgFeatureRenderer",
- "color1" : "sienna"
+ "color1" : "sienna",
+ "type" : "SvgFeatureRenderer"
},
"displayId" : "contig_submissions-p_pacificus_PRJNA12644-LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
- "name" : "Contig submissions",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/Contig submissions/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- }
- },
- "description" : "This track shows the location and coordinates of contigs (mostly cosmids) submitted to GenBank/EMBL."
+ },
+ "type" : "NCListAdapter"
+ }
},
{
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/C. brenneri proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "C. brenneri proteins",
- "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "assemblyNames" : [
- "p_pacificus_PRJNA12644"
- ],
"category" : [
"Sequence Similarity",
"Proteins"
],
- "trackId" : "p_pacificus_PRJNA12644_C_brenneri_proteins",
+ "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "C_brenneri_proteins-p_pacificus_PRJNA12644-LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
+ "showLabels" : false,
+ "height" : 4,
"color1" : "orange"
},
+ "displayId" : "C_brenneri_proteins-p_pacificus_PRJNA12644-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "assemblyNames" : [
+ "p_pacificus_PRJNA12644"
+ ],
+ "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "C. brenneri proteins",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/C. brenneri proteins/{refseq}/trackData.jsonz"
+ }
+ },
+ "trackId" : "p_pacificus_PRJNA12644_C_brenneri_proteins"
},
{
+ "category" : [
+ "Genes",
+ "Supporting Evidence"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "p_pacificus_PRJNA12644"
+ ],
+ "description" : "Native (same-species) Expressed Sequence Tags (ESTs), aligned to the genome using BLAT. This track shows the best unique location for each EST. The paired 5' and 3' ESTs from the same cDNA clone are connected by a dashed line and a colored light green. ESTs with no mate are yellow, and ESTs with a mate that is 'far away' are dark green.",
+ "name" : "ESTs",
+ "trackId" : "p_pacificus_PRJNA12644_ests",
"displays" : [
{
"displayId" : "ests-p_pacificus_PRJNA12644-LinearBasicDisplay",
"renderer" : {
- "color1" : "jexl:parent(feature)=='undefined'?'red':get(parent(feature),'has_mate')==1?'limegreen':get(parent(feature),'has_mate')==2?'green':get(parent(feature),'has_mate')==0?'gold':'black'",
"maxHeight" : 5000,
- "type" : "SvgFeatureRenderer"
+ "type" : "SvgFeatureRenderer",
+ "color1" : "jexl:parent(feature)=='undefined'?'red':get(parent(feature),'has_mate')==1?'limegreen':get(parent(feature),'has_mate')==2?'green':get(parent(feature),'has_mate')==0?'gold':'black'"
},
"type" : "LinearBasicDisplay"
}
@@ -56349,23 +55355,12 @@
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "trackId" : "p_pacificus_PRJNA12644_ests",
- "category" : [
- "Genes",
- "Supporting Evidence"
- ],
- "assemblyNames" : [
- "p_pacificus_PRJNA12644"
- ],
- "description" : "Native (same-species) Expressed Sequence Tags (ESTs), aligned to the genome using BLAT. This track shows the best unique location for each EST. The paired 5' and 3' ESTs from the same cDNA clone are connected by a dashed line and a colored light green. ESTs with no mate are yellow, and ESTs with a mate that is 'far away' are dark green.",
- "name" : "ESTs",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/ESTs (best)/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "NCListAdapter"
}
},
{
@@ -56376,87 +55371,75 @@
"assemblyNames" : [
"p_pacificus_PRJNA12644"
],
+ "type" : "FeatureTrack",
+ "description" : "Exact tandem and inverted repetitive elements.",
"trackId" : "p_pacificus_PRJNA12644_tandem_and_inverted_repeats",
+ "name" : "Tandem and Inverted Repeats",
"displays" : [
{
"displayId" : "tandem_and_inverted_repeats-p_pacificus_PRJNA12644-LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
"type" : "SvgFeatureRenderer",
+ "color1" : "bisque",
"showLabels" : false,
- "color1" : "bisque"
+ "showDescriptions" : false
},
"type" : "LinearBasicDisplay"
}
],
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/Tandem and Inverted Repeats/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "Tandem and Inverted Repeats",
- "description" : "Exact tandem and inverted repetitive elements."
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/Tandem and Inverted Repeats/{refseq}/trackData.jsonz"
+ }
+ }
},
{
+ "assemblyNames" : [
+ "p_pacificus_PRJNA12644"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "trackId" : "p_pacificus_PRJNA12644_C_japonica_proteins",
+ "name" : "C. japonica proteins",
+ "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "C_japonica_proteins-p_pacificus_PRJNA12644-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
+ "showLabels" : false,
+ "height" : 4,
"color1" : "orange"
},
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')"
}
],
- "trackId" : "p_pacificus_PRJNA12644_C_japonica_proteins",
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "p_pacificus_PRJNA12644"
- ],
- "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "C. japonica proteins",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/C. japonica proteins/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/C. japonica proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
}
- },
- "type" : "FeatureTrack"
+ }
},
{
- "displays" : [
- {
- "renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "orange",
- "height" : 4
- },
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
- "displayId" : "O_volvulus_proteins-p_pacificus_PRJNA12644-LinearBasicDisplay"
- }
- ],
"trackId" : "p_pacificus_PRJNA12644_O_volvulus_proteins",
+ "name" : "O. volvulus proteins",
+ "description" : "Matches to WormBase O. volvulus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"assemblyNames" : [
"p_pacificus_PRJNA12644"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "description" : "Matches to WormBase O. volvulus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "O. volvulus proteins",
"adapter" : {
"rootUrlTemplate" : {
"locationType" : "UriLocation",
@@ -56464,65 +55447,75 @@
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack"
+ "displays" : [
+ {
+ "displayId" : "O_volvulus_proteins-p_pacificus_PRJNA12644-LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "orange",
+ "height" : 4,
+ "showLabels" : false
+ },
+ "mouseover" : "jexl:get(feature,'clone')",
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/Nanopore matches/{refseq}/trackData.jsonz"
- }
- },
"name" : "Nanopore matches",
+ "trackId" : "p_pacificus_PRJNA12644_nanopore_matches",
"description" : "This Nanopore transcript data is from the paper 'The full-length transcriptome of C. elegans using direct RNA sequencing' Roach et al. https://doi.org/10.1101/598763. Where several transcripts are nearly identical, they are represented by a single transcript and the number of transcripts is recorded in the read coverage. Sequencing is from 3' to 5' and randomly terminates, so the 5' end of transcripts is often incomplete.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "p_pacificus_PRJNA12644"
+ ],
"category" : [
"Genes",
"Supporting Evidence"
],
- "assemblyNames" : [
- "p_pacificus_PRJNA12644"
- ],
- "trackId" : "p_pacificus_PRJNA12644_nanopore_matches",
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/Nanopore matches/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "nanopore_matches-p_pacificus_PRJNA12644-LinearBasicDisplay",
"renderer" : {
+ "showLabels" : false,
"height" : 4,
"color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA'?'lightblue':'green'",
- "maxHeight" : 5000,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "type" : "SvgFeatureRenderer",
+ "maxHeight" : 5000
},
- "displayId" : "nanopore_matches-p_pacificus_PRJNA12644-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
]
},
{
+ "type" : "FeatureTrack",
"displays" : [
{
+ "displayId" : "H_sapiens_proteins-p_pacificus_PRJNA12644-LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
"height" : 4,
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "orange"
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "H_sapiens_proteins-p_pacificus_PRJNA12644-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "p_pacificus_PRJNA12644_H_sapiens_proteins",
+ "assemblyNames" : [
+ "p_pacificus_PRJNA12644"
+ ],
"category" : [
"Sequence Similarity",
"Proteins"
],
- "assemblyNames" : [
- "p_pacificus_PRJNA12644"
- ],
- "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "H. sapiens proteins",
"adapter" : {
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/H. sapiens proteins/{refseq}/trackData.jsonz",
@@ -56530,52 +55523,45 @@
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack"
+ "name" : "H. sapiens proteins",
+ "trackId" : "p_pacificus_PRJNA12644_H_sapiens_proteins",
+ "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
},
{
+ "description" : "Matches to WormBase S. ratti proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "S. ratti proteins",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/S. ratti proteins/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/S. ratti proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "name" : "S. ratti proteins",
- "description" : "Matches to WormBase S. ratti proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "p_pacificus_PRJNA12644_S_ratti_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"p_pacificus_PRJNA12644"
],
- "trackId" : "p_pacificus_PRJNA12644_S_ratti_proteins",
"displays" : [
{
"displayId" : "S_ratti_proteins-p_pacificus_PRJNA12644-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "orange",
- "height" : 4
- }
+ "height" : 4,
+ "showLabels" : false,
+ "color1" : "orange"
+ },
+ "mouseover" : "jexl:get(feature,'clone')",
+ "type" : "LinearBasicDisplay"
}
]
},
{
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
"type" : "FeatureTrack",
- "name" : "Low complextity region (Dust)",
- "description" : "Low-complexity regions identified by Dust.",
"assemblyNames" : [
"p_pacificus_PRJNA12644"
],
@@ -56583,227 +55569,246 @@
"Genome Structure",
"Repeats"
],
+ "name" : "Low complextity region (Dust)",
"trackId" : "p_pacificus_PRJNA12644_low_complextity_region_(dust)",
+ "description" : "Low-complexity regions identified by Dust.",
"displays" : [
{
"renderer" : {
- "color1" : "bisque",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
"height" : 4,
- "showDescriptions" : false
+ "showLabels" : false,
+ "color1" : "bisque"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "low_complextity_region_(dust)-p_pacificus_PRJNA12644-LinearBasicDisplay"
+ "displayId" : "low_complextity_region_(dust)-p_pacificus_PRJNA12644-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ]
- },
- {
+ ],
"adapter" : {
"rootUrlTemplate" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/Non-C. elegans Isoseq collection (best)/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
+ }
+ },
+ {
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/Non-C. elegans Isoseq collection (best)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
},
- "type" : "FeatureTrack",
"name" : "Non-C. elegans Isoseq collection (best)",
- "description" : "IsoSeq from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each IsoSeqsequence.",
- "assemblyNames" : [
- "p_pacificus_PRJNA12644"
- ],
- "category" : [
- "Sequence Similarity",
- "Nucleotide"
- ],
"trackId" : "non-c._elegans_isoseq_collection_(best)-p_pacificus_PRJNA12644",
+ "description" : "IsoSeq from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each IsoSeqsequence.",
+ "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "non-c._elegans_isoseq_collection_(best)-p_pacificus_PRJNA12644-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"color1" : "green",
"height" : 4
- }
+ },
+ "displayId" : "non-c._elegans_isoseq_collection_(best)-p_pacificus_PRJNA12644-LinearBasicDisplay"
}
+ ],
+ "assemblyNames" : [
+ "p_pacificus_PRJNA12644"
+ ],
+ "category" : [
+ "Sequence Similarity",
+ "Nucleotide"
]
},
{
- "name" : "WormBase nematode mRNAs/ESTs (best)",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/WormBase nematode mRNAs_ESTs (best)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "description" : "ESTs and mRNAs from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each cDNA sequence. mRNAs are shown in light blue; ESTs in green.",
- "trackId" : "wormbase_nematode_mrnas/ests_(best)-p_pacificus_PRJNA12644",
"category" : [
"Sequence Similarity",
"Nucleotide"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"p_pacificus_PRJNA12644"
],
+ "description" : "ESTs and mRNAs from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each cDNA sequence. mRNAs are shown in light blue; ESTs in green.",
+ "name" : "WormBase nematode mRNAs/ESTs (best)",
+ "trackId" : "wormbase_nematode_mrnas/ests_(best)-p_pacificus_PRJNA12644",
"displays" : [
{
"displayId" : "wormbase_nematode_mrnas/ests_(best)-p_pacificus_PRJNA12644-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "type" : "SvgFeatureRenderer",
+ "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA_BEST'?'lightblue':get(feature,'source')=='BLAT_Caen_EST_BEST'?'green':'black'",
"labels" : {
"name" : "jexl:get(feature,'species') || get(feature,'id')"
},
- "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA_BEST'?'lightblue':get(feature,'source')=='BLAT_Caen_EST_BEST'?'green':'black'"
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
},
"type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/WormBase nematode mRNAs_ESTs (best)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
+ "description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"trackId" : "p_pacificus_PRJNA12644_other_uniprot_proteins",
- "assemblyNames" : [
- "p_pacificus_PRJNA12644"
- ],
+ "name" : "Other UniProt proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "assemblyNames" : [
+ "p_pacificus_PRJNA12644"
+ ],
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/Other UniProt proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "other_uniprot_proteins-p_pacificus_PRJNA12644-LinearBasicDisplay",
"renderer" : {
+ "color1" : "orange",
+ "showLabels" : false,
"showDescriptions" : false,
"height" : 4,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "orange"
- },
- "displayId" : "other_uniprot_proteins-p_pacificus_PRJNA12644-LinearBasicDisplay"
- }
- ],
- "name" : "Other UniProt proteins",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/Other UniProt proteins/{refseq}/trackData.jsonz"
+ "type" : "SvgFeatureRenderer"
+ }
}
- },
- "type" : "FeatureTrack",
- "description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ ]
},
{
- "category" : [
- "Expression"
- ],
- "assemblyNames" : [
- "p_pacificus_PRJNA12644"
- ],
- "trackId" : "p_pacificus_PRJNA12644_rnaseq_asymmetries",
+ "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "rnaseq_asymmetries-p_pacificus_PRJNA12644-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "rnaseq_asymmetries-p_pacificus_PRJNA12644-LinearBasicDisplay",
+ "mouseover" : "jexl:'Score: '+get(feature,'score')",
"renderer" : {
- "displayMode" : "collapse",
+ "color1" : "jexl:get(feature,'source')=='RNASeq_R_asymmetry'?'red': get(feature,'source')=='RNASeq_F_asymmetry'?'green':'black'",
"height" : 24,
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "jexl:get(feature,'source')=='RNASeq_R_asymmetry'?'red': get(feature,'source')=='RNASeq_F_asymmetry'?'green':'black'"
- },
- "mouseover" : "jexl:'Score: '+get(feature,'score')"
+ "displayMode" : "collapse",
+ "type" : "SvgFeatureRenderer"
+ }
}
],
- "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "p_pacificus_PRJNA12644"
+ ],
+ "category" : [
+ "Expression"
+ ],
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/RNASeq Asymmetries/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/RNASeq Asymmetries/{refseq}/trackData.jsonz"
+ }
},
"name" : "RNASeq Asymmetries",
+ "trackId" : "p_pacificus_PRJNA12644_rnaseq_asymmetries",
"description" : "Red boxes indicate regions where there are more than 2 times as many forward sense RNASeq reads aligned to the genome as reverse sense reads. This asymmetrical signal has been found empirically to be a sensitive marker for the ends of transcripts. Green boxes indicate regions where there are more than 2 times as many reverse sense RNASeq reads aligned to the genome as forward sense reads. This asymmetrical signal has been found empirically to be sensitive marker for the ends of transcripts. The height of all boxes indicates the relative score of the feature."
},
{
+ "category" : [
+ "Expression"
+ ],
+ "assemblyNames" : [
+ "p_pacificus_PRJNA12644"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "These boxes indicate alignments of short read sequences from all available RNASeq projects. The number of reads has been normalised by averaging over the number of libraries. The height of all boxes indicates the relative score of the feature.",
+ "trackId" : "p_pacificus_PRJNA12644_rnaseq",
+ "name" : "RNASeq",
"displays" : [
{
- "displayId" : "rnaseq-p_pacificus_PRJNA12644-LinearBasicDisplay",
"mouseover" : "jexl:'Score: '+get(feature,'score')",
"renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "black",
+ "height" : "jexl:get(feature,'score')>100?50:floor(get(feature,'score')/2)>4?floor(get(feature,'score')/2):4",
"showDescriptions" : false,
+ "showLabels" : false,
"displayMode" : "collapse",
- "height" : "jexl:get(feature,'score')>100?50:floor(get(feature,'score')/2)>4?floor(get(feature,'score')/2):4"
+ "type" : "SvgFeatureRenderer"
},
+ "displayId" : "rnaseq-p_pacificus_PRJNA12644-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
- "trackId" : "p_pacificus_PRJNA12644_rnaseq",
- "assemblyNames" : [
- "p_pacificus_PRJNA12644"
- ],
- "category" : [
- "Expression"
- ],
- "description" : "These boxes indicate alignments of short read sequences from all available RNASeq projects. The number of reads has been normalised by averaging over the number of libraries. The height of all boxes indicates the relative score of the feature.",
- "name" : "RNASeq",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/RNASeq/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
}
- },
- "type" : "FeatureTrack"
+ }
},
{
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/B. malayi proteins/{refseq}/trackData.jsonz"
+ }
+ },
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
+ "height" : 4,
"showLabels" : false,
- "height" : 4
+ "color1" : "orange"
},
- "type" : "LinearBasicDisplay",
"displayId" : "B_malayi_proteins-p_pacificus_PRJNA12644-LinearBasicDisplay"
}
],
+ "name" : "B. malayi proteins",
"trackId" : "p_pacificus_PRJNA12644_B_malayi_proteins",
+ "description" : "Matches to WormBase B. malayi proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"p_pacificus_PRJNA12644"
],
"category" : [
"Sequence Similarity",
"Proteins"
- ],
- "description" : "Matches to WormBase B. malayi proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "B. malayi proteins",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/B. malayi proteins/{refseq}/trackData.jsonz"
- }
- },
- "type" : "FeatureTrack"
+ ]
},
{
- "assemblyNames" : [
- "p_pacificus_PRJNA12644"
- ],
+ "description" : "This track contains Affymetrix GeneChip and Washington University GSC microarray probe sets.",
+ "name" : "Microarray oligo probes",
+ "trackId" : "p_pacificus_PRJNA12644_microarray_oligo_probes",
"category" : [
"Reagents"
],
- "trackId" : "p_pacificus_PRJNA12644_microarray_oligo_probes",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "p_pacificus_PRJNA12644"
+ ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/Microarray oligo probes/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
@@ -56811,212 +55816,201 @@
{
"displayId" : "microarray_oligo_probes-p_pacificus_PRJNA12644-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
"type" : "SvgFeatureRenderer",
+ "height" : 4,
"color1" : "black"
},
"type" : "LinearBasicDisplay"
}
- ],
+ ]
+ },
+ {
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/Microarray oligo probes/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/C. briggsae proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "name" : "Microarray oligo probes",
- "description" : "This track contains Affymetrix GeneChip and Washington University GSC microarray probe sets."
- },
- {
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "C_briggsae_proteins-p_pacificus_PRJNA12644-LinearBasicDisplay",
"renderer" : {
- "color1" : "orange",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "height" : 4
+ "color1" : "orange",
+ "height" : 4,
+ "showLabels" : false
},
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
- "displayId" : "C_briggsae_proteins-p_pacificus_PRJNA12644-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')"
}
],
+ "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "C. briggsae proteins",
+ "trackId" : "p_pacificus_PRJNA12644_C_briggsae_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"p_pacificus_PRJNA12644"
- ],
- "trackId" : "p_pacificus_PRJNA12644_C_briggsae_proteins",
- "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "type" : "FeatureTrack",
+ ]
+ },
+ {
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/C. briggsae proteins/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/C. remanei proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
}
},
- "name" : "C. briggsae proteins"
- },
- {
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "p_pacificus_PRJNA12644"
- ],
- "trackId" : "p_pacificus_PRJNA12644_C_remanei_proteins",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "C_remanei_proteins-p_pacificus_PRJNA12644-LinearBasicDisplay",
"renderer" : {
"height" : 4,
+ "showLabels" : false,
"color1" : "orange",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
- "displayId" : "C_remanei_proteins-p_pacificus_PRJNA12644-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')"
}
],
+ "name" : "C. remanei proteins",
+ "trackId" : "p_pacificus_PRJNA12644_C_remanei_proteins",
+ "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "p_pacificus_PRJNA12644"
+ ],
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ]
+ },
+ {
+ "trackId" : "p_pacificus_PRJNA12644_T_muris_proteins",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/C. remanei proteins/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/T. muris proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ }
},
- "name" : "C. remanei proteins",
- "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
- },
- {
+ "name" : "T. muris proteins",
+ "description" : "Matches to WormBase T. muris proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"displays" : [
{
"displayId" : "T_muris_proteins-p_pacificus_PRJNA12644-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "color1" : "orange",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "height" : 4
+ "color1" : "orange",
+ "height" : 4,
+ "showLabels" : false
},
- "mouseover" : "jexl:get(feature,'clone')",
"type" : "LinearBasicDisplay"
}
],
"assemblyNames" : [
"p_pacificus_PRJNA12644"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
- ],
- "trackId" : "p_pacificus_PRJNA12644_T_muris_proteins",
- "description" : "Matches to WormBase T. muris proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "type" : "FeatureTrack",
+ ]
+ },
+ {
+ "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "P. pacificus proteins",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/T. muris proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/P. pacificus proteins/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
},
- "name" : "T. muris proteins"
- },
- {
"trackId" : "p_pacificus_PRJNA12644_P_pacificus_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"p_pacificus_PRJNA12644"
],
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
"type" : "SvgFeatureRenderer",
+ "color1" : "orange",
"showLabels" : false,
- "color1" : "orange"
+ "height" : 4
},
- "type" : "LinearBasicDisplay",
"displayId" : "P_pacificus_proteins-p_pacificus_PRJNA12644-LinearBasicDisplay"
}
- ],
- "name" : "P. pacificus proteins",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/P. pacificus proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ ]
},
{
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display.",
- "name" : "RNASeq introns",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/RNASeq introns/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/RNASeq introns/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
"displays" : [
{
"type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'score')+' reads'",
+ "displayId" : "rnaseq_introns-p_pacificus_PRJNA12644-LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)",
- "type" : "SvgFeatureRenderer",
+ "color1" : "green",
"showLabels" : false,
- "color1" : "green"
+ "height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)",
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "rnaseq_introns-p_pacificus_PRJNA12644-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'score')+' reads'"
}
],
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display.",
+ "name" : "RNASeq introns",
"trackId" : "p_pacificus_PRJNA12644_rnaseq_introns",
"category" : [
"Expression"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"p_pacificus_PRJNA12644"
]
},
{
- "trackId" : "p_pacificus_PRJNA12644_rnaseq_splice_junctions_(common)",
- "category" : [
- "Expression"
- ],
- "assemblyNames" : [
- "p_pacificus_PRJNA12644"
- ],
+ "type" : "FeatureTrack",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'score')+' reads'",
"renderer" : {
- "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer",
"color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "showDescriptions" : false,
+ "showLabels" : false
},
- "type" : "LinearBasicDisplay",
"displayId" : "rnaseq_splice_junctions_(common)-p_pacificus_PRJNA12644-LinearBasicDisplay"
}
],
+ "assemblyNames" : [
+ "p_pacificus_PRJNA12644"
+ ],
+ "category" : [
+ "Expression"
+ ],
"name" : "RNASeq Splice Junctions (common)",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -57024,73 +56018,68 @@
"locationType" : "UriLocation"
}
},
+ "trackId" : "p_pacificus_PRJNA12644_rnaseq_splice_junctions_(common)",
"description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads."
},
{
- "name" : "RNASeq Splice Junctions (rare)",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ }
},
- "type" : "FeatureTrack",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
- "trackId" : "p_pacificus_PRJNA12644_rnaseq_splice_junctions_(rare)",
- "assemblyNames" : [
- "p_pacificus_PRJNA12644"
- ],
- "category" : [
- "Expression"
- ],
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "rnaseq_splice_junctions_(rare)-p_pacificus_PRJNA12644-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'score')+' reads'",
"renderer" : {
+ "showLabels" : false,
"height" : "jexl:4",
- "type" : "SvgFeatureRenderer",
"showDescriptions" : false,
- "showLabels" : false,
- "maxHeight" : 5000,
- "color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))"
- },
- "mouseover" : "jexl:get(feature,'score')+' reads'",
- "type" : "LinearBasicDisplay"
+ "color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
+ "type" : "SvgFeatureRenderer",
+ "maxHeight" : 5000
+ }
}
+ ],
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
+ "name" : "RNASeq Splice Junctions (rare)",
+ "trackId" : "p_pacificus_PRJNA12644_rnaseq_splice_junctions_(rare)",
+ "category" : [
+ "Expression"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "p_pacificus_PRJNA12644"
]
},
{
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "p_pacificus_PRJNA12644"
+ ],
"displays" : [
{
+ "displayId" : "TTCN_sequence_search_p_pacificus_PRJNA12644-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "showDescriptions" : false,
"color1" : "SlateBlue",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "TTCN_sequence_search_p_pacificus_PRJNA12644-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "p_pacificus_PRJNA12644_TTCN_sequence_search",
- "assemblyNames" : [
- "p_pacificus_PRJNA12644"
- ],
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
"name" : "Cas12e TTCN PAM sites",
"adapter" : {
- "search" : "TTC.",
"sequenceAdapter" : {
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_pacificus.PRJNA12644.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
- },
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_pacificus.PRJNA12644.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
@@ -57099,20 +56088,22 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_pacificus.PRJNA12644.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
- "type" : "BgzipFastaAdapter"
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_pacificus.PRJNA12644.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ }
},
- "type" : "SequenceSearchAdapter"
+ "type" : "SequenceSearchAdapter",
+ "search" : "TTC."
},
- "type" : "FeatureTrack"
+ "trackId" : "p_pacificus_PRJNA12644_TTCN_sequence_search",
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time."
},
{
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
"name" : "Cas12a TTN PAM sites",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
"fastaLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_pacificus.PRJNA12644.WS284.genomic.fa.gz"
@@ -57121,27 +56112,31 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_pacificus.PRJNA12644.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_pacificus.PRJNA12644.WS284.genomic.fa.gz.gzi"
}
},
+ "type" : "SequenceSearchAdapter",
"search" : "TT."
},
+ "trackId" : "p_pacificus_PRJNA12644_TTN_sequence_search",
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
+ "type" : "FeatureTrack",
"displays" : [
{
"displayId" : "TTN_sequence_search_p_pacificus_PRJNA12644-LinearBasicDisplay",
"renderer" : {
- "color1" : "Indigo",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
"height" : 4,
- "showDescriptions" : false
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "color1" : "Indigo",
+ "type" : "SvgFeatureRenderer"
},
"type" : "LinearBasicDisplay"
}
],
- "trackId" : "p_pacificus_PRJNA12644_TTN_sequence_search",
"assemblyNames" : [
"p_pacificus_PRJNA12644"
],
@@ -57151,269 +56146,180 @@
]
},
{
- "type" : "FeatureTrack",
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
"adapter" : {
+ "search" : "..G[AG][AG]T",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_pacificus.PRJNA12644.WS284.genomic.fa.gz.gzi"
- },
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_pacificus.PRJNA12644.WS284.genomic.fa.gz.fai",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_pacificus.PRJNA12644.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
},
"fastaLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_pacificus.PRJNA12644.WS284.genomic.fa.gz"
},
- "type" : "BgzipFastaAdapter"
- },
- "search" : "..G[AG][AG]T",
- "type" : "SequenceSearchAdapter"
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_pacificus.PRJNA12644.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
+ }
+ }
},
"name" : "SaCas9 NNGRRT PAM sites",
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
- "assemblyNames" : [
- "p_pacificus_PRJNA12644"
- ],
+ "trackId" : "p_pacificus_PRJNA12644_NNGRRT_sequence_search",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "trackId" : "p_pacificus_PRJNA12644_NNGRRT_sequence_search",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "p_pacificus_PRJNA12644"
+ ],
"displays" : [
{
- "displayId" : "NNGRRT_sequence_search_p_pacificus_PRJNA12644-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 4,
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
+ "showLabels" : false,
+ "height" : 4,
+ "showDescriptions" : false,
"color1" : "DarkViolet"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "NNGRRT_sequence_search_p_pacificus_PRJNA12644-LinearBasicDisplay"
}
]
},
{
- "type" : "FeatureTrack",
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
"adapter" : {
- "search" : ".GG",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_pacificus.PRJNA12644.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
- },
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_pacificus.PRJNA12644.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_pacificus.PRJNA12644.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_pacificus.PRJNA12644.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
- },
- "type" : "BgzipFastaAdapter"
+ }
},
- "type" : "SequenceSearchAdapter"
+ "search" : ".GG"
},
"name" : "SpCas9 NGG PAM sites",
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
+ "trackId" : "p_pacificus_PRJNA12644_NGG_sequence_search",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "assemblyNames" : [
- "p_pacificus_PRJNA12644"
- ],
- "trackId" : "p_pacificus_PRJNA12644_NGG_sequence_search",
+ "type" : "FeatureTrack",
"displays" : [
{
"displayId" : "NGG_sequence_search_p_pacificus_PRJNA12644-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "color1" : "RebeccaPurple",
"height" : 4,
"showDescriptions" : false,
- "color1" : "RebeccaPurple",
"showLabels" : false,
"type" : "SvgFeatureRenderer"
- }
+ },
+ "type" : "LinearBasicDisplay"
}
+ ],
+ "assemblyNames" : [
+ "p_pacificus_PRJNA12644"
]
},
{
- "trackId" : "p_pacificus_PRJNA12644_rnaseq_introns",
- "assemblyNames" : [
- "p_pacificus_PRJNA12644"
- ],
- "category" : [
- "Expression"
- ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
+ "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
+ "maxHeight" : 5000,
"type" : "SvgFeatureRenderer",
- "color1" : "green",
- "showDescriptions" : false,
- "height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)"
+ "color3" : "#965567"
},
- "mouseover" : "jexl:get(feature,'score')+' reads'",
- "displayId" : "rnaseq_introns-p_pacificus_PRJNA12644-LinearBasicDisplay"
+ "displayId" : "curated_genes_(protein_coding)-p_redivivus_PRJNA186477-LinearBasicDisplay"
}
],
- "name" : "RNASeq introns",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/RNASeq introns/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display."
- },
- {
- "displays" : [
- {
- "renderer" : {
- "showDescriptions" : false,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "jexl:get(feature,'score')>1000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/1000))))+'00'+hex(round(255-(140*(get(feature,'score')/1000)))):'#00'+hex(round(255-(140*(get(feature,'score')/1000))))+hex(round(255-(140*(get(feature,'score')/1000))))"
- },
- "mouseover" : "jexl:get(feature,'score')+' reads'",
- "type" : "LinearBasicDisplay",
- "displayId" : "rnaseq_splice_junctions_(common)-p_pacificus_PRJNA12644-LinearBasicDisplay"
- }
- ],
- "trackId" : "p_pacificus_PRJNA12644_rnaseq_splice_junctions_(common)",
"category" : [
- "Expression"
+ "Genes",
+ "Curated Genes"
],
"assemblyNames" : [
- "p_pacificus_PRJNA12644"
+ "p_redivivus_PRJNA186477"
],
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
- "name" : "RNASeq Splice Junctions (common)",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/RNASeq Splice Junctions (common)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- }
- },
- {
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz"
- }
- },
- "name" : "RNASeq Splice Junctions (rare)",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
- "assemblyNames" : [
- "p_pacificus_PRJNA12644"
- ],
- "category" : [
- "Expression"
- ],
- "trackId" : "p_pacificus_PRJNA12644_rnaseq_splice_junctions_(rare)",
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "showLabels" : false,
- "color1" : "jexl:get(feature,'score')>1000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/1000))))+'00'+hex(round(255-(140*(get(feature,'score')/1000)))):'#00'+hex(round(255-(140*(get(feature,'score')/1000))))+hex(round(255-(140*(get(feature,'score')/1000))))",
- "maxHeight" : 5000,
- "showDescriptions" : false,
- "type" : "SvgFeatureRenderer",
- "height" : "jexl:4"
- },
- "mouseover" : "jexl:get(feature,'score')+' reads'",
- "displayId" : "rnaseq_splice_junctions_(rare)-p_pacificus_PRJNA12644-LinearBasicDisplay"
- }
- ]
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
+ "trackId" : "p_redivivus_PRJNA186477_curated_genes_protein_coding",
+ "name" : "Curated Genes (protein coding)"
},
{
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
+ "name" : "Curated Genes",
+ "trackId" : "p_redivivus_PRJNA186477_curated_genes",
"category" : [
"Genes",
"Curated Genes"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"p_redivivus_PRJNA186477"
],
- "trackId" : "p_redivivus_PRJNA186477_curated_genes_protein_coding",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color3" : "#965567",
- "type" : "SvgFeatureRenderer",
- "maxHeight" : 5000,
- "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'"
- },
- "displayId" : "curated_genes_(protein_coding)-p_redivivus_PRJNA186477-LinearBasicDisplay"
- }
- ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/Curated_Genes/{refseq}/trackData.jsonz"
}
},
- "type" : "FeatureTrack",
- "name" : "Curated Genes (protein coding)",
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track."
- },
- {
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
- "name" : "Curated Genes",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/Curated_Genes/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
"displays" : [
{
- "displayId" : "curated_genes-p_redivivus_PRJNA186477-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
- "color3" : "#965567",
"color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
- "maxHeight" : 5000,
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
},
+ "color3" : "#965567",
+ "maxHeight" : 5000,
"type" : "SvgFeatureRenderer"
- }
+ },
+ "displayId" : "curated_genes-p_redivivus_PRJNA186477-LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
- },
- "trackId" : "p_redivivus_PRJNA186477_curated_genes",
- "assemblyNames" : [
- "p_redivivus_PRJNA186477"
- ],
- "category" : [
- "Genes",
- "Curated Genes"
- ]
+ }
},
{
+ "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"name" : "C. japonica proteins",
+ "trackId" : "p_redivivus_PRJNA186477_C_japonica_proteins",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "p_redivivus_PRJNA186477"
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -57421,54 +56327,32 @@
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/C. japonica proteins/{refseq}/trackData.jsonz"
}
},
- "type" : "FeatureTrack",
- "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "trackId" : "p_redivivus_PRJNA186477_C_japonica_proteins",
- "assemblyNames" : [
- "p_redivivus_PRJNA186477"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
"displays" : [
{
- "type" : "LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
"height" : 4,
- "color1" : "orange",
"showLabels" : false,
+ "color1" : "orange",
"type" : "SvgFeatureRenderer"
},
- "displayId" : "C_japonica_proteins-p_redivivus_PRJNA186477-LinearBasicDisplay"
+ "displayId" : "C_japonica_proteins-p_redivivus_PRJNA186477-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
]
},
{
+ "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "C. elegans proteins",
"trackId" : "p_redivivus_PRJNA186477_C_elegans_proteins",
- "assemblyNames" : [
- "p_redivivus_PRJNA186477"
- ],
"category" : [
"Sequence Similarity",
"Proteins"
],
- "displays" : [
- {
- "displayId" : "C_elegans_proteins-p_redivivus_PRJNA186477-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "height" : 4,
- "color1" : "orange",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "mouseover" : "jexl:get(feature,'clone')"
- }
- ],
- "name" : "C. elegans proteins",
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "p_redivivus_PRJNA186477"
+ ],
"adapter" : {
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/C. elegans proteins/{refseq}/trackData.jsonz",
@@ -57476,69 +56360,81 @@
},
"type" : "NCListAdapter"
},
- "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
- },
- {
- "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/C. brenneri proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "name" : "C. brenneri proteins",
"displays" : [
{
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "orange",
- "height" : 4
+ "height" : 4,
+ "showLabels" : false
},
+ "displayId" : "C_elegans_proteins-p_redivivus_PRJNA186477-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ]
+ },
+ {
+ "displays" : [
+ {
"type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
+ "renderer" : {
+ "color1" : "orange",
+ "height" : 4,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
+ },
"displayId" : "C_brenneri_proteins-p_redivivus_PRJNA186477-LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "p_redivivus_PRJNA186477"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "trackId" : "p_redivivus_PRJNA186477_C_brenneri_proteins"
- },
- {
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/H. sapiens proteins/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/C. brenneri proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "name" : "H. sapiens proteins",
- "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "p_redivivus_PRJNA186477"
+ ],
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "name" : "C. brenneri proteins",
+ "trackId" : "p_redivivus_PRJNA186477_C_brenneri_proteins",
+ "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ },
+ {
+ "trackId" : "p_redivivus_PRJNA186477_H_sapiens_proteins",
+ "name" : "H. sapiens proteins",
+ "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"assemblyNames" : [
"p_redivivus_PRJNA186477"
],
- "trackId" : "p_redivivus_PRJNA186477_H_sapiens_proteins",
+ "type" : "FeatureTrack",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/H. sapiens proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
- "displayId" : "H_sapiens_proteins-p_redivivus_PRJNA186477-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "H_sapiens_proteins-p_redivivus_PRJNA186477-LinearBasicDisplay",
"renderer" : {
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "height" : 4
+ "color1" : "orange",
+ "height" : 4,
+ "showLabels" : false
},
"mouseover" : "jexl:get(feature,'clone')"
}
@@ -57546,117 +56442,105 @@
},
{
"trackId" : "p_redivivus_PRJNA186477_other_uniprot_proteins",
+ "name" : "Other UniProt proteins",
+ "description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"assemblyNames" : [
"p_redivivus_PRJNA186477"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "showDescriptions" : false,
- "height" : 4,
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "orange"
- },
- "displayId" : "other_uniprot_proteins-p_redivivus_PRJNA186477-LinearBasicDisplay"
- }
- ],
- "name" : "Other UniProt proteins",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/Other UniProt proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation)."
- },
- {
- "type" : "FeatureTrack",
- "adapter" : {
"rootUrlTemplate" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/C. briggsae proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/Other UniProt proteins/{refseq}/trackData.jsonz"
+ }
},
- "name" : "C. briggsae proteins",
- "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "p_redivivus_PRJNA186477"
- ],
- "trackId" : "p_redivivus_PRJNA186477_C_briggsae_proteins",
"displays" : [
{
- "displayId" : "C_briggsae_proteins-p_redivivus_PRJNA186477-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
+ "displayId" : "other_uniprot_proteins-p_redivivus_PRJNA186477-LinearBasicDisplay",
"renderer" : {
+ "showLabels" : false,
+ "showDescriptions" : false,
"height" : 4,
"color1" : "orange",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')"
+ "type" : "LinearBasicDisplay"
}
]
},
{
- "name" : "S. cerevisiae proteins",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "trackId" : "p_redivivus_PRJNA186477_S_cerevisiae_proteins",
+ "trackId" : "p_redivivus_PRJNA186477_C_briggsae_proteins",
+ "name" : "C. briggsae proteins",
+ "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"assemblyNames" : [
"p_redivivus_PRJNA186477"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/C. briggsae proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "C_briggsae_proteins-p_redivivus_PRJNA186477-LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
"color1" : "orange",
+ "showLabels" : false,
"height" : 4
},
- "mouseover" : "jexl:get(feature,'clone')",
- "displayId" : "S_cerevisiae_proteins-p_redivivus_PRJNA186477-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')"
}
]
},
{
"displays" : [
{
- "displayId" : "P_pacificus_proteins-p_redivivus_PRJNA186477-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
+ "displayId" : "S_cerevisiae_proteins-p_redivivus_PRJNA186477-LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "orange",
- "height" : 4
+ "height" : 4,
+ "showLabels" : false,
+ "color1" : "orange"
},
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')"
+ }
+ ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz"
}
+ },
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "assemblyNames" : [
+ "p_redivivus_PRJNA186477"
],
+ "type" : "FeatureTrack",
+ "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "p_redivivus_PRJNA186477_S_cerevisiae_proteins",
+ "name" : "S. cerevisiae proteins"
+ },
+ {
+ "type" : "FeatureTrack",
"assemblyNames" : [
"p_redivivus_PRJNA186477"
],
@@ -57664,196 +56548,215 @@
"Sequence Similarity",
"Proteins"
],
+ "name" : "P. pacificus proteins",
"trackId" : "p_redivivus_PRJNA186477_P_pacificus_proteins",
"description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "type" : "FeatureTrack",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
+ "renderer" : {
+ "color1" : "orange",
+ "height" : 4,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "P_pacificus_proteins-p_redivivus_PRJNA186477-LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/P. pacificus proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
}
- },
- "name" : "P. pacificus proteins"
+ }
},
{
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/C. remanei proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "name" : "C. remanei proteins",
- "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "assemblyNames" : [
- "p_redivivus_PRJNA186477"
- ],
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "p_redivivus_PRJNA186477"
+ ],
+ "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "C. remanei proteins",
"trackId" : "p_redivivus_PRJNA186477_C_remanei_proteins",
"displays" : [
{
"displayId" : "C_remanei_proteins-p_redivivus_PRJNA186477-LinearBasicDisplay",
"renderer" : {
+ "color1" : "orange",
"height" : 4,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "orange"
+ "type" : "SvgFeatureRenderer"
},
"mouseover" : "jexl:get(feature,'clone')",
"type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/C. remanei proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
"displays" : [
{
- "displayId" : "repeat_region_(repeatmasker)-p_redivivus_PRJNA186477-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 4,
+ "color1" : "bisque",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "bisque"
+ "height" : 4,
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "repeat_region_(repeatmasker)-p_redivivus_PRJNA186477-LinearBasicDisplay"
}
],
- "trackId" : "p_redivivus_PRJNA186477_repeat_region_(repeatmasker)",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"category" : [
"Genome Structure",
"Repeats"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"p_redivivus_PRJNA186477"
],
"description" : "Repetitive regions identified by RepeatMasker.",
"name" : "Repeat Region (RepeatMasker)",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- }
+ "trackId" : "p_redivivus_PRJNA186477_repeat_region_(repeatmasker)"
},
{
- "name" : "INSDC nematode cDNAs",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "grey",
+ "height" : 4,
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "$ASEMBLY_insdc_nematode_cdnas-LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/$ASEMBLY/tracks/INSDC nematode cDNAs/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/$ASEMBLY/tracks/INSDC nematode cDNAs/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "description" : "cDNAs from this species from INSDC that have been aligned to the genome using STAR.",
- "trackId" : "$ASEMBLY_insdc_nematode_cdnas",
"category" : [
"Sequence Similarity",
"Nucleotide"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"$ASEMBLY"
],
- "displays" : [
- {
- "displayId" : "$ASEMBLY_insdc_nematode_cdnas-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "grey",
- "showDescriptions" : false,
- "height" : 4
- }
- }
- ]
+ "description" : "cDNAs from this species from INSDC that have been aligned to the genome using STAR.",
+ "name" : "INSDC nematode cDNAs",
+ "trackId" : "$ASEMBLY_insdc_nematode_cdnas"
},
{
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "D_melanogaster_proteins-p_redivivus_PRJNA186477-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
"type" : "SvgFeatureRenderer",
+ "height" : 4,
"showLabels" : false,
"color1" : "orange"
},
"mouseover" : "jexl:get(feature,'clone')",
- "displayId" : "D_melanogaster_proteins-p_redivivus_PRJNA186477-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "p_redivivus_PRJNA186477"
- ],
+ "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "D. melanogaster proteins",
+ "trackId" : "p_redivivus_PRJNA186477_D_melanogaster_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "trackId" : "p_redivivus_PRJNA186477_D_melanogaster_proteins",
- "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
"type" : "FeatureTrack",
- "name" : "D. melanogaster proteins"
+ "assemblyNames" : [
+ "p_redivivus_PRJNA186477"
+ ]
},
{
- "description" : "Low-complexity regions identified by Dust.",
+ "trackId" : "p_redivivus_PRJNA186477_low_complextity_region_(dust)",
"name" : "Low complextity region (Dust)",
+ "description" : "Low-complexity regions identified by Dust.",
+ "assemblyNames" : [
+ "p_redivivus_PRJNA186477"
+ ],
"type" : "FeatureTrack",
+ "category" : [
+ "Genome Structure",
+ "Repeats"
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz"
}
},
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "low_complextity_region_(dust)-p_redivivus_PRJNA186477-LinearBasicDisplay",
"renderer" : {
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "bisque",
+ "height" : 4,
"showDescriptions" : false,
- "height" : 4
+ "color1" : "bisque",
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "low_complextity_region_(dust)-p_redivivus_PRJNA186477-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
- ],
- "trackId" : "p_redivivus_PRJNA186477_low_complextity_region_(dust)",
- "category" : [
- "Genome Structure",
- "Repeats"
- ],
- "assemblyNames" : [
- "p_redivivus_PRJNA186477"
]
},
{
"displays" : [
{
- "displayId" : "tandem_and_inverted_repeats-p_redivivus_PRJNA186477-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
+ "showDescriptions" : false,
"color1" : "bisque",
- "showDescriptions" : false
- }
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "tandem_and_inverted_repeats-p_redivivus_PRJNA186477-LinearBasicDisplay"
}
],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/Tandem and Inverted Repeats/{refseq}/trackData.jsonz"
+ }
+ },
"category" : [
"Genome Structure",
"Repeats"
@@ -57861,29 +56764,32 @@
"assemblyNames" : [
"p_redivivus_PRJNA186477"
],
- "trackId" : "p_redivivus_PRJNA186477_tandem_and_inverted_repeats",
- "description" : "Exact tandem and inverted repetitive elements.",
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/Tandem and Inverted Repeats/{refseq}/trackData.jsonz"
- }
- },
+ "description" : "Exact tandem and inverted repetitive elements.",
+ "trackId" : "p_redivivus_PRJNA186477_tandem_and_inverted_repeats",
"name" : "Tandem and Inverted Repeats"
},
{
+ "displays" : [
+ {
+ "displayId" : "B_malayi_proteins-p_redivivus_PRJNA186477-LinearBasicDisplay",
+ "renderer" : {
+ "showLabels" : false,
+ "height" : 4,
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
+ },
+ "mouseover" : "jexl:get(feature,'clone')",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/tracks/B. malayi proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
+ }
},
- "type" : "FeatureTrack",
- "name" : "B. malayi proteins",
- "description" : "Matches to WormBase B. malayi proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"category" : [
"Sequence Similarity",
"Proteins"
@@ -57891,213 +56797,217 @@
"assemblyNames" : [
"p_redivivus_PRJNA186477"
],
+ "type" : "FeatureTrack",
+ "description" : "Matches to WormBase B. malayi proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"trackId" : "p_redivivus_PRJNA186477_B_malayi_proteins",
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
- "renderer" : {
- "height" : 4,
- "color1" : "orange",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "displayId" : "B_malayi_proteins-p_redivivus_PRJNA186477-LinearBasicDisplay"
- }
- ]
+ "name" : "B. malayi proteins"
},
{
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
- "type" : "FeatureTrack",
"adapter" : {
"search" : "TTC.",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz.fai",
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
- "fastaLocation" : {
+ "faiLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz.fai"
},
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
- },
- "type" : "BgzipFastaAdapter"
- },
- "type" : "SequenceSearchAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz.gzi"
+ }
+ }
},
- "name" : "Cas12e TTCN PAM sites",
"displays" : [
{
- "displayId" : "TTCN_sequence_search_p_redivivus_PRJNA186477-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "TTCN_sequence_search_p_redivivus_PRJNA186477-LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "SlateBlue",
"showDescriptions" : false,
- "height" : 4
+ "height" : 4,
+ "showLabels" : false,
+ "color1" : "SlateBlue"
}
}
],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
+ "trackId" : "p_redivivus_PRJNA186477_TTCN_sequence_search",
+ "name" : "Cas12e TTCN PAM sites",
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
"assemblyNames" : [
"p_redivivus_PRJNA186477"
],
- "trackId" : "p_redivivus_PRJNA186477_TTCN_sequence_search"
+ "type" : "FeatureTrack",
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ]
},
{
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
- "type" : "FeatureTrack",
- "adapter" : {
- "sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
- "faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz.fai"
- },
- "fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz"
- },
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
- }
- },
- "search" : "TT.",
- "type" : "SequenceSearchAdapter"
- },
- "name" : "Cas12a TTN PAM sites",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 4,
"type" : "SvgFeatureRenderer",
"showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 4,
"color1" : "Indigo"
},
- "type" : "LinearBasicDisplay",
"displayId" : "TTN_sequence_search_p_redivivus_PRJNA186477-LinearBasicDisplay"
}
],
+ "adapter" : {
+ "sequenceAdapter" : {
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
+ },
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ }
+ },
+ "type" : "SequenceSearchAdapter",
+ "search" : "TT."
+ },
"assemblyNames" : [
"p_redivivus_PRJNA186477"
],
+ "type" : "FeatureTrack",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "trackId" : "p_redivivus_PRJNA186477_TTN_sequence_search"
+ "trackId" : "p_redivivus_PRJNA186477_TTN_sequence_search",
+ "name" : "Cas12a TTN PAM sites",
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time."
},
{
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
- "type" : "FeatureTrack",
"adapter" : {
+ "search" : "..G[AG][AG]T",
"type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
"faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz.fai"
},
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
}
- },
- "search" : "..G[AG][AG]T"
+ }
},
- "name" : "SaCas9 NNGRRT PAM sites",
"displays" : [
{
"displayId" : "NNGRRT_sequence_search_p_redivivus_PRJNA186477-LinearBasicDisplay",
"renderer" : {
+ "color1" : "DarkViolet",
"height" : 4,
"showDescriptions" : false,
- "color1" : "DarkViolet",
"showLabels" : false,
"type" : "SvgFeatureRenderer"
},
"type" : "LinearBasicDisplay"
}
],
+ "name" : "SaCas9 NNGRRT PAM sites",
+ "trackId" : "p_redivivus_PRJNA186477_NNGRRT_sequence_search",
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"p_redivivus_PRJNA186477"
],
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
- ],
- "trackId" : "p_redivivus_PRJNA186477_NNGRRT_sequence_search"
+ ]
},
{
- "adapter" : {
- "sequenceAdapter" : {
- "gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz.gzi"
- },
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
- },
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
- },
- "type" : "BgzipFastaAdapter"
- },
- "search" : ".GG",
- "type" : "SequenceSearchAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "SpCas9 NGG PAM sites",
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
- "assemblyNames" : [
- "p_redivivus_PRJNA186477"
- ],
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "trackId" : "p_redivivus_PRJNA186477_NGG_sequence_search",
- "displays" : [
- {
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "p_redivivus_PRJNA186477"
+ ],
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
+ "name" : "SpCas9 NGG PAM sites",
+ "trackId" : "p_redivivus_PRJNA186477_NGG_sequence_search",
+ "displays" : [
+ {
"displayId" : "NGG_sequence_search_p_redivivus_PRJNA186477-LinearBasicDisplay",
"renderer" : {
"color1" : "RebeccaPurple",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
"height" : 4,
- "showDescriptions" : false
+ "type" : "SvgFeatureRenderer"
},
"type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "SequenceSearchAdapter",
+ "sequenceAdapter" : {
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
+ },
+ "faiLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz.fai"
+ },
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ }
+ },
+ "search" : ".GG"
+ }
},
{
- "name" : "mRNAs/ncRNAs (best)",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/mRNAs_ncRNAs (best)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/mRNAs_ncRNAs (best)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
+ "displays" : [
+ {
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "jexl:startsWith(get(feature,'source'),'BLAT_mRNA_')==true?'yellow':'gray'",
+ "outline" : "black",
+ "height" : 6
+ },
+ "displayId" : "mrnas/ncrnas_(best)-s_ratti_PRJEB125-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"description" : "Native (same species) full length cDNAs and ncRNAs aligned to the genome using BLAT. This track shows the best unique location for each cDNA.",
"trackId" : "s_ratti_PRJEB125_mrnas/ncrnas_(best)",
+ "name" : "mRNAs/ncRNAs (best)",
"category" : [
"Genes",
"Supporting Evidence"
@@ -58105,173 +57015,169 @@
"assemblyNames" : [
"s_ratti_PRJEB125"
],
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "jexl:startsWith(get(feature,'source'),'BLAT_mRNA_')==true?'yellow':'gray'",
- "outline" : "black"
- },
- "displayId" : "mrnas/ncrnas_(best)-s_ratti_PRJEB125-LinearBasicDisplay"
- }
- ],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- }
+ "type" : "FeatureTrack"
},
{
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "s_ratti_PRJEB125"
+ ],
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
+ "name" : "Curated Genes (noncoding)",
+ "trackId" : "s_ratti_PRJEB125_curated_genes_noncoding",
+ "description" : "Non-coding curated gene models, including ncRNA, tRNA, miRNA, snRNA, snoRNA, piRNA, lincRNA and antisense RNA.",
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "gray",
"type" : "SvgFeatureRenderer",
+ "color1" : "gray",
"height" : 6
},
- "displayId" : "curated_genes_(noncoding)-s_ratti_PRJEB125-LinearBasicDisplay"
+ "displayId" : "curated_genes_(noncoding)-s_ratti_PRJEB125-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
- "trackId" : "s_ratti_PRJEB125_curated_genes_noncoding",
- "assemblyNames" : [
- "s_ratti_PRJEB125"
- ],
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "description" : "Non-coding curated gene models, including ncRNA, tRNA, miRNA, snRNA, snoRNA, piRNA, lincRNA and antisense RNA.",
- "name" : "Curated Genes (noncoding)",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Curated Genes (noncoding)/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack"
+ }
+ }
},
{
- "name" : "Trans-spliced acceptor",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Trans-spliced acceptor/{refseq}/trackData.jsonz"
- }
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "type" : "FeatureTrack",
- "description" : "This track contains SL1 and SL2 trans-spliced acceptors from a variety of sources: SL1 and SL2 trans-spliced acceptors published by Blumenthal et al, Nature (2002), Trans-Spliced Exon Coupled RNA End Determination (TEC-RED) Hwang et al, PNAS (2004), EST/mRNA sequence data, RNASeq read data from ENA. SL1 acceptors are show in red, SL2 in green. Direction of transcription is indicated by arrow direction.",
- "trackId" : "s_ratti_PRJEB125_trans-spliced_acceptor",
- "assemblyNames" : [
- "s_ratti_PRJEB125"
- ],
- "category" : [
- "Sequence Features",
- "Signals & Motifs"
- ],
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "jexl:get(feature,'source')=='SL1'?'red':get(feature,'source')=='SL2'?'green':'black'",
- "type" : "SvgFeatureRenderer",
"labels" : {
"description" : "jexl:get(feature,'source') || get(feature,'description')"
- }
+ },
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "trans-spliced_acceptor-s_ratti_PRJEB125-LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- }
- },
- {
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Curated_Genes/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Trans-spliced acceptor/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "name" : "Curated Genes",
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
- "category" : [
- "Genes",
- "Curated Genes"
- ],
"assemblyNames" : [
"s_ratti_PRJEB125"
],
- "trackId" : "s_ratti_PRJEB125_curated_genes",
+ "type" : "FeatureTrack",
+ "category" : [
+ "Sequence Features",
+ "Signals & Motifs"
+ ],
+ "trackId" : "s_ratti_PRJEB125_trans-spliced_acceptor",
+ "name" : "Trans-spliced acceptor",
+ "description" : "This track contains SL1 and SL2 trans-spliced acceptors from a variety of sources: SL1 and SL2 trans-spliced acceptors published by Blumenthal et al, Nature (2002), Trans-Spliced Exon Coupled RNA End Determination (TEC-RED) Hwang et al, PNAS (2004), EST/mRNA sequence data, RNASeq read data from ENA. SL1 acceptors are show in red, SL2 in green. Direction of transcription is indicated by arrow direction."
+ },
+ {
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Curated_Genes/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"formatDetails" : {
"feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
},
"displays" : [
{
"displayId" : "curated_genes-s_ratti_PRJEB125-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
+ "type" : "SvgFeatureRenderer",
"maxHeight" : 5000,
+ "color3" : "#965567",
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
},
- "type" : "SvgFeatureRenderer",
- "color3" : "#965567"
- }
+ "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'"
+ },
+ "type" : "LinearBasicDisplay"
}
- ]
- },
- {
- "name" : "Curated Genes (protein coding)",
+ ],
+ "name" : "Curated Genes",
+ "trackId" : "s_ratti_PRJEB125_curated_genes",
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
"type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
- "trackId" : "s_ratti_PRJEB125_curated_genes_protein_coding",
"assemblyNames" : [
"s_ratti_PRJEB125"
],
"category" : [
"Genes",
"Curated Genes"
- ],
+ ]
+ },
+ {
"displays" : [
{
"displayId" : "curated_genes_(protein_coding)-s_ratti_PRJEB125-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "maxHeight" : 5000,
"color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
- "color3" : "#965567"
+ "color3" : "#965567",
+ "maxHeight" : 5000,
+ "type" : "SvgFeatureRenderer"
},
"type" : "LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- }
+ },
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "s_ratti_PRJEB125"
+ ],
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
+ "name" : "Curated Genes (protein coding)",
+ "trackId" : "s_ratti_PRJEB125_curated_genes_protein_coding",
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track."
},
{
+ "description" : "This track shows the locations of the cosmids, fosmids, and YACs used for the physical mapping and sequencing of the C. elegans genome. The clone termini do not necessarily correspond to the termini of submitted GenBank/EMBL entries. In some cases the exact termini of the clones is not known. For example, YACs were sequenced using PCR amplification across gaps in the cosmid maps. When a clone end is not known, it is shown as an arrow extending to the end of the display. Such data is to be treated with caution. The Vancouver fosmids can be ordered directly from GeneService.",
+ "name" : "YACs, Fosmids, & Cosmids",
+ "trackId" : "s_ratti_PRJEB125_yacs_fosmids_cosmids",
"category" : [
"Reagents"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"s_ratti_PRJEB125"
],
- "trackId" : "s_ratti_PRJEB125_yacs_fosmids_cosmids",
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/YACs, Fosmids, & Cosmids/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
@@ -58279,23 +57185,13 @@
{
"displayId" : "yacs,_fosmids,_&_cosmids-s_ratti_PRJEB125-LinearBasicDisplay",
"renderer" : {
- "height" : 3,
"type" : "SvgFeatureRenderer",
+ "height" : 3,
"color1" : "black"
},
"type" : "LinearBasicDisplay"
}
- ],
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/YACs, Fosmids, & Cosmids/{refseq}/trackData.jsonz"
- }
- },
- "type" : "FeatureTrack",
- "name" : "YACs, Fosmids, & Cosmids",
- "description" : "This track shows the locations of the cosmids, fosmids, and YACs used for the physical mapping and sequencing of the C. elegans genome. The clone termini do not necessarily correspond to the termini of submitted GenBank/EMBL entries. In some cases the exact termini of the clones is not known. For example, YACs were sequenced using PCR amplification across gaps in the cosmid maps. When a clone end is not known, it is shown as an arrow extending to the end of the display. Such data is to be treated with caution. The Vancouver fosmids can be ordered directly from GeneService."
+ ]
},
{
"formatDetails" : {
@@ -58303,15 +57199,23 @@
},
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "protein_motifs-s_ratti_PRJEB125-LinearBasicDisplay",
"renderer" : {
- "height" : 7,
"color1" : "jexl:parent(feature)=='undefined'?'purple':get(parent(feature),'predictiontype')=='tmhmm'?'magenta':get(parent(feature),'predictiontype')=='seg'?'lightseagreen':get(parent(feature),'predictiontype')=='signalp'?'aquamarine':get(parent(feature),'predictiontype')=='ncoils'?'chartreuse':\nget(parent(feature),'predictiontype')=='pfam'?'lightsalmon':'purple'",
+ "height" : 7,
"type" : "SvgFeatureRenderer"
},
- "displayId" : "protein_motifs-s_ratti_PRJEB125-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Protein motifs/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
+ "type" : "FeatureTrack",
"assemblyNames" : [
"s_ratti_PRJEB125"
],
@@ -58319,78 +57223,58 @@
"Sequence Features",
"Translated Features"
],
+ "name" : "Protein motifs",
"trackId" : "s_ratti_PRJEB125_protein_motifs",
- "description" : "This track shows the extent of predicted protein motifs. Note these spans correspond to amino acid coordinates interpolated onto the physical map. Included are signal peptide (signalp), coiled coil (ncoils) and transmembrane (tmhmm) domains, regions of low complexity (seg), and Pfam annotated motif homologies.",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Protein motifs/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "name" : "Protein motifs"
+ "description" : "This track shows the extent of predicted protein motifs. Note these spans correspond to amino acid coordinates interpolated onto the physical map. Included are signal peptide (signalp), coiled coil (ncoils) and transmembrane (tmhmm) domains, regions of low complexity (seg), and Pfam annotated motif homologies."
},
{
- "description" : "Historical gene predictions.",
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
+ "assemblyNames" : [
+ "s_ratti_PRJEB125"
+ ],
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Gene Models (historical)/{refseq}/trackData.jsonz"
- }
- },
+ "description" : "Historical gene predictions.",
+ "trackId" : "s_ratti_PRJEB125_gene_models_(historical)",
"name" : "Gene Models (historical)",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
"type" : "SvgFeatureRenderer",
"labels" : {
"description" : "jexl:get(feature,'type')"
- }
+ },
+ "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'"
},
"displayId" : "gene_models_(historical)-s_ratti_PRJEB125-LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "s_ratti_PRJEB125"
- ],
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "trackId" : "s_ratti_PRJEB125_gene_models_(historical)"
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Gene Models (historical)/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
"trackId" : "s_ratti_PRJEB125_other_uniprot_proteins",
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
+ "name" : "Other UniProt proteins",
+ "description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"assemblyNames" : [
"s_ratti_PRJEB125"
],
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "orange",
- "showDescriptions" : false,
- "height" : 4
- },
- "displayId" : "other_uniprot_proteins-s_ratti_PRJEB125-LinearBasicDisplay"
- }
- ],
- "name" : "Other UniProt proteins",
"type" : "FeatureTrack",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -58398,33 +57282,45 @@
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Other UniProt proteins/{refseq}/trackData.jsonz"
}
},
- "description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation)."
- },
- {
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "jexl:get(feature,'source')=='RNASeq_R_asymmetry'?'red': get(feature,'source')=='RNASeq_F_asymmetry'?'green':'black'",
- "displayMode" : "collapse",
- "height" : 24
+ "height" : 4,
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "color1" : "orange"
},
- "mouseover" : "jexl:'Score: '+get(feature,'score')",
- "displayId" : "rnaseq_asymmetries-s_ratti_PRJEB125-LinearBasicDisplay"
+ "displayId" : "other_uniprot_proteins-s_ratti_PRJEB125-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ],
- "trackId" : "s_ratti_PRJEB125_rnaseq_asymmetries",
+ ]
+ },
+ {
"category" : [
"Expression"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"s_ratti_PRJEB125"
],
"description" : "Red boxes indicate regions where there are more than 2 times as many forward sense RNASeq reads aligned to the genome as reverse sense reads. This asymmetrical signal has been found empirically to be a sensitive marker for the ends of transcripts. Green boxes indicate regions where there are more than 2 times as many reverse sense RNASeq reads aligned to the genome as forward sense reads. This asymmetrical signal has been found empirically to be sensitive marker for the ends of transcripts. The height of all boxes indicates the relative score of the feature.",
"name" : "RNASeq Asymmetries",
- "type" : "FeatureTrack",
+ "trackId" : "s_ratti_PRJEB125_rnaseq_asymmetries",
+ "displays" : [
+ {
+ "renderer" : {
+ "displayMode" : "collapse",
+ "type" : "SvgFeatureRenderer",
+ "color1" : "jexl:get(feature,'source')=='RNASeq_R_asymmetry'?'red': get(feature,'source')=='RNASeq_F_asymmetry'?'green':'black'",
+ "height" : 24,
+ "showLabels" : false
+ },
+ "mouseover" : "jexl:'Score: '+get(feature,'score')",
+ "displayId" : "rnaseq_asymmetries-s_ratti_PRJEB125-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -58434,425 +57330,422 @@
}
},
{
- "name" : "C. elegans proteins",
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/C. elegans proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "trackId" : "s_ratti_PRJEB125_C_elegans_proteins",
"assemblyNames" : [
"s_ratti_PRJEB125"
],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
"displays" : [
{
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "orange",
- "height" : 4
+ "showLabels" : false,
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "C_elegans_proteins-s_ratti_PRJEB125-LinearBasicDisplay"
+ "displayId" : "C_elegans_proteins-s_ratti_PRJEB125-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ]
- },
- {
+ ],
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "name" : "C. elegans proteins",
"adapter" : {
"rootUrlTemplate" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Contig submissions/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/C. elegans proteins/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "name" : "Contig submissions",
+ "trackId" : "s_ratti_PRJEB125_C_elegans_proteins",
+ "description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ },
+ {
"description" : "This track shows the location and coordinates of contigs (mostly cosmids) submitted to GenBank/EMBL.",
+ "name" : "Contig submissions",
+ "trackId" : "s_ratti_PRJEB125_contig_submissions",
"category" : [
"Genome Structure",
"Assembly & Curation"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"s_ratti_PRJEB125"
],
- "trackId" : "s_ratti_PRJEB125_contig_submissions",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Contig submissions/{refseq}/trackData.jsonz"
+ }
+ },
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "contig_submissions-s_ratti_PRJEB125-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"color1" : "sienna",
"height" : 7
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "contig_submissions-s_ratti_PRJEB125-LinearBasicDisplay"
+ }
}
]
},
{
+ "assemblyNames" : [
+ "s_ratti_PRJEB125"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "assemblyNames" : [
- "s_ratti_PRJEB125"
- ],
"trackId" : "s_ratti_PRJEB125_S_ratti_proteins",
+ "name" : "S. ratti proteins",
+ "description" : "Matches to WormBase S. ratti proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "S_ratti_proteins-s_ratti_PRJEB125-LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
"color1" : "orange",
- "type" : "SvgFeatureRenderer",
+ "height" : 4,
"showLabels" : false,
- "height" : 4
- },
- "type" : "LinearBasicDisplay"
+ "type" : "SvgFeatureRenderer"
+ }
}
],
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/S. ratti proteins/{refseq}/trackData.jsonz"
- }
- },
- "type" : "FeatureTrack",
- "name" : "S. ratti proteins",
- "description" : "Matches to WormBase S. ratti proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/S. ratti proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
- "description" : "IsoSeq from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each IsoSeqsequence.",
+ "category" : [
+ "Sequence Similarity",
+ "Nucleotide"
+ ],
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Non-C. elegans Isoseq collection (best)/{refseq}/trackData.jsonz"
- }
- },
- "name" : "Non-C. elegans Isoseq collection (best)",
"displays" : [
{
+ "displayId" : "non-c._elegans_isoseq_collection_(best)-s_ratti_PRJEB125-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
+ "type" : "SvgFeatureRenderer",
"color1" : "green",
- "type" : "SvgFeatureRenderer"
+ "height" : 4
},
- "type" : "LinearBasicDisplay",
- "displayId" : "non-c._elegans_isoseq_collection_(best)-s_ratti_PRJEB125-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "category" : [
- "Sequence Similarity",
- "Nucleotide"
- ],
"assemblyNames" : [
"s_ratti_PRJEB125"
],
- "trackId" : "non-c._elegans_isoseq_collection_(best)-s_ratti_PRJEB125"
- },
- {
- "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "description" : "IsoSeq from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each IsoSeqsequence.",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/C. brenneri proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Non-C. elegans Isoseq collection (best)/{refseq}/trackData.jsonz"
+ }
},
- "type" : "FeatureTrack",
- "name" : "C. brenneri proteins",
+ "name" : "Non-C. elegans Isoseq collection (best)",
+ "trackId" : "non-c._elegans_isoseq_collection_(best)-s_ratti_PRJEB125"
+ },
+ {
+ "assemblyNames" : [
+ "s_ratti_PRJEB125"
+ ],
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "orange",
- "height" : 4
+ "height" : 4,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
"displayId" : "C_brenneri_proteins-s_ratti_PRJEB125-LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "s_ratti_PRJEB125"
- ],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "trackId" : "s_ratti_PRJEB125_C_brenneri_proteins"
+ "trackId" : "s_ratti_PRJEB125_C_brenneri_proteins",
+ "name" : "C. brenneri proteins",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/C. brenneri proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
+ "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
},
{
"description" : "Matches to WormBase B. malayi proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/B. malayi proteins/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/B. malayi proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
}
},
"name" : "B. malayi proteins",
+ "trackId" : "s_ratti_PRJEB125_B_malayi_proteins",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "s_ratti_PRJEB125"
+ ],
"displays" : [
{
+ "displayId" : "B_malayi_proteins-s_ratti_PRJEB125-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
"color1" : "orange",
+ "height" : 4,
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 4
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
- "displayId" : "B_malayi_proteins-s_ratti_PRJEB125-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "s_ratti_PRJEB125"
- ],
- "trackId" : "s_ratti_PRJEB125_B_malayi_proteins"
+ ]
},
{
"type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/RNASeq introns/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "name" : "RNASeq introns",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display.",
- "category" : [
- "Expression"
- ],
"assemblyNames" : [
"s_ratti_PRJEB125"
],
- "trackId" : "s_ratti_PRJEB125_rnaseq_introns",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)",
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "green"
+ "color1" : "green",
+ "height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)",
+ "showDescriptions" : false,
+ "showLabels" : false
},
"mouseover" : "jexl:get(feature,'score')+' reads'",
- "type" : "LinearBasicDisplay",
"displayId" : "rnaseq_introns-s_ratti_PRJEB125-LinearBasicDisplay"
}
- ]
- },
- {
- "displays" : [
- {
- "displayId" : "rnaseq_splice_junctions_(common)-s_ratti_PRJEB125-LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'score')+' reads'",
- "renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
- "showDescriptions" : false
- },
- "type" : "LinearBasicDisplay"
- }
- ],
- "trackId" : "s_ratti_PRJEB125_rnaseq_splice_junctions_(common)",
- "assemblyNames" : [
- "s_ratti_PRJEB125"
],
"category" : [
"Expression"
],
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
- "name" : "RNASeq Splice Junctions (common)",
+ "name" : "RNASeq introns",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/RNASeq Splice Junctions (common)/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/RNASeq introns/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack"
+ "trackId" : "s_ratti_PRJEB125_rnaseq_introns",
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display."
},
{
- "name" : "RNASeq Splice Junctions (rare)",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz"
- }
- },
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
- "trackId" : "s_ratti_PRJEB125_rnaseq_splice_junctions_(rare)",
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
+ "name" : "RNASeq Splice Junctions (common)",
+ "trackId" : "s_ratti_PRJEB125_rnaseq_splice_junctions_(common)",
"category" : [
"Expression"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"s_ratti_PRJEB125"
],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/RNASeq Splice Junctions (common)/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "rnaseq_splice_junctions_(common)-s_ratti_PRJEB125-LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'score')+' reads'",
"renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "maxHeight" : 5000,
"color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
"showDescriptions" : false,
- "height" : "jexl:4"
- },
- "displayId" : "rnaseq_splice_junctions_(rare)-s_ratti_PRJEB125-LinearBasicDisplay"
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
+ }
}
]
},
{
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/T. muris proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "name" : "T. muris proteins",
- "description" : "Matches to WormBase T. muris proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"assemblyNames" : [
"s_ratti_PRJEB125"
],
+ "type" : "FeatureTrack",
"category" : [
- "Sequence Similarity",
- "Proteins"
+ "Expression"
],
- "trackId" : "s_ratti_PRJEB125_T_muris_proteins",
+ "trackId" : "s_ratti_PRJEB125_rnaseq_splice_junctions_(rare)",
+ "name" : "RNASeq Splice Junctions (rare)",
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
"displays" : [
{
- "displayId" : "T_muris_proteins-s_ratti_PRJEB125-LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "rnaseq_splice_junctions_(rare)-s_ratti_PRJEB125-LinearBasicDisplay",
"renderer" : {
- "color1" : "orange",
- "showLabels" : false,
+ "maxHeight" : 5000,
"type" : "SvgFeatureRenderer",
- "height" : 4
+ "showDescriptions" : false,
+ "height" : "jexl:4",
+ "showLabels" : false,
+ "color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))"
},
+ "mouseover" : "jexl:get(feature,'score')+' reads'",
"type" : "LinearBasicDisplay"
}
- ]
- },
- {
- "description" : "These boxes indicate alignments of short read sequences from all available RNASeq projects. The number of reads has been normalised by averaging over the number of libraries. The height of all boxes indicates the relative score of the feature.",
- "type" : "FeatureTrack",
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/RNASeq/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz"
}
- },
- "name" : "RNASeq",
+ }
+ },
+ {
"displays" : [
{
- "displayId" : "rnaseq-s_ratti_PRJEB125-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
- "displayMode" : "collapse",
- "showDescriptions" : false,
- "height" : "jexl:get(feature,'score')>100?50:floor(get(feature,'score')/2)>4?floor(get(feature,'score')/2):4",
"type" : "SvgFeatureRenderer",
+ "color1" : "orange",
"showLabels" : false,
- "color1" : "black"
+ "height" : 4
},
- "mouseover" : "jexl:'Score: '+get(feature,'score')"
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "T_muris_proteins-s_ratti_PRJEB125-LinearBasicDisplay"
+ }
+ ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/T. muris proteins/{refseq}/trackData.jsonz"
}
+ },
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"s_ratti_PRJEB125"
],
+ "description" : "Matches to WormBase T. muris proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "T. muris proteins",
+ "trackId" : "s_ratti_PRJEB125_T_muris_proteins"
+ },
+ {
"category" : [
"Expression"
],
- "trackId" : "s_ratti_PRJEB125_rnaseq"
- },
- {
- "trackId" : "s_ratti_PRJEB125_P_pacificus_proteins",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"s_ratti_PRJEB125"
],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
+ "description" : "These boxes indicate alignments of short read sequences from all available RNASeq projects. The number of reads has been normalised by averaging over the number of libraries. The height of all boxes indicates the relative score of the feature.",
+ "name" : "RNASeq",
+ "trackId" : "s_ratti_PRJEB125_rnaseq",
"displays" : [
{
- "displayId" : "P_pacificus_proteins-s_ratti_PRJEB125-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "orange",
- "showLabels" : false,
+ "displayMode" : "collapse",
"type" : "SvgFeatureRenderer",
- "height" : 4
+ "color1" : "black",
+ "showDescriptions" : false,
+ "height" : "jexl:get(feature,'score')>100?50:floor(get(feature,'score')/2)>4?floor(get(feature,'score')/2):4",
+ "showLabels" : false
},
- "mouseover" : "jexl:get(feature,'clone')"
+ "mouseover" : "jexl:'Score: '+get(feature,'score')",
+ "displayId" : "rnaseq-s_ratti_PRJEB125-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "name" : "P. pacificus proteins",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/P. pacificus proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
- "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/RNASeq/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
- "description" : "Low-complexity regions identified by Dust.",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/P. pacificus proteins/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "name" : "Low complextity region (Dust)",
+ "name" : "P. pacificus proteins",
+ "trackId" : "s_ratti_PRJEB125_P_pacificus_proteins",
+ "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "s_ratti_PRJEB125"
+ ],
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "bisque",
- "showDescriptions" : false,
+ "color1" : "orange",
+ "showLabels" : false,
"height" : 4
},
- "displayId" : "low_complextity_region_(dust)-s_ratti_PRJEB125-LinearBasicDisplay"
+ "displayId" : "P_pacificus_proteins-s_ratti_PRJEB125-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ],
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ]
+ },
+ {
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "displayId" : "low_complextity_region_(dust)-s_ratti_PRJEB125-LinearBasicDisplay",
+ "renderer" : {
+ "height" : 4,
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "color1" : "bisque",
+ "type" : "SvgFeatureRenderer"
+ }
}
],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ },
"category" : [
"Genome Structure",
"Repeats"
@@ -58860,47 +57753,60 @@
"assemblyNames" : [
"s_ratti_PRJEB125"
],
- "trackId" : "s_ratti_PRJEB125_low_complextity_region_(dust)"
+ "type" : "FeatureTrack",
+ "description" : "Low-complexity regions identified by Dust.",
+ "trackId" : "s_ratti_PRJEB125_low_complextity_region_(dust)",
+ "name" : "Low complextity region (Dust)"
},
{
- "description" : "ESTs and mRNAs from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each cDNA sequence. mRNAs are shown in light blue; ESTs in green.",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/WormBase nematode mRNAs_ESTs (best)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
+ "assemblyNames" : [
+ "s_ratti_PRJEB125"
+ ],
"type" : "FeatureTrack",
+ "category" : [
+ "Sequence Similarity",
+ "Nucleotide"
+ ],
+ "trackId" : "wormbase_nematode_mrnas/ests_(best)-s_ratti_PRJEB125",
"name" : "WormBase nematode mRNAs/ESTs (best)",
+ "description" : "ESTs and mRNAs from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each cDNA sequence. mRNAs are shown in light blue; ESTs in green.",
"displays" : [
{
- "displayId" : "wormbase_nematode_mrnas/ests_(best)-s_ratti_PRJEB125-LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 4,
"color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA_BEST'?'lightblue':get(feature,'source')=='BLAT_Caen_EST_BEST'?'green':'black'",
- "type" : "SvgFeatureRenderer",
"labels" : {
"name" : "jexl:get(feature,'species') || get(feature,'id')"
}
},
+ "displayId" : "wormbase_nematode_mrnas/ests_(best)-s_ratti_PRJEB125-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "s_ratti_PRJEB125"
- ],
- "category" : [
- "Sequence Similarity",
- "Nucleotide"
- ],
- "trackId" : "wormbase_nematode_mrnas/ests_(best)-s_ratti_PRJEB125"
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/WormBase nematode mRNAs_ESTs (best)/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/ESTs (best)/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"displays" : [
{
- "displayId" : "ests-s_ratti_PRJEB125-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "ests-s_ratti_PRJEB125-LinearBasicDisplay",
"renderer" : {
"color1" : "jexl:parent(feature)=='undefined'?'red':get(parent(feature),'has_mate')==1?'limegreen':get(parent(feature),'has_mate')==2?'green':get(parent(feature),'has_mate')==0?'gold':'black'",
"maxHeight" : 5000,
@@ -58908,52 +57814,40 @@
}
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
+ "description" : "Native (same-species) Expressed Sequence Tags (ESTs), aligned to the genome using BLAT. This track shows the best unique location for each EST. The paired 5' and 3' ESTs from the same cDNA clone are connected by a dashed line and a colored light green. ESTs with no mate are yellow, and ESTs with a mate that is 'far away' are dark green.",
+ "name" : "ESTs",
"trackId" : "s_ratti_PRJEB125_ests",
"category" : [
"Genes",
"Supporting Evidence"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"s_ratti_PRJEB125"
- ],
- "description" : "Native (same-species) Expressed Sequence Tags (ESTs), aligned to the genome using BLAT. This track shows the best unique location for each EST. The paired 5' and 3' ESTs from the same cDNA clone are connected by a dashed line and a colored light green. ESTs with no mate are yellow, and ESTs with a mate that is 'far away' are dark green.",
- "name" : "ESTs",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/ESTs (best)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- }
+ ]
},
{
- "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "name" : "D. melanogaster proteins",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "orange",
- "type" : "SvgFeatureRenderer",
+ "height" : 4,
"showLabels" : false,
- "height" : 4
+ "type" : "SvgFeatureRenderer"
},
"mouseover" : "jexl:get(feature,'clone')",
"displayId" : "D_melanogaster_proteins-s_ratti_PRJEB125-LinearBasicDisplay"
}
],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz"
+ }
+ },
+ "type" : "FeatureTrack",
"assemblyNames" : [
"s_ratti_PRJEB125"
],
@@ -58961,77 +57855,79 @@
"Sequence Similarity",
"Proteins"
],
- "trackId" : "s_ratti_PRJEB125_D_melanogaster_proteins"
+ "name" : "D. melanogaster proteins",
+ "trackId" : "s_ratti_PRJEB125_D_melanogaster_proteins",
+ "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
},
{
"displays" : [
{
- "displayId" : "H_sapiens_proteins-s_ratti_PRJEB125-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
"height" : 4,
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "orange"
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "H_sapiens_proteins-s_ratti_PRJEB125-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
- "trackId" : "s_ratti_PRJEB125_H_sapiens_proteins",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/H. sapiens proteins/{refseq}/trackData.jsonz"
+ }
+ },
"assemblyNames" : [
"s_ratti_PRJEB125"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "s_ratti_PRJEB125_H_sapiens_proteins",
"name" : "H. sapiens proteins",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/H. sapiens proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- }
+ "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
},
{
- "name" : "Nanopore matches",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Nanopore matches/{refseq}/trackData.jsonz"
- }
- },
"type" : "FeatureTrack",
- "description" : "This Nanopore transcript data is from the paper 'The full-length transcriptome of C. elegans using direct RNA sequencing' Roach et al. https://doi.org/10.1101/598763. Where several transcripts are nearly identical, they are represented by a single transcript and the number of transcripts is recorded in the read coverage. Sequencing is from 3' to 5' and randomly terminates, so the 5' end of transcripts is often incomplete.",
- "trackId" : "s_ratti_PRJEB125_nanopore_matches",
"assemblyNames" : [
"s_ratti_PRJEB125"
],
- "category" : [
- "Genes",
- "Supporting Evidence"
- ],
"displays" : [
{
+ "displayId" : "nanopore_matches-s_ratti_PRJEB125-LinearBasicDisplay",
"renderer" : {
+ "showLabels" : false,
"height" : 4,
+ "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA'?'lightblue':'green'",
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "maxHeight" : 5000,
- "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA'?'lightblue':'green'"
+ "maxHeight" : 5000
},
- "type" : "LinearBasicDisplay",
- "displayId" : "nanopore_matches-s_ratti_PRJEB125-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "category" : [
+ "Genes",
+ "Supporting Evidence"
+ ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Nanopore matches/{refseq}/trackData.jsonz"
+ }
+ },
+ "name" : "Nanopore matches",
+ "trackId" : "s_ratti_PRJEB125_nanopore_matches",
+ "description" : "This Nanopore transcript data is from the paper 'The full-length transcriptome of C. elegans using direct RNA sequencing' Roach et al. https://doi.org/10.1101/598763. Where several transcripts are nearly identical, they are represented by a single transcript and the number of transcripts is recorded in the read coverage. Sequencing is from 3' to 5' and randomly terminates, so the 5' end of transcripts is often incomplete."
},
{
+ "trackId" : "s_ratti_PRJEB125_O_volvulus_proteins",
"name" : "O. volvulus proteins",
- "type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -59040,138 +57936,139 @@
}
},
"description" : "Matches to WormBase O. volvulus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "trackId" : "s_ratti_PRJEB125_O_volvulus_proteins",
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "s_ratti_PRJEB125"
- ],
"displays" : [
{
- "displayId" : "O_volvulus_proteins-s_ratti_PRJEB125-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "showLabels" : false,
+ "height" : 4,
+ "color1" : "orange"
},
"mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "O_volvulus_proteins-s_ratti_PRJEB125-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
+ ],
+ "assemblyNames" : [
+ "s_ratti_PRJEB125"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
]
},
{
- "name" : "Repeat Region (RepeatMasker)",
+ "description" : "Repetitive regions identified by RepeatMasker.",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "description" : "Repetitive regions identified by RepeatMasker.",
+ "name" : "Repeat Region (RepeatMasker)",
"trackId" : "s_ratti_PRJEB125_repeat_region_(repeatmasker)",
"category" : [
"Genome Structure",
"Repeats"
],
- "assemblyNames" : [
- "s_ratti_PRJEB125"
- ],
+ "type" : "FeatureTrack",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "repeat_region_(repeatmasker)-s_ratti_PRJEB125-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "showDescriptions" : false,
"color1" : "bisque",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false
- },
- "type" : "LinearBasicDisplay"
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "height" : 4,
+ "type" : "SvgFeatureRenderer"
+ }
}
+ ],
+ "assemblyNames" : [
+ "s_ratti_PRJEB125"
]
},
{
- "name" : "C. remanei proteins",
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/C. remanei proteins/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/C. remanei proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showLabels" : false,
+ "height" : 4,
+ "color1" : "orange"
+ },
+ "displayId" : "C_remanei_proteins-s_ratti_PRJEB125-LinearBasicDisplay"
+ }
+ ],
"description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "C. remanei proteins",
"trackId" : "s_ratti_PRJEB125_C_remanei_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"s_ratti_PRJEB125"
- ],
- "displays" : [
- {
- "displayId" : "C_remanei_proteins-s_ratti_PRJEB125-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "orange",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "height" : 4
- },
- "mouseover" : "jexl:get(feature,'clone')"
- }
]
},
{
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/C. briggsae proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "C. briggsae proteins",
- "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "assemblyNames" : [
- "s_ratti_PRJEB125"
- ],
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "assemblyNames" : [
+ "s_ratti_PRJEB125"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"trackId" : "s_ratti_PRJEB125_C_briggsae_proteins",
+ "name" : "C. briggsae proteins",
"displays" : [
{
- "displayId" : "C_briggsae_proteins-s_ratti_PRJEB125-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
"color1" : "orange",
- "type" : "SvgFeatureRenderer",
+ "height" : 4,
"showLabels" : false,
- "height" : 4
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "C_briggsae_proteins-s_ratti_PRJEB125-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/C. briggsae proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ }
},
{
+ "category" : [
+ "Genome Structure",
+ "Assembly & Curation"
+ ],
+ "assemblyNames" : [
+ "s_ratti_PRJEB125"
+ ],
+ "type" : "FeatureTrack",
"description" : "This track shows the location and coordinates of contigs created during the assembly of the C. elegans genome.",
+ "trackId" : "s_ratti_PRJEB125_links_and_superlinks",
"name" : "Links and Superlinks",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Links and Superlinks/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
"displays" : [
{
"renderer" : {
@@ -59179,24 +58076,33 @@
"color1" : "black",
"height" : 4
},
- "type" : "LinearBasicDisplay",
- "displayId" : "links_and_superlinks-s_ratti_PRJEB125-LinearBasicDisplay"
+ "displayId" : "links_and_superlinks-s_ratti_PRJEB125-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "trackId" : "s_ratti_PRJEB125_links_and_superlinks",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Links and Superlinks/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ }
+ },
+ {
+ "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "S. cerevisiae proteins",
+ "trackId" : "s_ratti_PRJEB125_S_cerevisiae_proteins",
"category" : [
- "Genome Structure",
- "Assembly & Curation"
+ "Sequence Similarity",
+ "Proteins"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"s_ratti_PRJEB125"
- ]
- },
- {
- "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -59204,73 +58110,76 @@
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz"
}
},
- "type" : "FeatureTrack",
- "name" : "S. cerevisiae proteins",
"displays" : [
{
"displayId" : "S_cerevisiae_proteins-s_ratti_PRJEB125-LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
- "color1" : "orange",
- "height" : 4
+ "height" : 4,
+ "showLabels" : false,
+ "color1" : "orange"
},
"mouseover" : "jexl:get(feature,'clone')",
"type" : "LinearBasicDisplay"
}
+ ]
+ },
+ {
+ "category" : [
+ "Genome Structure",
+ "Repeats"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"s_ratti_PRJEB125"
],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "trackId" : "s_ratti_PRJEB125_S_cerevisiae_proteins"
- },
- {
"description" : "Exact tandem and inverted repetitive elements.",
"name" : "Tandem and Inverted Repeats",
- "type" : "FeatureTrack",
+ "trackId" : "s_ratti_PRJEB125_tandem_and_inverted_repeats",
+ "displays" : [
+ {
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "showLabels" : false,
+ "showDescriptions" : false,
+ "color1" : "bisque"
+ },
+ "displayId" : "tandem_and_inverted_repeats-s_ratti_PRJEB125-LinearBasicDisplay"
+ }
+ ],
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Tandem and Inverted Repeats/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Tandem and Inverted Repeats/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
- },
+ }
+ },
+ {
"displays" : [
{
- "displayId" : "tandem_and_inverted_repeats-s_ratti_PRJEB125-LinearBasicDisplay",
+ "displayId" : "genbank_submissions-s_ratti_PRJEB125-LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "bisque"
+ "color1" : "sienna",
+ "height" : 4
},
+ "mouseover" : "jexl:get(feature,'genbank')",
"type" : "LinearBasicDisplay"
}
],
- "trackId" : "s_ratti_PRJEB125_tandem_and_inverted_repeats",
- "category" : [
- "Genome Structure",
- "Repeats"
- ],
- "assemblyNames" : [
- "s_ratti_PRJEB125"
- ]
- },
- {
- "type" : "FeatureTrack",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Genbank submissions/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/Genbank submissions/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
},
- "name" : "Genbank submissions",
- "description" : "The C. elegans genome was submitted to the GenBank and EMBL databases in in the form of a set of minimally-overlapping segments. This track shows the position of these accessioned entries.",
+ "type" : "FeatureTrack",
"assemblyNames" : [
"s_ratti_PRJEB125"
],
@@ -59278,111 +58187,76 @@
"Genome Structure",
"Assembly & Curation"
],
+ "name" : "Genbank submissions",
"trackId" : "s_ratti_PRJEB125_genbank_submissions",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "color1" : "sienna",
- "height" : 4
- },
- "mouseover" : "jexl:get(feature,'genbank')",
- "displayId" : "genbank_submissions-s_ratti_PRJEB125-LinearBasicDisplay"
- }
- ]
+ "description" : "The C. elegans genome was submitted to the GenBank and EMBL databases in in the form of a set of minimally-overlapping segments. This track shows the position of these accessioned entries."
},
{
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/C. japonica proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
"type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "orange",
+ "showLabels" : false,
"height" : 4
},
+ "mouseover" : "jexl:get(feature,'clone')",
"displayId" : "C_japonica_proteins-s_ratti_PRJEB125-LinearBasicDisplay"
}
],
+ "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "C. japonica proteins",
"trackId" : "s_ratti_PRJEB125_C_japonica_proteins",
- "assemblyNames" : [
- "s_ratti_PRJEB125"
- ],
"category" : [
"Sequence Similarity",
"Proteins"
],
- "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "C. japonica proteins",
"type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/C. japonica proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- }
- },
- {
"assemblyNames" : [
"s_ratti_PRJEB125"
- ],
- "trackId" : "s_ratti_PRJEB125_community_annotation",
+ ]
+ },
+ {
+ "adapter" : {
+ "type" : "Gff3Adapter",
+ "gffLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://raw.githubusercontent.com/HallemLab/Parasite_Genome_Annotations/main/GFF3s/strongyloides_ratti.PRJEB125.community.annotations.edit_log.gff3"
+ }
+ },
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "s_ratti_PRJEB125_community_annotation-LinearBasicDisplay",
"renderer" : {
"color3" : "#965567",
- "color1" : "jexl:get(feature,'strand')>0?'darkviolet':'darkturquoise'",
- "type" : "SvgFeatureRenderer"
+ "type" : "SvgFeatureRenderer",
+ "color1" : "jexl:get(feature,'strand')>0?'darkviolet':'darkturquoise'"
},
- "displayId" : "s_ratti_PRJEB125_community_annotation-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
},
{
"type" : "LinearArcDisplay",
"displayId" : "s_ratti_PRJEB125_community_annotation-LinearArcDisplay"
}
],
+ "name" : "Community Annotation",
+ "trackId" : "s_ratti_PRJEB125_community_annotation",
"type" : "FeatureTrack",
- "adapter" : {
- "gffLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://raw.githubusercontent.com/HallemLab/Parasite_Genome_Annotations/main/GFF3s/strongyloides_ratti.PRJEB125.community.annotations.edit_log.gff3"
- },
- "type" : "Gff3Adapter"
- },
- "name" : "Community Annotation"
- },
- {
- "trackId" : "s_ratti_PRJEB125_TTCN_sequence_search",
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
"assemblyNames" : [
"s_ratti_PRJEB125"
- ],
- "displays" : [
- {
- "displayId" : "TTCN_sequence_search_s_ratti_PRJEB125-LinearBasicDisplay",
- "renderer" : {
- "height" : 4,
- "showDescriptions" : false,
- "color1" : "SlateBlue",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay"
- }
- ],
- "name" : "Cas12e TTCN PAM sites",
- "type" : "FeatureTrack",
+ ]
+ },
+ {
"adapter" : {
+ "search" : "TTC.",
"sequenceAdapter" : {
"faiLocation" : {
"locationType" : "UriLocation",
@@ -59393,393 +58267,314 @@
"locationType" : "UriLocation"
},
"gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/s_ratti.PRJEB125.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/s_ratti.PRJEB125.WS284.genomic.fa.gz.gzi"
},
"type" : "BgzipFastaAdapter"
},
- "search" : "TTC.",
"type" : "SequenceSearchAdapter"
},
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time."
- },
- {
- "trackId" : "s_ratti_PRJEB125_TTN_sequence_search",
- "assemblyNames" : [
- "s_ratti_PRJEB125"
- ],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
"displays" : [
{
- "displayId" : "TTN_sequence_search_s_ratti_PRJEB125-LinearBasicDisplay",
+ "displayId" : "TTCN_sequence_search_s_ratti_PRJEB125-LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
+ "color1" : "SlateBlue",
"showDescriptions" : false,
"height" : 4,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "Indigo"
+ "showLabels" : false
},
"type" : "LinearBasicDisplay"
}
],
- "name" : "Cas12a TTN PAM sites",
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
+ "name" : "Cas12e TTCN PAM sites",
+ "trackId" : "s_ratti_PRJEB125_TTCN_sequence_search",
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "s_ratti_PRJEB125"
+ ]
+ },
+ {
"adapter" : {
+ "search" : "TT.",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
"fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/s_ratti.PRJEB125.WS284.genomic.fa.gz"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/s_ratti.PRJEB125.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
},
"faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/s_ratti.PRJEB125.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/s_ratti.PRJEB125.WS284.genomic.fa.gz.fai"
},
"gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/s_ratti.PRJEB125.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/s_ratti.PRJEB125.WS284.genomic.fa.gz.gzi"
},
"type" : "BgzipFastaAdapter"
- },
- "search" : "TT.",
- "type" : "SequenceSearchAdapter"
+ }
},
+ "displays" : [
+ {
+ "displayId" : "TTN_sequence_search_s_ratti_PRJEB125-LinearBasicDisplay",
+ "renderer" : {
+ "color1" : "Indigo",
+ "height" : 4,
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
+ },
+ "type" : "LinearBasicDisplay"
+ }
+ ],
+ "name" : "Cas12a TTN PAM sites",
+ "trackId" : "s_ratti_PRJEB125_TTN_sequence_search",
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
"type" : "FeatureTrack",
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time."
+ "assemblyNames" : [
+ "s_ratti_PRJEB125"
+ ],
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ]
},
{
- "type" : "FeatureTrack",
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
+ "name" : "SaCas9 NNGRRT PAM sites",
"adapter" : {
"type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
"fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/s_ratti.PRJEB125.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/s_ratti.PRJEB125.WS284.genomic.fa.gz"
},
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/s_ratti.PRJEB125.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
"gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/s_ratti.PRJEB125.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/s_ratti.PRJEB125.WS284.genomic.fa.gz.gzi"
},
"type" : "BgzipFastaAdapter"
},
"search" : "..G[AG][AG]T"
},
- "name" : "SaCas9 NNGRRT PAM sites",
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
+ "trackId" : "s_ratti_PRJEB125_NNGRRT_sequence_search",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"s_ratti_PRJEB125"
],
- "trackId" : "s_ratti_PRJEB125_NNGRRT_sequence_search",
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "color1" : "DarkViolet",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
+ "showDescriptions" : false,
"height" : 4,
- "showDescriptions" : false
+ "color1" : "DarkViolet",
+ "type" : "SvgFeatureRenderer"
},
"displayId" : "NNGRRT_sequence_search_s_ratti_PRJEB125-LinearBasicDisplay"
}
]
},
{
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
- "assemblyNames" : [
- "s_ratti_PRJEB125"
- ],
- "trackId" : "s_ratti_PRJEB125_NGG_sequence_search",
"displays" : [
{
- "displayId" : "NGG_sequence_search_s_ratti_PRJEB125-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
"color1" : "RebeccaPurple",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
"height" : 4,
- "showDescriptions" : false
+ "showDescriptions" : false,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay"
+ "displayId" : "NGG_sequence_search_s_ratti_PRJEB125-LinearBasicDisplay"
}
],
"adapter" : {
"type" : "SequenceSearchAdapter",
- "search" : ".GG",
"sequenceAdapter" : {
- "faiLocation" : {
+ "gziLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/s_ratti.PRJEB125.WS284.genomic.fa.gz.fai"
- },
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/s_ratti.PRJEB125.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/s_ratti.PRJEB125.WS284.genomic.fa.gz.gzi"
},
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/s_ratti.PRJEB125.WS284.genomic.fa.gz.gzi",
+ "type" : "BgzipFastaAdapter",
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/s_ratti.PRJEB125.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
- "type" : "BgzipFastaAdapter"
- }
+ "fastaLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/s_ratti.PRJEB125.WS284.genomic.fa.gz"
+ }
+ },
+ "search" : ".GG"
},
"type" : "FeatureTrack",
+ "assemblyNames" : [
+ "s_ratti_PRJEB125"
+ ],
+ "category" : [
+ "Externally Sourced Resources",
+ "CRISPR predictions"
+ ],
"name" : "SpCas9 NGG PAM sites",
+ "trackId" : "s_ratti_PRJEB125_NGG_sequence_search",
"description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time."
},
{
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display.",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/RNASeq introns/{refseq}/trackData.jsonz"
- }
- },
"type" : "FeatureTrack",
- "name" : "RNASeq introns",
- "displays" : [
- {
- "mouseover" : "jexl:get(feature,'score')+' reads'",
- "renderer" : {
- "color1" : "green",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)",
- "showDescriptions" : false
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "rnaseq_introns-s_ratti_PRJEB125-LinearBasicDisplay"
- }
- ],
"assemblyNames" : [
- "s_ratti_PRJEB125"
+ "t_muris_PRJEB126"
],
"category" : [
- "Expression"
+ "Genes",
+ "Curated Genes"
],
- "trackId" : "s_ratti_PRJEB125_rnaseq_introns"
- },
- {
+ "name" : "Curated Genes (protein coding)",
+ "trackId" : "t_muris_PRJEB126_curated_genes_protein_coding",
+ "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
"displays" : [
{
- "displayId" : "rnaseq_splice_junctions_(common)-s_ratti_PRJEB125-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
+ "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
"type" : "SvgFeatureRenderer",
- "color1" : "jexl:get(feature,'score')>1000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/1000))))+'00'+hex(round(255-(140*(get(feature,'score')/1000)))):'#00'+hex(round(255-(140*(get(feature,'score')/1000))))+hex(round(255-(140*(get(feature,'score')/1000))))",
- "showDescriptions" : false
+ "maxHeight" : 5000,
+ "color3" : "#965567"
},
- "mouseover" : "jexl:get(feature,'score')+' reads'",
- "type" : "LinearBasicDisplay"
+ "displayId" : "curated_genes_(protein_coding)-t_muris_PRJEB126-LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "s_ratti_PRJEB125"
- ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz"
+ }
+ }
+ },
+ {
+ "description" : "Native (same species) full length cDNAs and ncRNAs aligned to the genome using BLAT. This track shows the best unique location for each cDNA.",
+ "trackId" : "t_muris_PRJEB126_mrnas/ncrnas_(best)",
+ "name" : "mRNAs/ncRNAs (best)",
"category" : [
- "Expression"
+ "Genes",
+ "Supporting Evidence"
+ ],
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
],
- "trackId" : "s_ratti_PRJEB125_rnaseq_splice_junctions_(common)",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
"type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/RNASeq Splice Junctions (common)/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/mRNAs_ncRNAs (best)/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "name" : "RNASeq Splice Junctions (common)"
- },
- {
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "mrnas/ncrnas_(best)-t_muris_PRJEB126-LinearBasicDisplay",
"renderer" : {
- "height" : "jexl:4",
"type" : "SvgFeatureRenderer",
- "showDescriptions" : false,
- "maxHeight" : 5000,
- "color1" : "jexl:get(feature,'score')>1000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/1000))))+'00'+hex(round(255-(140*(get(feature,'score')/1000)))):'#00'+hex(round(255-(140*(get(feature,'score')/1000))))+hex(round(255-(140*(get(feature,'score')/1000))))",
- "showLabels" : false
+ "color1" : "jexl:startsWith(get(feature,'source'),'BLAT_mRNA_')==true?'yellow':'gray'",
+ "outline" : "black",
+ "height" : 6
},
- "mouseover" : "jexl:get(feature,'score')+' reads'",
- "displayId" : "rnaseq_splice_junctions_(rare)-s_ratti_PRJEB125-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "category" : [
- "Expression"
- ],
- "assemblyNames" : [
- "s_ratti_PRJEB125"
- ],
- "trackId" : "s_ratti_PRJEB125_rnaseq_splice_junctions_(rare)",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "name" : "RNASeq Splice Junctions (rare)"
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ }
},
{
- "type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/Curated Genes (protein coding)/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/Gene Models (historical)/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "name" : "Curated Genes (protein coding)",
- "description" : "A subset of the full Curated Genes set limited to protein-coding genes only. Only the CDS is represented. Full models (with UTRs) can be seen on the 'Curated Genes' track.",
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ],
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "trackId" : "t_muris_PRJEB126_curated_genes_protein_coding",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "gene_models_(historical)-t_muris_PRJEB126-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
- "maxHeight" : 5000,
- "color3" : "#965567"
+ "labels" : {
+ "description" : "jexl:get(feature,'type')"
+ }
},
- "displayId" : "curated_genes_(protein_coding)-t_muris_PRJEB126-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
- ]
- },
- {
- "trackId" : "t_muris_PRJEB126_mrnas/ncrnas_(best)",
+ ],
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
+ },
+ "trackId" : "t_muris_PRJEB126_gene_models_(historical)",
+ "name" : "Gene Models (historical)",
+ "description" : "Historical gene predictions.",
"assemblyNames" : [
"t_muris_PRJEB126"
],
+ "type" : "FeatureTrack",
"category" : [
"Genes",
- "Supporting Evidence"
- ],
+ "Curated Genes"
+ ]
+ },
+ {
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
+ },
"displays" : [
{
- "displayId" : "mrnas/ncrnas_(best)-t_muris_PRJEB126-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
+ "displayId" : "protein_motifs-t_muris_PRJEB126-LinearBasicDisplay",
"renderer" : {
- "height" : 6,
- "outline" : "black",
- "color1" : "jexl:startsWith(get(feature,'source'),'BLAT_mRNA_')==true?'yellow':'gray'",
+ "color1" : "jexl:parent(feature)=='undefined'?'purple':get(parent(feature),'predictiontype')=='tmhmm'?'magenta':get(parent(feature),'predictiontype')=='seg'?'lightseagreen':get(parent(feature),'predictiontype')=='signalp'?'aquamarine':get(parent(feature),'predictiontype')=='ncoils'?'chartreuse':\nget(parent(feature),'predictiontype')=='pfam'?'lightsalmon':'purple'",
+ "height" : 7,
"type" : "SvgFeatureRenderer"
- }
+ },
+ "type" : "LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
- "name" : "mRNAs/ncRNAs (best)",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/mRNAs_ncRNAs (best)/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/Protein motifs/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
+ }
},
"type" : "FeatureTrack",
- "description" : "Native (same species) full length cDNAs and ncRNAs aligned to the genome using BLAT. This track shows the best unique location for each cDNA."
- },
- {
- "trackId" : "t_muris_PRJEB126_gene_models_(historical)",
"assemblyNames" : [
"t_muris_PRJEB126"
],
"category" : [
- "Genes",
- "Curated Genes"
+ "Sequence Features",
+ "Translated Features"
],
- "displays" : [
- {
- "renderer" : {
- "color1" : "jexl:get(feature,'strand')>0?'violet':'turquoise'",
- "labels" : {
- "description" : "jexl:get(feature,'type')"
- },
- "type" : "SvgFeatureRenderer"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "gene_models_(historical)-t_muris_PRJEB126-LinearBasicDisplay"
- }
- ],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
- "name" : "Gene Models (historical)",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/Gene Models (historical)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "description" : "Historical gene predictions."
- },
- {
- "description" : "This track shows the extent of predicted protein motifs. Note these spans correspond to amino acid coordinates interpolated onto the physical map. Included are signal peptide (signalp), coiled coil (ncoils) and transmembrane (tmhmm) domains, regions of low complexity (seg), and Pfam annotated motif homologies.",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/Protein motifs/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
"name" : "Protein motifs",
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- },
- "displays" : [
- {
- "displayId" : "protein_motifs-t_muris_PRJEB126-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "color1" : "jexl:parent(feature)=='undefined'?'purple':get(parent(feature),'predictiontype')=='tmhmm'?'magenta':get(parent(feature),'predictiontype')=='seg'?'lightseagreen':get(parent(feature),'predictiontype')=='signalp'?'aquamarine':get(parent(feature),'predictiontype')=='ncoils'?'chartreuse':\nget(parent(feature),'predictiontype')=='pfam'?'lightsalmon':'purple'",
- "type" : "SvgFeatureRenderer",
- "height" : 7
- }
- }
- ],
- "category" : [
- "Sequence Features",
- "Translated Features"
- ],
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ],
- "trackId" : "t_muris_PRJEB126_protein_motifs"
+ "trackId" : "t_muris_PRJEB126_protein_motifs",
+ "description" : "This track shows the extent of predicted protein motifs. Note these spans correspond to amino acid coordinates interpolated onto the physical map. Included are signal peptide (signalp), coiled coil (ncoils) and transmembrane (tmhmm) domains, regions of low complexity (seg), and Pfam annotated motif homologies."
},
{
- "description" : "This track shows the locations of the cosmids, fosmids, and YACs used for the physical mapping and sequencing of the C. elegans genome. The clone termini do not necessarily correspond to the termini of submitted GenBank/EMBL entries. In some cases the exact termini of the clones is not known. For example, YACs were sequenced using PCR amplification across gaps in the cosmid maps. When a clone end is not known, it is shown as an arrow extending to the end of the display. Such data is to be treated with caution. The Vancouver fosmids can be ordered directly from GeneService.",
- "name" : "YACs, Fosmids, & Cosmids",
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -59787,48 +58582,71 @@
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/YACs, Fosmids, & Cosmids/{refseq}/trackData.jsonz"
}
},
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "yacs,_fosmids,_&_cosmids-t_muris_PRJEB126-LinearBasicDisplay",
"renderer" : {
- "height" : 3,
+ "type" : "SvgFeatureRenderer",
"color1" : "black",
- "type" : "SvgFeatureRenderer"
+ "height" : 3
},
+ "displayId" : "yacs,_fosmids,_&_cosmids-t_muris_PRJEB126-LinearBasicDisplay",
"type" : "LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
+ "description" : "This track shows the locations of the cosmids, fosmids, and YACs used for the physical mapping and sequencing of the C. elegans genome. The clone termini do not necessarily correspond to the termini of submitted GenBank/EMBL entries. In some cases the exact termini of the clones is not known. For example, YACs were sequenced using PCR amplification across gaps in the cosmid maps. When a clone end is not known, it is shown as an arrow extending to the end of the display. Such data is to be treated with caution. The Vancouver fosmids can be ordered directly from GeneService.",
"trackId" : "t_muris_PRJEB126_yacs_fosmids_cosmids",
+ "name" : "YACs, Fosmids, & Cosmids",
"category" : [
"Reagents"
],
"assemblyNames" : [
"t_muris_PRJEB126"
- ]
+ ],
+ "type" : "FeatureTrack"
},
{
+ "trackId" : "t_muris_PRJEB126_curated_genes",
+ "name" : "Curated Genes",
+ "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Genes",
+ "Curated Genes"
+ ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/Curated_Genes/{refseq}/trackData.jsonz"
+ }
+ },
"formatDetails" : {
"feature" : "jexl:{ curie:null,Alliance:feature.curie?''+feature.curie+'':null,JBrowse1: ''+feature.name+'', WormBase: feature.source=='WormBase'?'Gene Page':''}"
},
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "curated_genes-t_muris_PRJEB126-LinearBasicDisplay",
"renderer" : {
- "type" : "SvgFeatureRenderer",
+ "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
"labels" : {
"name" : "jexl:get(feature,'locus') || get(feature,'sequence_name')"
},
- "color1" : "jexl:get(feature,'type')!='CDS'?'gray':get(feature,'strand')>0?'violet':'turquoise'",
+ "type" : "SvgFeatureRenderer",
"maxHeight" : 5000,
"color3" : "#965567"
- },
- "displayId" : "curated_genes-t_muris_PRJEB126-LinearBasicDisplay"
+ }
}
- ],
+ ]
+ },
+ {
+ "type" : "FeatureTrack",
"assemblyNames" : [
"t_muris_PRJEB126"
],
@@ -59836,67 +58654,53 @@
"Genes",
"Curated Genes"
],
- "trackId" : "t_muris_PRJEB126_curated_genes",
- "description" : "Protein-coding gene structures result from the integration of a variety of prediction methods and data sources followed by manual review and revison by WormBase curators. tRNAs are predicted by tRNAscan, and other non-coding RNA transcripts are taken from a variety of literature sources. The purple and blue colors indicate transcripts on the forward and reverse strands respectively. Dark purple areas represent 5' and 3' UTRs of protein-coding transcripts, assigned automatically using the extents of overlapping ESTs and full-length cDNAs. The UTR predictions have not been reviewed by WormBase curators, and some are known to contain artifacts. Grey transcripts represent either non-coding transcripts of protein coding genes or transcripts of non-coding genes.",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/Curated_Genes/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "name" : "Curated Genes"
- },
- {
- "description" : "Non-coding curated gene models, including ncRNA, tRNA, miRNA, snRNA, snoRNA, piRNA, lincRNA and antisense RNA.",
"name" : "Curated Genes (noncoding)",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/Curated Genes (noncoding)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
+ "trackId" : "t_muris_PRJEB126_curated_genes_noncoding",
+ "description" : "Non-coding curated gene models, including ncRNA, tRNA, miRNA, snRNA, snoRNA, piRNA, lincRNA and antisense RNA.",
+ "formatDetails" : {
+ "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
},
"displays" : [
{
+ "displayId" : "curated_genes_(noncoding)-t_muris_PRJEB126-LinearBasicDisplay",
"renderer" : {
"height" : 6,
- "type" : "SvgFeatureRenderer",
- "color1" : "gray"
+ "color1" : "gray",
+ "type" : "SvgFeatureRenderer"
},
- "type" : "LinearBasicDisplay",
- "displayId" : "curated_genes_(noncoding)-t_muris_PRJEB126-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "formatDetails" : {
- "feature" : "jexl:{ JBrowse1: ''+feature.name+''}"
- },
- "trackId" : "t_muris_PRJEB126_curated_genes_noncoding",
- "category" : [
- "Genes",
- "Curated Genes"
- ],
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ]
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/Curated Genes (noncoding)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
"displays" : [
{
- "type" : "LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "color1" : "orange",
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "height" : 4
+ "height" : 4,
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
},
- "displayId" : "O_volvulus_proteins-t_muris_PRJEB126-LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "O_volvulus_proteins-t_muris_PRJEB126-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "t_muris_PRJEB126_O_volvulus_proteins",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/O. volvulus proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
+ "type" : "FeatureTrack",
"assemblyNames" : [
"t_muris_PRJEB126"
],
@@ -59904,51 +58708,55 @@
"Sequence Similarity",
"Proteins"
],
- "description" : "Matches to WormBase O. volvulus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"name" : "O. volvulus proteins",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/O. volvulus proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack"
+ "trackId" : "t_muris_PRJEB126_O_volvulus_proteins",
+ "description" : "Matches to WormBase O. volvulus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation)."
},
{
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
+ ],
+ "type" : "FeatureTrack",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "trackId" : "t_muris_PRJEB126_C_japonica_proteins",
+ "name" : "C. japonica proteins",
+ "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "C_japonica_proteins-t_muris_PRJEB126-LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
"color1" : "orange",
+ "height" : 4,
"showLabels" : false,
"type" : "SvgFeatureRenderer"
},
- "displayId" : "C_japonica_proteins-t_muris_PRJEB126-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "trackId" : "t_muris_PRJEB126_C_japonica_proteins",
- "description" : "Matches to WormBase C. japonica proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/C. japonica proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- }
- },
- "name" : "C. japonica proteins"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
+ "description" : "Native (same species) RNAseq data was assembled with Trinity and then aligned to the genome with BLAT",
+ "name" : "Trinity-assembled RNAseq",
+ "trackId" : "t_muris_PRJEB126_trinity-assembled_rnaseq",
+ "category" : [
+ "Genes",
+ "Supporting Evidence"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
+ ],
"adapter" : {
"type" : "NCListAdapter",
"rootUrlTemplate" : {
@@ -59956,64 +58764,63 @@
"locationType" : "UriLocation"
}
},
- "type" : "FeatureTrack",
- "name" : "Trinity-assembled RNAseq",
- "description" : "Native (same species) RNAseq data was assembled with Trinity and then aligned to the genome with BLAT",
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ],
- "category" : [
- "Genes",
- "Supporting Evidence"
- ],
- "trackId" : "t_muris_PRJEB126_trinity-assembled_rnaseq",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "trinity-assembled_rnaseq-t_muris_PRJEB126-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
- "showLabels" : false,
"color1" : "mediumpurple",
- "height" : 5
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "trinity-assembled_rnaseq-t_muris_PRJEB126-LinearBasicDisplay"
+ "height" : 5,
+ "showLabels" : false
+ }
}
]
},
{
- "description" : "Matches to WormBase T. muris proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/T. muris proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/T. muris proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
},
- "type" : "FeatureTrack",
- "name" : "T. muris proteins",
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "T_muris_proteins-t_muris_PRJEB126-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
+ "showLabels" : false,
+ "height" : 4,
"color1" : "orange"
- },
- "mouseover" : "jexl:get(feature,'clone')",
- "displayId" : "T_muris_proteins-t_muris_PRJEB126-LinearBasicDisplay"
+ }
}
],
+ "description" : "Matches to WormBase T. muris proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "t_muris_PRJEB126_T_muris_proteins",
+ "name" : "T. muris proteins",
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
"assemblyNames" : [
"t_muris_PRJEB126"
],
+ "type" : "FeatureTrack"
+ },
+ {
+ "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "t_muris_PRJEB126_P_pacificus_proteins",
+ "name" : "P. pacificus proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
- "trackId" : "t_muris_PRJEB126_T_muris_proteins"
- },
- {
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
+ ],
"type" : "FeatureTrack",
"adapter" : {
"type" : "NCListAdapter",
@@ -60022,101 +58829,91 @@
"locationType" : "UriLocation"
}
},
- "name" : "P. pacificus proteins",
- "description" : "Matches to WormBase P. pacificus proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "trackId" : "t_muris_PRJEB126_P_pacificus_proteins",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "P_pacificus_proteins-t_muris_PRJEB126-LinearBasicDisplay",
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
"height" : 4,
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "orange"
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')",
- "displayId" : "P_pacificus_proteins-t_muris_PRJEB126-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
]
},
{
- "name" : "S. cerevisiae proteins",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
"type" : "FeatureTrack",
- "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "trackId" : "t_muris_PRJEB126_S_cerevisiae_proteins",
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
+ ],
"category" : [
"Sequence Similarity",
"Proteins"
],
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ],
+ "name" : "S. cerevisiae proteins",
+ "trackId" : "t_muris_PRJEB126_S_cerevisiae_proteins",
+ "description" : "Matches to WormBase S. cerevisiae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"displays" : [
{
"displayId" : "S_cerevisiae_proteins-t_muris_PRJEB126-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
"color1" : "orange",
- "height" : 4
- }
+ "height" : 4,
+ "showLabels" : false
+ },
+ "type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/S. cerevisiae proteins/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
+ ],
+ "type" : "FeatureTrack",
"description" : "Matches to WormBase C. elegans proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "trackId" : "t_muris_PRJEB126_C_elegans_proteins",
"name" : "C. elegans proteins",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/C. elegans proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack",
"displays" : [
{
- "displayId" : "C_elegans_proteins-t_muris_PRJEB126-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
+ "height" : 4,
"showLabels" : false,
- "height" : 4
- }
+ "color1" : "orange"
+ },
+ "displayId" : "C_elegans_proteins-t_muris_PRJEB126-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "trackId" : "t_muris_PRJEB126_C_elegans_proteins",
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ]
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/C. elegans proteins/{refseq}/trackData.jsonz"
+ }
+ }
},
{
"displays" : [
{
- "displayId" : "contig_submissions-t_muris_PRJEB126-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "contig_submissions-t_muris_PRJEB126-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
"color1" : "sienna",
@@ -60127,70 +58924,62 @@
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "trackId" : "t_muris_PRJEB126_contig_submissions",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/Contig submissions/{refseq}/trackData.jsonz"
+ }
+ },
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
+ ],
"category" : [
"Genome Structure",
"Assembly & Curation"
],
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ],
- "description" : "This track shows the location and coordinates of contigs (mostly cosmids) submitted to GenBank/EMBL.",
"name" : "Contig submissions",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/Contig submissions/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack"
+ "trackId" : "t_muris_PRJEB126_contig_submissions",
+ "description" : "This track shows the location and coordinates of contigs (mostly cosmids) submitted to GenBank/EMBL."
},
{
+ "name" : "RNASeq Asymmetries",
+ "trackId" : "t_muris_PRJEB126_rnaseq_asymmetries",
"description" : "Red boxes indicate regions where there are more than 2 times as many forward sense RNASeq reads aligned to the genome as reverse sense reads. This asymmetrical signal has been found empirically to be a sensitive marker for the ends of transcripts. Green boxes indicate regions where there are more than 2 times as many reverse sense RNASeq reads aligned to the genome as forward sense reads. This asymmetrical signal has been found empirically to be sensitive marker for the ends of transcripts. The height of all boxes indicates the relative score of the feature.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
+ ],
+ "category" : [
+ "Expression"
+ ],
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/RNASeq Asymmetries/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/RNASeq Asymmetries/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "name" : "RNASeq Asymmetries",
"displays" : [
{
- "displayId" : "rnaseq_asymmetries-t_muris_PRJEB126-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"mouseover" : "jexl:'Score: '+get(feature,'score')",
"renderer" : {
- "color1" : "jexl:get(feature,'source')=='RNASeq_R_asymmetry'?'red': get(feature,'source')=='RNASeq_F_asymmetry'?'green':'black'",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
"height" : 24,
- "displayMode" : "collapse"
- }
+ "showLabels" : false,
+ "color1" : "jexl:get(feature,'source')=='RNASeq_R_asymmetry'?'red': get(feature,'source')=='RNASeq_F_asymmetry'?'green':'black'",
+ "displayMode" : "collapse",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "rnaseq_asymmetries-t_muris_PRJEB126-LinearBasicDisplay"
}
- ],
- "category" : [
- "Expression"
- ],
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ],
- "trackId" : "t_muris_PRJEB126_rnaseq_asymmetries"
+ ]
},
{
- "name" : "B. malayi proteins",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/B. malayi proteins/{refseq}/trackData.jsonz"
- }
- },
"description" : "Matches to WormBase B. malayi proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"trackId" : "t_muris_PRJEB126_B_malayi_proteins",
+ "name" : "B. malayi proteins",
"category" : [
"Sequence Similarity",
"Proteins"
@@ -60198,47 +58987,55 @@
"assemblyNames" : [
"t_muris_PRJEB126"
],
+ "type" : "FeatureTrack",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/B. malayi proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
+ "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
- "height" : 4,
"color1" : "orange",
+ "height" : 4,
"showLabels" : false,
"type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
- "displayId" : "B_malayi_proteins-t_muris_PRJEB126-LinearBasicDisplay"
+ "displayId" : "B_malayi_proteins-t_muris_PRJEB126-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
]
},
{
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/S. ratti proteins/{refseq}/trackData.jsonz"
- }
- },
- "type" : "FeatureTrack",
"name" : "S. ratti proteins",
+ "trackId" : "t_muris_PRJEB126_S_ratti_proteins",
"description" : "Matches to WormBase S. ratti proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
+ ],
"category" : [
"Sequence Similarity",
"Proteins"
],
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ],
- "trackId" : "t_muris_PRJEB126_S_ratti_proteins",
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/S. ratti proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
"type" : "LinearBasicDisplay",
"renderer" : {
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
"color1" : "orange",
- "height" : 4
+ "height" : 4,
+ "showLabels" : false,
+ "type" : "SvgFeatureRenderer"
},
"mouseover" : "jexl:get(feature,'clone')",
"displayId" : "S_ratti_proteins-t_muris_PRJEB126-LinearBasicDisplay"
@@ -60246,228 +59043,219 @@
]
},
{
- "name" : "ESTs",
"type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/ESTs (best)/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "description" : "Native (same-species) Expressed Sequence Tags (ESTs), aligned to the genome using BLAT. This track shows the best unique location for each EST. The paired 5' and 3' ESTs from the same cDNA clone are connected by a dashed line and a colored light green. ESTs with no mate are yellow, and ESTs with a mate that is 'far away' are dark green.",
- "trackId" : "t_muris_PRJEB126_ests",
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
+ ],
"category" : [
"Genes",
"Supporting Evidence"
],
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ],
+ "name" : "ESTs",
+ "trackId" : "t_muris_PRJEB126_ests",
+ "description" : "Native (same-species) Expressed Sequence Tags (ESTs), aligned to the genome using BLAT. This track shows the best unique location for each EST. The paired 5' and 3' ESTs from the same cDNA clone are connected by a dashed line and a colored light green. ESTs with no mate are yellow, and ESTs with a mate that is 'far away' are dark green.",
"displays" : [
{
- "displayId" : "ests-t_muris_PRJEB126-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
+ "color1" : "jexl:parent(feature)=='undefined'?'red':get(parent(feature),'has_mate')==1?'limegreen':get(parent(feature),'has_mate')==2?'green':get(parent(feature),'has_mate')==0?'gold':'black'",
"type" : "SvgFeatureRenderer",
- "maxHeight" : 5000,
- "color1" : "jexl:parent(feature)=='undefined'?'red':get(parent(feature),'has_mate')==1?'limegreen':get(parent(feature),'has_mate')==2?'green':get(parent(feature),'has_mate')==0?'gold':'black'"
- }
+ "maxHeight" : 5000
+ },
+ "displayId" : "ests-t_muris_PRJEB126-LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
- }
- },
- {
- "name" : "RNASeq introns",
+ },
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/RNASeq introns/{refseq}/trackData.jsonz"
- }
- },
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/ESTs (best)/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ }
+ },
+ {
"type" : "FeatureTrack",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display.",
- "trackId" : "t_muris_PRJEB126_rnaseq_introns",
"assemblyNames" : [
"t_muris_PRJEB126"
],
"category" : [
"Expression"
],
+ "name" : "RNASeq introns",
+ "trackId" : "t_muris_PRJEB126_rnaseq_introns",
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display.",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "rnaseq_introns-t_muris_PRJEB126-LinearBasicDisplay",
"renderer" : {
"showDescriptions" : false,
"height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "green"
- },
+ "color1" : "green",
+ "type" : "SvgFeatureRenderer"
+ },
"mouseover" : "jexl:get(feature,'score')+' reads'",
- "displayId" : "rnaseq_introns-t_muris_PRJEB126-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/RNASeq introns/{refseq}/trackData.jsonz"
+ }
+ }
},
{
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ],
"category" : [
"Expression"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
+ ],
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
+ "name" : "RNASeq Splice Junctions (common)",
"trackId" : "t_muris_PRJEB126_rnaseq_splice_junctions_(common)",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "rnaseq_splice_junctions_(common)-t_muris_PRJEB126-LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "type" : "SvgFeatureRenderer",
+ "color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
"showLabels" : false,
- "color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))"
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
},
"mouseover" : "jexl:get(feature,'score')+' reads'",
- "displayId" : "rnaseq_splice_junctions_(common)-t_muris_PRJEB126-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/RNASeq Splice Junctions (common)/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/RNASeq Splice Junctions (common)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "name" : "RNASeq Splice Junctions (common)",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads."
+ }
},
{
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
- "name" : "RNASeq Splice Junctions (rare)",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz"
- }
- },
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
+ ],
"type" : "FeatureTrack",
+ "category" : [
+ "Expression"
+ ],
+ "trackId" : "t_muris_PRJEB126_rnaseq_splice_junctions_(rare)",
+ "name" : "RNASeq Splice Junctions (rare)",
+ "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
"displays" : [
{
"displayId" : "rnaseq_splice_junctions_(rare)-t_muris_PRJEB126-LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
"showLabels" : false,
- "maxHeight" : 5000,
- "color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
+ "showDescriptions" : false,
"height" : "jexl:4",
- "type" : "SvgFeatureRenderer"
+ "color1" : "jexl:get(feature,'score')>20000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/20000))))+'00'+hex(round(255-(140*(get(feature,'score')/20000)))):'#00'+hex(round(255-(140*(get(feature,'score')/20000))))+hex(round(255-(140*(get(feature,'score')/20000))))",
+ "type" : "SvgFeatureRenderer",
+ "maxHeight" : 5000
},
"mouseover" : "jexl:get(feature,'score')+' reads'",
"type" : "LinearBasicDisplay"
}
],
- "trackId" : "t_muris_PRJEB126_rnaseq_splice_junctions_(rare)",
- "category" : [
- "Expression"
- ],
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ]
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ }
},
{
+ "name" : "Repeat Region (RepeatMasker)",
+ "trackId" : "t_muris_PRJEB126_repeat_region_(repeatmasker)",
+ "description" : "Repetitive regions identified by RepeatMasker.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
+ ],
+ "category" : [
+ "Genome Structure",
+ "Repeats"
+ ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ }
+ },
"displays" : [
{
"displayId" : "repeat_region_(repeatmasker)-t_muris_PRJEB126-LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 4,
"showDescriptions" : false,
- "color1" : "bisque",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "color1" : "bisque"
},
"type" : "LinearBasicDisplay"
}
- ],
- "trackId" : "t_muris_PRJEB126_repeat_region_(repeatmasker)",
- "category" : [
- "Genome Structure",
- "Repeats"
- ],
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ],
- "description" : "Repetitive regions identified by RepeatMasker.",
- "name" : "Repeat Region (RepeatMasker)",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/Repeat Region (RepeatMasker)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- }
+ ]
},
{
"displays" : [
{
"displayId" : "wormbase_nematode_mrnas/ests_(best)-t_muris_PRJEB126-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 4,
- "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA_BEST'?'lightblue':get(feature,'source')=='BLAT_Caen_EST_BEST'?'green':'black'",
"labels" : {
"name" : "jexl:get(feature,'species') || get(feature,'id')"
},
- "type" : "SvgFeatureRenderer"
- }
+ "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA_BEST'?'lightblue':get(feature,'source')=='BLAT_Caen_EST_BEST'?'green':'black'"
+ },
+ "type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/WormBase nematode mRNAs_ESTs (best)/{refseq}/trackData.jsonz"
+ },
+ "type" : "NCListAdapter"
+ },
"category" : [
"Sequence Similarity",
"Nucleotide"
],
- "trackId" : "wormbase_nematode_mrnas/ests_(best)-t_muris_PRJEB126",
- "description" : "ESTs and mRNAs from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each cDNA sequence. mRNAs are shown in light blue; ESTs in green.",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/WormBase nematode mRNAs_ESTs (best)/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
+ ],
"type" : "FeatureTrack",
+ "description" : "ESTs and mRNAs from other WormBase core species aligned to the genome using UCSC's BLAT. This track shows the best location for each cDNA sequence. mRNAs are shown in light blue; ESTs in green.",
+ "trackId" : "wormbase_nematode_mrnas/ests_(best)-t_muris_PRJEB126",
"name" : "WormBase nematode mRNAs/ESTs (best)"
},
{
"displays" : [
{
- "displayId" : "other_uniprot_proteins-t_muris_PRJEB126-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 4,
- "type" : "SvgFeatureRenderer",
+ "color1" : "orange",
"showLabels" : false,
- "color1" : "orange"
- }
+ "height" : 4,
+ "showDescriptions" : false,
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "other_uniprot_proteins-t_muris_PRJEB126-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
],
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
- "trackId" : "t_muris_PRJEB126_other_uniprot_proteins",
- "description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"adapter" : {
"rootUrlTemplate" : {
"locationType" : "UriLocation",
@@ -60475,288 +59263,320 @@
},
"type" : "NCListAdapter"
},
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
+ ],
"type" : "FeatureTrack",
- "name" : "Other UniProt proteins"
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "trackId" : "t_muris_PRJEB126_other_uniprot_proteins",
+ "name" : "Other UniProt proteins",
+ "description" : "Matches to proteins from a slimmed-down version of UniProt (with proteins from WormBase core nematodes, human, fly and yeast removed), aligned with BLASTX (nucleotide to protein, via six-frame translation)."
},
{
- "displays" : [
- {
- "displayId" : "rnaseq-t_muris_PRJEB126-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "color1" : "black",
- "displayMode" : "collapse",
- "showDescriptions" : false,
- "height" : "jexl:get(feature,'score')>100?50:floor(get(feature,'score')/2)>4?floor(get(feature,'score')/2):4"
- },
- "mouseover" : "jexl:'Score: '+get(feature,'score')"
- }
- ],
+ "description" : "These boxes indicate alignments of short read sequences from all available RNASeq projects. The number of reads has been normalised by averaging over the number of libraries. The height of all boxes indicates the relative score of the feature.",
+ "trackId" : "t_muris_PRJEB126_rnaseq",
+ "name" : "RNASeq",
"category" : [
"Expression"
],
"assemblyNames" : [
"t_muris_PRJEB126"
],
- "trackId" : "t_muris_PRJEB126_rnaseq",
- "description" : "These boxes indicate alignments of short read sequences from all available RNASeq projects. The number of reads has been normalised by averaging over the number of libraries. The height of all boxes indicates the relative score of the feature.",
"type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/RNASeq/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/RNASeq/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "name" : "RNASeq"
+ "displays" : [
+ {
+ "mouseover" : "jexl:'Score: '+get(feature,'score')",
+ "renderer" : {
+ "displayMode" : "collapse",
+ "showLabels" : false,
+ "height" : "jexl:get(feature,'score')>100?50:floor(get(feature,'score')/2)>4?floor(get(feature,'score')/2):4",
+ "showDescriptions" : false,
+ "color1" : "black",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "rnaseq-t_muris_PRJEB126-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
+ }
+ ]
},
{
- "name" : "C. remanei proteins",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/C. remanei proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "type" : "FeatureTrack",
- "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "trackId" : "t_muris_PRJEB126_C_remanei_proteins",
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ],
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
+ ],
+ "description" : "Matches to WormBase C. remanei proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "C. remanei proteins",
+ "trackId" : "t_muris_PRJEB126_C_remanei_proteins",
"displays" : [
{
- "type" : "LinearBasicDisplay",
"renderer" : {
"height" : 4,
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "orange"
+ "color1" : "orange",
+ "type" : "SvgFeatureRenderer"
},
"mouseover" : "jexl:get(feature,'clone')",
- "displayId" : "C_remanei_proteins-t_muris_PRJEB126-LinearBasicDisplay"
+ "displayId" : "C_remanei_proteins-t_muris_PRJEB126-LinearBasicDisplay",
+ "type" : "LinearBasicDisplay"
}
- ]
- },
- {
- "description" : "This track shows the location and coordinates of contigs created during the assembly of the C. elegans genome.",
- "name" : "Links and Superlinks",
- "type" : "FeatureTrack",
+ ],
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/Links and Superlinks/{refseq}/trackData.jsonz",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/C. remanei proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- },
- "type" : "NCListAdapter"
- },
+ }
+ }
+ },
+ {
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 4,
"type" : "SvgFeatureRenderer",
- "color1" : "black"
+ "color1" : "black",
+ "height" : 4
},
- "type" : "LinearBasicDisplay",
"displayId" : "links_and_superlinks-t_muris_PRJEB126-LinearBasicDisplay"
}
],
"formatDetails" : {
"feature" : "jexl:{ JBrowse1: ''+feature.refName+':'+feature.start+'..'+feature.end+''}"
},
- "trackId" : "t_muris_PRJEB126_links_and_superlinks",
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/Links and Superlinks/{refseq}/trackData.jsonz"
+ }
+ },
"category" : [
"Genome Structure",
"Assembly & Curation"
- ]
+ ],
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "This track shows the location and coordinates of contigs created during the assembly of the C. elegans genome.",
+ "trackId" : "t_muris_PRJEB126_links_and_superlinks",
+ "name" : "Links and Superlinks"
},
{
- "name" : "C. brenneri proteins",
- "type" : "FeatureTrack",
- "adapter" : {
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/C. brenneri proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
- },
- "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "trackId" : "t_muris_PRJEB126_C_brenneri_proteins",
"assemblyNames" : [
"t_muris_PRJEB126"
],
+ "type" : "FeatureTrack",
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "trackId" : "t_muris_PRJEB126_C_brenneri_proteins",
+ "name" : "C. brenneri proteins",
+ "description" : "Matches to WormBase C. brenneri proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"displayId" : "C_brenneri_proteins-t_muris_PRJEB126-LinearBasicDisplay",
"renderer" : {
- "height" : 4,
"color1" : "orange",
"showLabels" : false,
+ "height" : 4,
"type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay"
+ "mouseover" : "jexl:get(feature,'clone')"
}
- ]
+ ],
+ "adapter" : {
+ "type" : "NCListAdapter",
+ "rootUrlTemplate" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/C. brenneri proteins/{refseq}/trackData.jsonz"
+ }
+ }
},
{
+ "category" : [
+ "Sequence Similarity",
+ "Proteins"
+ ],
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
+ ],
+ "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "D. melanogaster proteins",
+ "trackId" : "t_muris_PRJEB126_D_melanogaster_proteins",
"displays" : [
{
- "displayId" : "D_melanogaster_proteins-t_muris_PRJEB126-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
"renderer" : {
+ "showLabels" : false,
"height" : 4,
"color1" : "orange",
- "showLabels" : false,
"type" : "SvgFeatureRenderer"
},
- "mouseover" : "jexl:get(feature,'clone')"
+ "mouseover" : "jexl:get(feature,'clone')",
+ "displayId" : "D_melanogaster_proteins-t_muris_PRJEB126-LinearBasicDisplay"
}
],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ }
+ },
+ {
+ "name" : "H. sapiens proteins",
+ "trackId" : "t_muris_PRJEB126_H_sapiens_proteins",
+ "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
+ ],
"category" : [
"Sequence Similarity",
"Proteins"
],
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ],
- "trackId" : "t_muris_PRJEB126_D_melanogaster_proteins",
- "description" : "Matches to WormBase D. melanogaster proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "type" : "FeatureTrack",
"adapter" : {
+ "type" : "NCListAdapter",
"rootUrlTemplate" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/D. melanogaster proteins/{refseq}/trackData.jsonz"
- },
- "type" : "NCListAdapter"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/H. sapiens proteins/{refseq}/trackData.jsonz"
+ }
},
- "name" : "D. melanogaster proteins"
- },
- {
"displays" : [
{
+ "type" : "LinearBasicDisplay",
"renderer" : {
- "height" : 4,
- "color1" : "orange",
"type" : "SvgFeatureRenderer",
- "showLabels" : false
+ "color1" : "orange",
+ "showLabels" : false,
+ "height" : 4
},
"mouseover" : "jexl:get(feature,'clone')",
- "type" : "LinearBasicDisplay",
"displayId" : "H_sapiens_proteins-t_muris_PRJEB126-LinearBasicDisplay"
}
- ],
- "trackId" : "t_muris_PRJEB126_H_sapiens_proteins",
+ ]
+ },
+ {
+ "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
+ "name" : "C. briggsae proteins",
+ "trackId" : "t_muris_PRJEB126_C_briggsae_proteins",
"category" : [
"Sequence Similarity",
"Proteins"
],
+ "type" : "FeatureTrack",
"assemblyNames" : [
"t_muris_PRJEB126"
],
- "description" : "Matches to WormBase H. sapiens proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "name" : "H. sapiens proteins",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/H. sapiens proteins/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
- }
- },
- "type" : "FeatureTrack"
- },
- {
- "name" : "C. briggsae proteins",
- "type" : "FeatureTrack",
"adapter" : {
- "type" : "NCListAdapter",
"rootUrlTemplate" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/C. briggsae proteins/{refseq}/trackData.jsonz",
"locationType" : "UriLocation"
- }
+ },
+ "type" : "NCListAdapter"
},
- "description" : "Matches to WormBase C. briggsae proteins, aligned with BLASTX (nucleotide to protein, via six-frame translation).",
- "trackId" : "t_muris_PRJEB126_C_briggsae_proteins",
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ],
- "category" : [
- "Sequence Similarity",
- "Proteins"
- ],
"displays" : [
{
"displayId" : "C_briggsae_proteins-t_muris_PRJEB126-LinearBasicDisplay",
- "mouseover" : "jexl:get(feature,'clone')",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"height" : 4,
- "color1" : "orange",
"showLabels" : false,
- "type" : "SvgFeatureRenderer"
+ "color1" : "orange"
},
+ "mouseover" : "jexl:get(feature,'clone')",
"type" : "LinearBasicDisplay"
}
]
},
{
- "name" : "Collapsed IsoSeq structures",
"adapter" : {
"rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/Collapsed IsoSeq structures/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/Collapsed IsoSeq structures/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
},
"type" : "NCListAdapter"
},
- "type" : "FeatureTrack",
- "description" : "Aligned and filtered full-length non-chimeric IsoSeq reads with similar alignments collapsed into one representative structure.",
- "trackId" : "t_muris_PRJEB126_collapsed_isoseq_structures",
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ],
- "category" : [
- "Genes",
- "Supporting Evidence"
- ],
"displays" : [
{
- "displayId" : "collapsed_isoseq_structures-t_muris_PRJEB126-LinearBasicDisplay",
"type" : "LinearBasicDisplay",
+ "displayId" : "collapsed_isoseq_structures-t_muris_PRJEB126-LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 4,
"type" : "SvgFeatureRenderer",
+ "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA_BEST'?'lightblue':'green'",
"showLabels" : false,
- "color1" : "jexl:get(feature,'source')=='BLAT_Caen_mRNA_BEST'?'lightblue':'green'"
+ "height" : 4,
+ "showDescriptions" : false
}
}
+ ],
+ "name" : "Collapsed IsoSeq structures",
+ "trackId" : "t_muris_PRJEB126_collapsed_isoseq_structures",
+ "description" : "Aligned and filtered full-length non-chimeric IsoSeq reads with similar alignments collapsed into one representative structure.",
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
+ ],
+ "category" : [
+ "Genes",
+ "Supporting Evidence"
]
},
{
+ "category" : [
+ "Genome Structure",
+ "Repeats"
+ ],
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
+ ],
+ "type" : "FeatureTrack",
+ "description" : "Exact tandem and inverted repetitive elements.",
+ "trackId" : "t_muris_PRJEB126_tandem_and_inverted_repeats",
+ "name" : "Tandem and Inverted Repeats",
"displays" : [
{
+ "type" : "LinearBasicDisplay",
+ "displayId" : "tandem_and_inverted_repeats-t_muris_PRJEB126-LinearBasicDisplay",
"renderer" : {
"showDescriptions" : false,
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "bisque"
- },
- "type" : "LinearBasicDisplay",
- "displayId" : "tandem_and_inverted_repeats-t_muris_PRJEB126-LinearBasicDisplay"
+ "color1" : "bisque",
+ "type" : "SvgFeatureRenderer"
+ }
}
],
+ "adapter" : {
+ "rootUrlTemplate" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/Tandem and Inverted Repeats/{refseq}/trackData.jsonz",
+ "locationType" : "UriLocation"
+ },
+ "type" : "NCListAdapter"
+ }
+ },
+ {
+ "description" : "Low-complexity regions identified by Dust.",
+ "trackId" : "t_muris_PRJEB126_low_complextity_region_(dust)",
+ "name" : "Low complextity region (Dust)",
"category" : [
"Genome Structure",
"Repeats"
@@ -60764,160 +59584,140 @@
"assemblyNames" : [
"t_muris_PRJEB126"
],
- "trackId" : "t_muris_PRJEB126_tandem_and_inverted_repeats",
- "description" : "Exact tandem and inverted repetitive elements.",
"type" : "FeatureTrack",
"adapter" : {
"rootUrlTemplate" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/Tandem and Inverted Repeats/{refseq}/trackData.jsonz"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz"
},
"type" : "NCListAdapter"
},
- "name" : "Tandem and Inverted Repeats"
- },
- {
"displays" : [
{
"displayId" : "low_complextity_region_(dust)-t_muris_PRJEB126-LinearBasicDisplay",
"renderer" : {
- "showDescriptions" : false,
- "height" : 4,
- "showLabels" : false,
"type" : "SvgFeatureRenderer",
+ "showLabels" : false,
+ "height" : 4,
+ "showDescriptions" : false,
"color1" : "bisque"
},
"type" : "LinearBasicDisplay"
}
+ ]
+ },
+ {
+ "adapter" : {
+ "bamLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/jbrowse/data/t_muris_PRJEB126/Tmuris_isoseq.bam",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BamAdapter",
+ "index" : {
+ "location" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/jbrowse/data/t_muris_PRJEB126/Tmuris_isoseq.bam.bai",
+ "locationType" : "UriLocation"
+ }
+ }
+ },
+ "displays" : [
+ {
+ "type" : "LinearAlignmentsDisplay",
+ "displayId" : "t_muris_PRJEB126_isoseq_collection_alignments-LinearAlignmentsDisplay"
+ },
+ {
+ "displayId" : "t_muris_PRJEB126_isoseq_collection_alignments-LinearPileupDisplay",
+ "type" : "LinearPileupDisplay"
+ },
+ {
+ "type" : "LinearSNPCoverageDisplay",
+ "displayId" : "t_muris_PRJEB126_isoseq_collection_alignments-LinearSNPCoverageDisplay"
+ }
],
+ "name" : "IsoSeq collection alignments",
+ "trackId" : "t_muris_PRJEB126_isoseq_collection_alignments",
+ "description" : "PacBio IsoSeq (RSII) reads from adult male and adult female T. muris libraries, generated by the Parasite Genomics group at the Wellcome Sanger Institute. Full-length non-chimeric reads were aligned with GMAP.",
+ "type" : "AlignmentsTrack",
"assemblyNames" : [
"t_muris_PRJEB126"
],
"category" : [
- "Genome Structure",
- "Repeats"
- ],
- "trackId" : "t_muris_PRJEB126_low_complextity_region_(dust)",
- "description" : "Low-complexity regions identified by Dust.",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/Low complextity region (Dust)/{refseq}/trackData.jsonz"
- }
- },
- "type" : "FeatureTrack",
- "name" : "Low complextity region (Dust)"
+ "Expression"
+ ]
},
{
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ],
- "category" : [
- "Expression"
- ],
- "trackId" : "t_muris_PRJEB126_isoseq_collection_alignments",
"displays" : [
{
- "displayId" : "t_muris_PRJEB126_isoseq_collection_alignments-LinearAlignmentsDisplay",
- "type" : "LinearAlignmentsDisplay"
- },
- {
- "type" : "LinearPileupDisplay",
- "displayId" : "t_muris_PRJEB126_isoseq_collection_alignments-LinearPileupDisplay"
- },
- {
- "displayId" : "t_muris_PRJEB126_isoseq_collection_alignments-LinearSNPCoverageDisplay",
- "type" : "LinearSNPCoverageDisplay"
+ "type" : "LinearBasicDisplay",
+ "renderer" : {
+ "showLabels" : false,
+ "height" : 4,
+ "showDescriptions" : false,
+ "color1" : "SlateBlue",
+ "type" : "SvgFeatureRenderer"
+ },
+ "displayId" : "TTCN_sequence_search_t_muris_PRJEB126-LinearBasicDisplay"
}
],
"adapter" : {
- "bamLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/jbrowse/data/t_muris_PRJEB126/Tmuris_isoseq.bam",
- "locationType" : "UriLocation"
- },
- "index" : {
- "location" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/jbrowse/data/t_muris_PRJEB126/Tmuris_isoseq.bam.bai"
- }
- },
- "type" : "BamAdapter"
- },
- "type" : "AlignmentsTrack",
- "name" : "IsoSeq collection alignments",
- "description" : "PacBio IsoSeq (RSII) reads from adult male and adult female T. muris libraries, generated by the Parasite Genomics group at the Wellcome Sanger Institute. Full-length non-chimeric reads were aligned with GMAP."
- },
- {
- "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time.",
- "name" : "Cas12e TTCN PAM sites",
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
- "faiLocation" : {
+ "fastaLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz.fai"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz"
},
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz",
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
- },
- "type" : "BgzipFastaAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz.gzi"
+ }
},
+ "type" : "SequenceSearchAdapter",
"search" : "TTC."
},
- "displays" : [
- {
- "displayId" : "TTCN_sequence_search_t_muris_PRJEB126-LinearBasicDisplay",
- "renderer" : {
- "color1" : "SlateBlue",
- "type" : "SvgFeatureRenderer",
- "showLabels" : false,
- "height" : 4,
- "showDescriptions" : false
- },
- "type" : "LinearBasicDisplay"
- }
+ "type" : "FeatureTrack",
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
],
- "trackId" : "t_muris_PRJEB126_TTCN_sequence_search",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ]
+ "name" : "Cas12e TTCN PAM sites",
+ "trackId" : "t_muris_PRJEB126_TTCN_sequence_search",
+ "description" : "Cas12e (CasX) PAM sites based on TTCN motif. Computed on the fly at load time."
},
{
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
+ ],
+ "type" : "FeatureTrack",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ],
"trackId" : "t_muris_PRJEB126_TTN_sequence_search",
+ "name" : "Cas12a TTN PAM sites",
+ "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time.",
"displays" : [
{
- "type" : "LinearBasicDisplay",
+ "displayId" : "TTN_sequence_search_t_muris_PRJEB126-LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"color1" : "Indigo",
"showLabels" : false,
- "type" : "SvgFeatureRenderer",
"height" : 4,
"showDescriptions" : false
},
- "displayId" : "TTN_sequence_search_t_muris_PRJEB126-LinearBasicDisplay"
+ "type" : "LinearBasicDisplay"
}
],
"adapter" : {
- "type" : "SequenceSearchAdapter",
"search" : "TT.",
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
"type" : "BgzipFastaAdapter",
"gziLocation" : {
@@ -60925,224 +59725,121 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz.gzi"
},
"fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
},
"faiLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz.fai"
}
}
- },
- "type" : "FeatureTrack",
- "name" : "Cas12a TTN PAM sites",
- "description" : "Cas12a (Cpf1) PAM sites based on TTN motif. Computed on the fly at load time."
+ }
},
{
- "displays" : [
- {
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "showDescriptions" : false,
- "height" : 4,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "DarkViolet"
- },
- "displayId" : "NNGRRT_sequence_search_t_muris_PRJEB126-LinearBasicDisplay"
- }
- ],
+ "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
"trackId" : "t_muris_PRJEB126_NNGRRT_sequence_search",
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ],
+ "name" : "SaCas9 NNGRRT PAM sites",
"category" : [
"Externally Sourced Resources",
"CRISPR predictions"
],
- "description" : "Staphylococcus aureus Cas9 PAM sites based on NNGRRT motif. Computed on the fly at load time.",
- "name" : "SaCas9 NNGRRT PAM sites",
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
+ ],
"type" : "FeatureTrack",
"adapter" : {
+ "type" : "SequenceSearchAdapter",
"sequenceAdapter" : {
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz.gzi"
},
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
- },
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
- },
- "type" : "BgzipFastaAdapter"
- },
- "search" : "..G[AG][AG]T",
- "type" : "SequenceSearchAdapter"
- }
- },
- {
- "name" : "SpCas9 NGG PAM sites",
- "adapter" : {
- "type" : "SequenceSearchAdapter",
- "sequenceAdapter" : {
- "type" : "BgzipFastaAdapter",
"faiLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz.fai"
},
"fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
- },
- "gziLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz"
}
},
- "search" : ".GG"
+ "search" : "..G[AG][AG]T"
},
- "type" : "FeatureTrack",
- "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
- "trackId" : "t_muris_PRJEB126_NGG_sequence_search",
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ],
- "category" : [
- "Externally Sourced Resources",
- "CRISPR predictions"
- ],
"displays" : [
{
"type" : "LinearBasicDisplay",
+ "displayId" : "NNGRRT_sequence_search_t_muris_PRJEB126-LinearBasicDisplay",
"renderer" : {
+ "type" : "SvgFeatureRenderer",
"showDescriptions" : false,
"height" : 4,
- "type" : "SvgFeatureRenderer",
"showLabels" : false,
- "color1" : "RebeccaPurple"
- },
- "displayId" : "NGG_sequence_search_t_muris_PRJEB126-LinearBasicDisplay"
+ "color1" : "DarkViolet"
+ }
}
]
},
{
- "displays" : [
- {
- "displayId" : "rnaseq_introns-t_muris_PRJEB126-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "showDescriptions" : false,
- "height" : "jexl:get(feature,'score')>100?50:get(feature,'score')<8?4:floor(get(feature,'score')/2)",
- "showLabels" : false,
- "type" : "SvgFeatureRenderer",
- "color1" : "green"
- },
- "mouseover" : "jexl:get(feature,'score')+' reads'"
- }
- ],
+ "trackId" : "t_muris_PRJEB126_NGG_sequence_search",
+ "name" : "SpCas9 NGG PAM sites",
+ "description" : "Streptococcus pyogenes Cas9 PAM sites based on NGG motif. Computed on the fly at load time.",
"assemblyNames" : [
"t_muris_PRJEB126"
],
+ "type" : "FeatureTrack",
"category" : [
- "Expression"
+ "Externally Sourced Resources",
+ "CRISPR predictions"
],
- "trackId" : "t_muris_PRJEB126_rnaseq_introns",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. The number of reads spanning the introns is indicated by the thickness of the display.",
- "type" : "FeatureTrack",
"adapter" : {
- "rootUrlTemplate" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/RNASeq introns/{refseq}/trackData.jsonz",
- "locationType" : "UriLocation"
+ "search" : ".GG",
+ "sequenceAdapter" : {
+ "faiLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz.fai"
+ },
+ "fastaLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz"
+ },
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ }
},
- "type" : "NCListAdapter"
+ "type" : "SequenceSearchAdapter"
},
- "name" : "RNASeq introns"
- },
- {
- "category" : [
- "Expression"
- ],
- "assemblyNames" : [
- "t_muris_PRJEB126"
- ],
- "trackId" : "t_muris_PRJEB126_rnaseq_splice_junctions_(common)",
"displays" : [
{
+ "displayId" : "NGG_sequence_search_t_muris_PRJEB126-LinearBasicDisplay",
"renderer" : {
"type" : "SvgFeatureRenderer",
+ "color1" : "RebeccaPurple",
"showLabels" : false,
- "color1" : "jexl:get(feature,'score')>1000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/1000))))+'00'+hex(round(255-(140*(get(feature,'score')/1000)))):'#00'+hex(round(255-(140*(get(feature,'score')/1000))))+hex(round(255-(140*(get(feature,'score')/1000))))",
+ "height" : 4,
"showDescriptions" : false
},
- "mouseover" : "jexl:get(feature,'score')+' reads'",
- "type" : "LinearBasicDisplay",
- "displayId" : "rnaseq_splice_junctions_(common)-t_muris_PRJEB126-LinearBasicDisplay"
- }
- ],
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/RNASeq Splice Junctions (common)/{refseq}/trackData.jsonz"
+ "type" : "LinearBasicDisplay"
}
- },
- "type" : "FeatureTrack",
- "name" : "RNASeq Splice Junctions (common)",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'common' in that there are more than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads."
+ ]
},
{
- "type" : "FeatureTrack",
- "adapter" : {
- "type" : "NCListAdapter",
- "rootUrlTemplate" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/tracks/RNASeq Splice Junctions (rare)/{refseq}/trackData.jsonz"
- }
- },
- "name" : "RNASeq Splice Junctions (rare)",
- "description" : "These are introns formed by aligned RNASeq reads spanning a region of the genome. Alignments of short read sequences from all available RNASeq projects were used. These junctions are considered 'rare' in that there are fewer than 500 reads confirming their existence. The number of reads spanning the introns is indicated by the darkness of the color (shades of cyan for reverse, shades of violet for forward). Darker is more reads.",
- "category" : [
- "Expression"
- ],
"assemblyNames" : [
- "t_muris_PRJEB126"
+ "c_brenneri_PRJNA20035",
+ "c_japonica_PRJNA12591"
],
- "trackId" : "t_muris_PRJEB126_rnaseq_splice_junctions_(rare)",
- "displays" : [
- {
- "displayId" : "rnaseq_splice_junctions_(rare)-t_muris_PRJEB126-LinearBasicDisplay",
- "type" : "LinearBasicDisplay",
- "renderer" : {
- "height" : "jexl:4",
- "showDescriptions" : false,
- "color1" : "jexl:get(feature,'score')>1000?(get(feature,'strand')>0?'#730073':'#007373'):get(feature,'strand')>0?'#'+hex(round(255-(140*(get(feature,'score')/1000))))+'00'+hex(round(255-(140*(get(feature,'score')/1000)))):'#00'+hex(round(255-(140*(get(feature,'score')/1000))))+hex(round(255-(140*(get(feature,'score')/1000))))",
- "maxHeight" : 5000,
- "showLabels" : false,
- "type" : "SvgFeatureRenderer"
- },
- "mouseover" : "jexl:get(feature,'score')+' reads'"
- }
- ]
- },
- {
- "name" : "C. brenneri to C. japonica",
"type" : "SyntenyTrack",
- "adapter" : {
- "pafLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_brenneri.c_japonica.paf"
- },
- "queryAssembly" : "c_japonica_PRJNA12591",
- "type" : "PAFAdapter",
- "targetAssembly" : "c_brenneri_PRJNA20035"
- },
+ "category" : [
+ "Synteny"
+ ],
+ "trackId" : "brenneri_to_japonica",
+ "name" : "C. brenneri to C. japonica",
"displays" : [
{
- "type" : "DotplotDisplay",
- "displayId" : "brenneri_to_japonica-DotplotDisplay"
+ "displayId" : "brenneri_to_japonica-DotplotDisplay",
+ "type" : "DotplotDisplay"
},
{
"displayId" : "brenneri_to_japonica-LinearComparativeDisplay",
@@ -61153,245 +59850,246 @@
"displayId" : "brenneri_to_japonica-LinearSyntenyDisplay"
}
],
- "trackId" : "brenneri_to_japonica",
+ "adapter" : {
+ "targetAssembly" : "c_brenneri_PRJNA20035",
+ "pafLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_brenneri.c_japonica.paf",
+ "locationType" : "UriLocation"
+ },
+ "type" : "PAFAdapter",
+ "queryAssembly" : "c_japonica_PRJNA12591"
+ }
+ },
+ {
"category" : [
"Synteny"
],
"assemblyNames" : [
"c_brenneri_PRJNA20035",
- "c_japonica_PRJNA12591"
- ]
- },
- {
- "name" : "C. brenneri to C. remanei",
- "adapter" : {
- "type" : "PAFAdapter",
- "targetAssembly" : "c_brenneri_PRJNA20035",
- "pafLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_brenneri.c_remanei.paf"
- },
- "queryAssembly" : "c_remanei_PRJNA53967"
- },
+ "c_remanei_PRJNA53967"
+ ],
"type" : "SyntenyTrack",
+ "trackId" : "brenneri_to_remanei",
+ "name" : "C. brenneri to C. remanei",
"displays" : [
{
"type" : "DotplotDisplay",
"displayId" : "brenneri_to_remanei-DotplotDisplay"
},
{
- "type" : "LinearComparativeDisplay",
- "displayId" : "brenneri_to_remanei-LinearComparativeDisplay"
+ "displayId" : "brenneri_to_remanei-LinearComparativeDisplay",
+ "type" : "LinearComparativeDisplay"
},
{
- "displayId" : "brenneri_to_remanei-LinearSyntenyDisplay",
- "type" : "LinearSyntenyDisplay"
+ "type" : "LinearSyntenyDisplay",
+ "displayId" : "brenneri_to_remanei-LinearSyntenyDisplay"
}
],
- "trackId" : "brenneri_to_remanei",
- "category" : [
- "Synteny"
- ],
- "assemblyNames" : [
- "c_brenneri_PRJNA20035",
- "c_remanei_PRJNA53967"
- ]
+ "adapter" : {
+ "targetAssembly" : "c_brenneri_PRJNA20035",
+ "pafLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_brenneri.c_remanei.paf",
+ "locationType" : "UriLocation"
+ },
+ "queryAssembly" : "c_remanei_PRJNA53967",
+ "type" : "PAFAdapter"
+ }
},
{
"name" : "C. briggsae to C. nigoni",
"adapter" : {
- "type" : "PAFAdapter",
- "targetAssembly" : "c_briggsae_PRJNA10731",
"pafLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_briggsae.c_nigoni.paf"
},
- "queryAssembly" : "c_nigoni_PRJNA384657"
+ "queryAssembly" : "c_nigoni_PRJNA384657",
+ "type" : "PAFAdapter",
+ "targetAssembly" : "c_briggsae_PRJNA10731"
},
- "type" : "SyntenyTrack",
"trackId" : "briggsae_to_nigoni",
+ "type" : "SyntenyTrack",
"assemblyNames" : [
"c_briggsae_PRJNA10731",
"c_nigoni_PRJNA384657"
],
- "category" : [
- "Synteny"
- ],
"displays" : [
{
- "displayId" : "briggsae_to_nigoni-DotplotDisplay",
- "type" : "DotplotDisplay"
+ "type" : "DotplotDisplay",
+ "displayId" : "briggsae_to_nigoni-DotplotDisplay"
},
{
"displayId" : "briggsae_to_nigoni-LinearComparativeDisplay",
"type" : "LinearComparativeDisplay"
},
{
- "displayId" : "briggsae_to_nigoni-LinearSyntenyDisplay",
- "type" : "LinearSyntenyDisplay"
+ "type" : "LinearSyntenyDisplay",
+ "displayId" : "briggsae_to_nigoni-LinearSyntenyDisplay"
}
+ ],
+ "category" : [
+ "Synteny"
]
},
{
- "name" : "C. briggsae to C. brenneri",
- "type" : "SyntenyTrack",
- "adapter" : {
- "queryAssembly" : "c_brenneri_PRJNA20035",
- "pafLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_briggsae.c_brenneri.paf",
- "locationType" : "UriLocation"
- },
- "type" : "PAFAdapter",
- "targetAssembly" : "c_briggsae_PRJNA10731"
- },
"displays" : [
{
- "type" : "DotplotDisplay",
- "displayId" : "briggsae_to_brenneri-DotplotDisplay"
+ "displayId" : "briggsae_to_brenneri-DotplotDisplay",
+ "type" : "DotplotDisplay"
},
{
"type" : "LinearComparativeDisplay",
"displayId" : "briggsae_to_brenneri-LinearComparativeDisplay"
},
{
- "displayId" : "briggsae_to_brenneri-LinearSyntenyDisplay",
- "type" : "LinearSyntenyDisplay"
+ "type" : "LinearSyntenyDisplay",
+ "displayId" : "briggsae_to_brenneri-LinearSyntenyDisplay"
}
],
- "trackId" : "briggsae_to_brenneri",
- "category" : [
- "Synteny"
- ],
+ "adapter" : {
+ "targetAssembly" : "c_briggsae_PRJNA10731",
+ "pafLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_briggsae.c_brenneri.paf",
+ "locationType" : "UriLocation"
+ },
+ "queryAssembly" : "c_brenneri_PRJNA20035",
+ "type" : "PAFAdapter"
+ },
+ "type" : "SyntenyTrack",
"assemblyNames" : [
"c_briggsae_PRJNA10731",
"c_brenneri_PRJNA20035"
- ]
+ ],
+ "category" : [
+ "Synteny"
+ ],
+ "name" : "C. briggsae to C. brenneri",
+ "trackId" : "briggsae_to_brenneri"
},
{
"displays" : [
{
- "type" : "DotplotDisplay",
- "displayId" : "briggsae_to_japonica-DotplotDisplay"
+ "displayId" : "briggsae_to_japonica-DotplotDisplay",
+ "type" : "DotplotDisplay"
},
{
- "type" : "LinearComparativeDisplay",
- "displayId" : "briggsae_to_japonica-LinearComparativeDisplay"
+ "displayId" : "briggsae_to_japonica-LinearComparativeDisplay",
+ "type" : "LinearComparativeDisplay"
},
{
"displayId" : "briggsae_to_japonica-LinearSyntenyDisplay",
"type" : "LinearSyntenyDisplay"
}
],
- "trackId" : "briggsae_to_japonica",
+ "adapter" : {
+ "targetAssembly" : "c_briggsae_PRJNA10731",
+ "queryAssembly" : "c_japonica_PRJNA12591",
+ "type" : "PAFAdapter",
+ "pafLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_briggsae.c_japonica.paf"
+ }
+ },
"assemblyNames" : [
"c_briggsae_PRJNA10731",
"c_japonica_PRJNA12591"
],
+ "type" : "SyntenyTrack",
"category" : [
"Synteny"
],
- "name" : "C. briggsae to C. japonica",
- "type" : "SyntenyTrack",
- "adapter" : {
- "type" : "PAFAdapter",
- "targetAssembly" : "c_briggsae_PRJNA10731",
- "pafLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_briggsae.c_japonica.paf",
- "locationType" : "UriLocation"
- },
- "queryAssembly" : "c_japonica_PRJNA12591"
- }
+ "trackId" : "briggsae_to_japonica",
+ "name" : "C. briggsae to C. japonica"
},
{
"adapter" : {
"pafLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_briggsae.c_remanei.paf"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_briggsae.c_remanei.paf",
+ "locationType" : "UriLocation"
},
"queryAssembly" : "c_remanei_PRJNA53967",
- "targetAssembly" : "c_briggsae_PRJNA10731",
- "type" : "PAFAdapter"
+ "type" : "PAFAdapter",
+ "targetAssembly" : "c_briggsae_PRJNA10731"
},
- "type" : "SyntenyTrack",
- "name" : "C. briggsae to C. remanei",
"displays" : [
{
- "type" : "DotplotDisplay",
- "displayId" : "briggsae_to_remanei-DotplotDisplay"
+ "displayId" : "briggsae_to_remanei-DotplotDisplay",
+ "type" : "DotplotDisplay"
},
{
- "type" : "LinearComparativeDisplay",
- "displayId" : "briggsae_to_remanei-LinearComparativeDisplay"
+ "displayId" : "briggsae_to_remanei-LinearComparativeDisplay",
+ "type" : "LinearComparativeDisplay"
},
{
"type" : "LinearSyntenyDisplay",
"displayId" : "briggsae_to_remanei-LinearSyntenyDisplay"
}
],
+ "name" : "C. briggsae to C. remanei",
+ "trackId" : "briggsae_to_remanei",
+ "type" : "SyntenyTrack",
"assemblyNames" : [
"c_briggsae_PRJNA10731",
"c_remanei_PRJNA53967"
],
"category" : [
"Synteny"
- ],
- "trackId" : "briggsae_to_remanei"
+ ]
},
{
- "name" : "C. elegans VC2010 to C. elegans Hawaiian",
- "type" : "SyntenyTrack",
"adapter" : {
"targetAssembly" : "c_elegans_PRJNA275000",
- "type" : "PAFAdapter",
"pafLocation" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_elegans_PRJEB28388.c_elegans_PRJNA275000.paf",
"locationType" : "UriLocation"
},
+ "type" : "PAFAdapter",
"queryAssembly" : "c_elegans_PRJEB28388"
},
"displays" : [
{
- "type" : "DotplotDisplay",
- "displayId" : "VC2010_to_Hawaiian-DotplotDisplay"
+ "displayId" : "VC2010_to_Hawaiian-DotplotDisplay",
+ "type" : "DotplotDisplay"
},
{
- "type" : "LinearComparativeDisplay",
- "displayId" : "VC2010_to_Hawaiian-LinearComparativeDisplay"
+ "displayId" : "VC2010_to_Hawaiian-LinearComparativeDisplay",
+ "type" : "LinearComparativeDisplay"
},
{
- "displayId" : "VC2010_to_Hawaiian-LinearSyntenyDisplay",
- "type" : "LinearSyntenyDisplay"
+ "type" : "LinearSyntenyDisplay",
+ "displayId" : "VC2010_to_Hawaiian-LinearSyntenyDisplay"
}
],
+ "name" : "C. elegans VC2010 to C. elegans Hawaiian",
"trackId" : "VC2010_to_Hawaiian",
- "category" : [
- "Synteny"
- ],
+ "type" : "SyntenyTrack",
"assemblyNames" : [
"c_elegans_PRJEB28388",
"c_elegans_PRJNA275000"
+ ],
+ "category" : [
+ "Synteny"
]
},
{
+ "trackId" : "N2_to_briggsae",
"name" : "C. elegans N2 to C. briggsae",
+ "assemblyNames" : [
+ "c_briggsae_PRJNA10731",
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "SyntenyTrack",
+ "category" : [
+ "Synteny"
+ ],
"adapter" : {
- "queryAssembly" : "c_briggsae_PRJNA10731",
+ "targetAssembly" : "c_elegans_PRJNA13758",
"pafLocation" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_elegans.c_briggsae.paf",
"locationType" : "UriLocation"
},
- "type" : "PAFAdapter",
- "targetAssembly" : "c_elegans_PRJNA13758"
+ "queryAssembly" : "c_briggsae_PRJNA10731",
+ "type" : "PAFAdapter"
},
- "type" : "SyntenyTrack",
- "trackId" : "N2_to_briggsae",
- "category" : [
- "Synteny"
- ],
- "assemblyNames" : [
- "c_briggsae_PRJNA10731",
- "c_elegans_PRJNA13758"
- ],
"displays" : [
{
"type" : "DotplotDisplay",
@@ -61402,13 +60100,23 @@
"type" : "LinearComparativeDisplay"
},
{
- "displayId" : "N2_to_briggsae-LinearSyntenyDisplay",
- "type" : "LinearSyntenyDisplay"
+ "type" : "LinearSyntenyDisplay",
+ "displayId" : "N2_to_briggsae-LinearSyntenyDisplay"
}
]
},
{
"trackId" : "N2_to_nigoni",
+ "adapter" : {
+ "targetAssembly" : "c_elegans_PRJNA13758",
+ "type" : "PAFAdapter",
+ "queryAssembly" : "c_nigoni_PRJNA384657",
+ "pafLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_elegans.c_nigoni.paf"
+ }
+ },
+ "name" : "C. elegans N2 to C. nigoni",
"category" : [
"Synteny"
],
@@ -61422,97 +60130,97 @@
"displayId" : "N2_to_nigoni-DotplotDisplay"
},
{
- "displayId" : "N2_to_nigoni-LinearComparativeDisplay",
- "type" : "LinearComparativeDisplay"
+ "type" : "LinearComparativeDisplay",
+ "displayId" : "N2_to_nigoni-LinearComparativeDisplay"
},
{
- "displayId" : "N2_to_nigoni-LinearSyntenyDisplay",
- "type" : "LinearSyntenyDisplay"
+ "type" : "LinearSyntenyDisplay",
+ "displayId" : "N2_to_nigoni-LinearSyntenyDisplay"
}
],
- "name" : "C. elegans N2 to C. nigoni",
- "adapter" : {
- "targetAssembly" : "c_elegans_PRJNA13758",
- "type" : "PAFAdapter",
- "queryAssembly" : "c_nigoni_PRJNA384657",
- "pafLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_elegans.c_nigoni.paf",
- "locationType" : "UriLocation"
- }
- },
"type" : "SyntenyTrack"
},
{
"adapter" : {
- "type" : "PAFAdapter",
"targetAssembly" : "c_elegans_PRJNA13758",
"pafLocation" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_elegans.c_brenneri.paf",
"locationType" : "UriLocation"
},
+ "type" : "PAFAdapter",
"queryAssembly" : "c_brenneri_PRJNA20035"
},
- "type" : "SyntenyTrack",
- "name" : "C. elegans N2 to C. brenneri",
"displays" : [
{
- "displayId" : "N2_to_brenneri-DotplotDisplay",
- "type" : "DotplotDisplay"
+ "type" : "DotplotDisplay",
+ "displayId" : "N2_to_brenneri-DotplotDisplay"
},
{
"type" : "LinearComparativeDisplay",
"displayId" : "N2_to_brenneri-LinearComparativeDisplay"
},
{
- "type" : "LinearSyntenyDisplay",
- "displayId" : "N2_to_brenneri-LinearSyntenyDisplay"
+ "displayId" : "N2_to_brenneri-LinearSyntenyDisplay",
+ "type" : "LinearSyntenyDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758",
- "c_brenneri_PRJNA20035"
- ],
+ "name" : "C. elegans N2 to C. brenneri",
+ "trackId" : "N2_to_brenneri",
"category" : [
"Synteny"
],
- "trackId" : "N2_to_brenneri"
- },
- {
- "name" : "C. elegans N2 to C. japonica",
"type" : "SyntenyTrack",
- "adapter" : {
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758",
+ "c_brenneri_PRJNA20035"
+ ]
+ },
+ {
+ "adapter" : {
+ "targetAssembly" : "c_elegans_PRJNA13758",
+ "type" : "PAFAdapter",
"queryAssembly" : "c_japonica_PRJNA12591",
"pafLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_elegans.c_japonica.paf"
- },
- "type" : "PAFAdapter",
- "targetAssembly" : "c_elegans_PRJNA13758"
+ }
},
- "trackId" : "N2_to_japonica",
- "category" : [
- "Synteny"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758",
- "c_japonica_PRJNA12591"
- ],
"displays" : [
{
- "displayId" : "N2_to_japonica-DotplotDisplay",
- "type" : "DotplotDisplay"
+ "type" : "DotplotDisplay",
+ "displayId" : "N2_to_japonica-DotplotDisplay"
},
{
"type" : "LinearComparativeDisplay",
"displayId" : "N2_to_japonica-LinearComparativeDisplay"
},
{
- "displayId" : "N2_to_japonica-LinearSyntenyDisplay",
- "type" : "LinearSyntenyDisplay"
+ "type" : "LinearSyntenyDisplay",
+ "displayId" : "N2_to_japonica-LinearSyntenyDisplay"
}
- ]
+ ],
+ "trackId" : "N2_to_japonica",
+ "name" : "C. elegans N2 to C. japonica",
+ "category" : [
+ "Synteny"
+ ],
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758",
+ "c_japonica_PRJNA12591"
+ ],
+ "type" : "SyntenyTrack"
},
{
+ "type" : "SyntenyTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758",
+ "c_remanei_PRJNA53967"
+ ],
+ "category" : [
+ "Synteny"
+ ],
+ "name" : "C. elegans N2 to C. remanei",
+ "trackId" : "N2_to_remanei",
"displays" : [
{
"type" : "DotplotDisplay",
@@ -61527,46 +60235,36 @@
"type" : "LinearSyntenyDisplay"
}
],
- "trackId" : "N2_to_remanei",
- "category" : [
- "Synteny"
- ],
- "assemblyNames" : [
- "c_elegans_PRJNA13758",
- "c_remanei_PRJNA53967"
- ],
- "name" : "C. elegans N2 to C. remanei",
- "type" : "SyntenyTrack",
"adapter" : {
+ "targetAssembly" : "c_elegans_PRJNA13758",
"queryAssembly" : "c_remanei_PRJNA53967",
+ "type" : "PAFAdapter",
"pafLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_elegans.c_remanei.paf",
- "locationType" : "UriLocation"
- },
- "targetAssembly" : "c_elegans_PRJNA13758",
- "type" : "PAFAdapter"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_elegans.c_remanei.paf"
+ }
}
},
{
"name" : "C. elegans N2 to C. elegans Hawaiian",
- "type" : "SyntenyTrack",
- "adapter" : {
- "type" : "PAFAdapter",
- "targetAssembly" : "c_elegans_PRJNA13758",
- "pafLocation" : {
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_elegans_PRJNA13758.c_elegans_PRJNA275000.paf",
- "locationType" : "UriLocation"
- },
- "queryAssembly" : "c_elegans_PRJNA275000"
- },
"trackId" : "N2_to_Hawaiian",
- "category" : [
- "Synteny"
- ],
+ "type" : "SyntenyTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758",
"c_elegans_PRJNA275000"
],
+ "category" : [
+ "Synteny"
+ ],
+ "adapter" : {
+ "pafLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_elegans_PRJNA13758.c_elegans_PRJNA275000.paf"
+ },
+ "type" : "PAFAdapter",
+ "queryAssembly" : "c_elegans_PRJNA275000",
+ "targetAssembly" : "c_elegans_PRJNA13758"
+ },
"displays" : [
{
"displayId" : "N2_to_Hawaiian-DotplotDisplay",
@@ -61584,200 +60282,215 @@
},
{
"adapter" : {
- "type" : "PAFAdapter",
"targetAssembly" : "c_elegans_PRJNA13758",
+ "type" : "PAFAdapter",
+ "queryAssembly" : "c_elegans_PRJEB28388",
"pafLocation" : {
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_elegans_PRJNA13758.c_elegans_PRJEB28388.paf",
"locationType" : "UriLocation"
- },
- "queryAssembly" : "c_elegans_PRJEB28388"
+ }
},
- "type" : "SyntenyTrack",
- "name" : "C. elegans N2 to C. elegans (VC2010)",
"displays" : [
{
"displayId" : "N2_to_VC2010-DotplotDisplay",
"type" : "DotplotDisplay"
},
{
- "type" : "LinearComparativeDisplay",
- "displayId" : "N2_to_VC2010-LinearComparativeDisplay"
+ "displayId" : "N2_to_VC2010-LinearComparativeDisplay",
+ "type" : "LinearComparativeDisplay"
},
{
- "displayId" : "N2_to_VC2010-LinearSyntenyDisplay",
- "type" : "LinearSyntenyDisplay"
+ "type" : "LinearSyntenyDisplay",
+ "displayId" : "N2_to_VC2010-LinearSyntenyDisplay"
}
],
+ "name" : "C. elegans N2 to C. elegans (VC2010)",
+ "trackId" : "N2_to_VC2010",
+ "category" : [
+ "Synteny"
+ ],
+ "type" : "SyntenyTrack",
"assemblyNames" : [
"c_elegans_PRJNA13758",
"c_elegans_PRJEB28388"
- ],
+ ]
+ },
+ {
"category" : [
"Synteny"
],
- "trackId" : "N2_to_VC2010"
- },
- {
+ "type" : "SyntenyTrack",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758",
+ "c_inopinata_PRJDB5687"
+ ],
+ "name" : "C. elegans N2 to C. inopinata",
+ "trackId" : "N2_to_inopinata",
"displays" : [
{
"type" : "DotplotDisplay",
"displayId" : "N2_to_inopinata-DotplotDisplay"
},
{
- "displayId" : "N2_to_inopinata-LinearComparativeDisplay",
- "type" : "LinearComparativeDisplay"
+ "type" : "LinearComparativeDisplay",
+ "displayId" : "N2_to_inopinata-LinearComparativeDisplay"
},
{
- "displayId" : "N2_to_inopinata-LinearSyntenyDisplay",
- "type" : "LinearSyntenyDisplay"
+ "type" : "LinearSyntenyDisplay",
+ "displayId" : "N2_to_inopinata-LinearSyntenyDisplay"
}
],
- "assemblyNames" : [
- "c_elegans_PRJNA13758",
- "c_inopinata_PRJDB5687"
- ],
- "category" : [
- "Synteny"
- ],
- "trackId" : "N2_to_inopinata",
"adapter" : {
+ "targetAssembly" : "c_elegans_PRJNA13758",
"pafLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_elegans.c_inopinata.paf"
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_elegans.c_inopinata.paf",
+ "locationType" : "UriLocation"
},
- "queryAssembly" : "c_inopinata_PRJDB5687",
- "targetAssembly" : "c_elegans_PRJNA13758",
- "type" : "PAFAdapter"
- },
- "type" : "SyntenyTrack",
- "name" : "C. elegans N2 to C. inopinata"
+ "type" : "PAFAdapter",
+ "queryAssembly" : "c_inopinata_PRJDB5687"
+ }
},
{
+ "category" : [
+ "Synteny"
+ ],
+ "type" : "SyntenyTrack",
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591",
+ "c_remanei_PRJNA53967"
+ ],
+ "name" : "C. japonica to C. remanei",
+ "trackId" : "japonica_to_remanei",
"displays" : [
{
"displayId" : "japonica_to_remanei-DotplotDisplay",
"type" : "DotplotDisplay"
},
{
- "displayId" : "japonica_to_remanei-LinearComparativeDisplay",
- "type" : "LinearComparativeDisplay"
+ "type" : "LinearComparativeDisplay",
+ "displayId" : "japonica_to_remanei-LinearComparativeDisplay"
},
{
"type" : "LinearSyntenyDisplay",
"displayId" : "japonica_to_remanei-LinearSyntenyDisplay"
}
],
- "trackId" : "japonica_to_remanei",
- "category" : [
- "Synteny"
- ],
- "assemblyNames" : [
- "c_japonica_PRJNA12591",
- "c_remanei_PRJNA53967"
- ],
- "name" : "C. japonica to C. remanei",
"adapter" : {
+ "targetAssembly" : "c_japonica_PRJNA12591",
+ "type" : "PAFAdapter",
+ "queryAssembly" : "c_remanei_PRJNA53967",
"pafLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/synteny_data/c_japonica.c_remanei.paf"
- },
- "queryAssembly" : "c_remanei_PRJNA53967",
- "type" : "PAFAdapter",
- "targetAssembly" : "c_japonica_PRJNA12591"
- },
- "type" : "SyntenyTrack"
+ }
+ }
}
],
+ "configuration" : {
+ "logoPath" : {
+ "locationType" : "UriLocation",
+ "uri" : "logo_wormbase_gradient-150px.png"
+ },
+ "theme" : {
+ "palette" : {
+ "tertiary" : {
+ "main" : "#9da9b6"
+ },
+ "secondary" : {
+ "main" : "#29405F"
+ }
+ }
+ }
+ },
"assemblies" : [
{
- "name" : "b_malayi_PRJNA10729",
+ "displayName" : "b_malayi_PRJNA10729",
"sequence" : {
- "displays" : [
- {
- "type" : "LinearReferenceSequenceDisplay",
- "displayId" : "b_malayi_PRJNA10729-LinearReferenceSequenceDisplay"
- }
- ],
- "type" : "ReferenceSequenceTrack",
"adapter" : {
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/b_malayi.PRJNA10729.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
- },
"fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/b_malayi.PRJNA10729.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/b_malayi.PRJNA10729.WS284.genomic.fa.gz"
},
- "gziLocation" : {
+ "faiLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/b_malayi.PRJNA10729.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/b_malayi.PRJNA10729.WS284.genomic.fa.gz.fai"
+ },
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/b_malayi.PRJNA10729.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
},
"type" : "BgzipFastaAdapter"
},
- "trackId" : "b_malayi_PRJNA10729-1646426635733"
+ "trackId" : "b_malayi_PRJNA10729-1646426635733",
+ "type" : "ReferenceSequenceTrack",
+ "displays" : [
+ {
+ "displayId" : "b_malayi_PRJNA10729-LinearReferenceSequenceDisplay",
+ "type" : "LinearReferenceSequenceDisplay"
+ }
+ ]
},
- "displayName" : "b_malayi_PRJNA10729"
+ "name" : "b_malayi_PRJNA10729"
},
{
+ "name" : "c_angaria_PRJNA51225",
"sequence" : {
+ "type" : "ReferenceSequenceTrack",
"displays" : [
{
- "type" : "LinearReferenceSequenceDisplay",
- "displayId" : "c_angaria_PRJNA51225-LinearReferenceSequenceDisplay"
+ "displayId" : "c_angaria_PRJNA51225-LinearReferenceSequenceDisplay",
+ "type" : "LinearReferenceSequenceDisplay"
}
],
- "trackId" : "c_angaria_PRJNA51225-1646426635733",
- "type" : "ReferenceSequenceTrack",
"adapter" : {
- "type" : "BgzipFastaAdapter",
"faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_angaria.PRJNA51225.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_angaria.PRJNA51225.WS284.genomic.fa.gz.fai"
},
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_angaria.PRJNA51225.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_angaria.PRJNA51225.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_angaria.PRJNA51225.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
}
- }
+ },
+ "trackId" : "c_angaria_PRJNA51225-1646426635733"
},
- "displayName" : "c_angaria_PRJNA51225",
- "name" : "c_angaria_PRJNA51225"
+ "displayName" : "c_angaria_PRJNA51225"
},
{
"sequence" : {
- "type" : "ReferenceSequenceTrack",
+ "trackId" : "c_becei_PRJEB28243-1646426635733",
"adapter" : {
- "type" : "BgzipFastaAdapter",
"gziLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz.gzi"
},
- "faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz.fai"
- },
+ "type" : "BgzipFastaAdapter",
"fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
+ },
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_becei.PRJEB28243.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
}
},
- "trackId" : "c_becei_PRJEB28243-1646426635733",
"displays" : [
{
- "displayId" : "c_becei_PRJEB28243-LinearReferenceSequenceDisplay",
- "type" : "LinearReferenceSequenceDisplay"
+ "type" : "LinearReferenceSequenceDisplay",
+ "displayId" : "c_becei_PRJEB28243-LinearReferenceSequenceDisplay"
}
- ]
+ ],
+ "type" : "ReferenceSequenceTrack"
},
- "displayName" : "c_becei_PRJEB28243",
- "name" : "c_becei_PRJEB28243"
+ "name" : "c_becei_PRJEB28243",
+ "displayName" : "c_becei_PRJEB28243"
},
{
- "displayName" : "c_bovis_PRJEB34497",
"sequence" : {
"displays" : [
{
@@ -61786,154 +60499,154 @@
}
],
"type" : "ReferenceSequenceTrack",
+ "trackId" : "c_bovis_PRJEB34497-1646426635733",
"adapter" : {
- "type" : "BgzipFastaAdapter",
- "gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_bovis.PRJEB34497.WS284.genomic.fa.gz.gzi"
- },
"fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_bovis.PRJEB34497.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_bovis.PRJEB34497.WS284.genomic.fa.gz"
},
"faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_bovis.PRJEB34497.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_bovis.PRJEB34497.WS284.genomic.fa.gz.fai"
+ },
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_bovis.PRJEB34497.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
}
- },
- "trackId" : "c_bovis_PRJEB34497-1646426635733"
+ }
},
- "name" : "c_bovis_PRJEB34497"
+ "name" : "c_bovis_PRJEB34497",
+ "displayName" : "c_bovis_PRJEB34497"
},
{
+ "displayName" : "c_brenneri_PRJNA20035",
"sequence" : {
+ "adapter" : {
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ },
+ "faiLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz.fai"
+ },
+ "fastaLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz"
+ }
+ },
+ "trackId" : "c_brenneri_PRJNA20035-1646426635733",
+ "type" : "ReferenceSequenceTrack",
"displays" : [
{
"displayId" : "c_brenneri_PRJNA20035-LinearReferenceSequenceDisplay",
"type" : "LinearReferenceSequenceDisplay"
}
- ],
- "trackId" : "c_brenneri_PRJNA20035-1646426635733",
+ ]
+ },
+ "name" : "c_brenneri_PRJNA20035"
+ },
+ {
+ "name" : "c_briggsae_PRJNA10731",
+ "sequence" : {
+ "trackId" : "c_briggsae_PRJNA10731-1646426635733",
"adapter" : {
- "type" : "BgzipFastaAdapter",
"faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz.fai",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_briggsae.PRJNA10731.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
"fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_briggsae.PRJNA10731.WS284.genomic.fa.gz"
},
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_brenneri.PRJNA20035.WS284.genomic.fa.gz.gzi",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_briggsae.PRJNA10731.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
}
},
+ "displays" : [
+ {
+ "type" : "LinearReferenceSequenceDisplay",
+ "displayId" : "c_briggsae_PRJNA10731-1646426635733-LinearReferenceSequenceDisplay"
+ }
+ ],
"type" : "ReferenceSequenceTrack"
},
- "displayName" : "c_brenneri_PRJNA20035",
- "name" : "c_brenneri_PRJNA20035"
+ "displayName" : "C. briggsae"
},
{
- "displayName" : "C. briggsae",
+ "name" : "c_elegans_PRJEB28388",
"sequence" : {
+ "type" : "ReferenceSequenceTrack",
"displays" : [
{
- "displayId" : "c_briggsae_PRJNA10731-1646426635733-LinearReferenceSequenceDisplay",
+ "displayId" : "c_elegans_PRJEB28388-LinearReferenceSequenceDisplay",
"type" : "LinearReferenceSequenceDisplay"
}
],
"adapter" : {
- "faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_briggsae.PRJNA10731.WS284.genomic.fa.gz.fai"
- },
"fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_briggsae.PRJNA10731.WS284.genomic.fa.gz",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJEB28388.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
- "gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_briggsae.PRJNA10731.WS284.genomic.fa.gz.gzi"
- },
- "type" : "BgzipFastaAdapter"
- },
- "type" : "ReferenceSequenceTrack",
- "trackId" : "c_briggsae_PRJNA10731-1646426635733"
- },
- "name" : "c_briggsae_PRJNA10731"
- },
- {
- "displayName" : "c_elegans_PRJEB28388",
- "sequence" : {
- "type" : "ReferenceSequenceTrack",
- "adapter" : {
- "type" : "BgzipFastaAdapter",
- "fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJEB28388.WS284.genomic.fa.gz"
- },
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJEB28388.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJEB28388.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
}
},
- "trackId" : "c_elegans_PRJEB28388-1646426635733",
- "displays" : [
- {
- "displayId" : "c_elegans_PRJEB28388-LinearReferenceSequenceDisplay",
- "type" : "LinearReferenceSequenceDisplay"
- }
- ]
+ "trackId" : "c_elegans_PRJEB28388-1646426635733"
},
- "name" : "c_elegans_PRJEB28388"
+ "displayName" : "c_elegans_PRJEB28388"
},
{
- "displayName" : "C. elegans N2",
+ "refNameAliases" : {
+ "adapter" : {
+ "location" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/test/jbrowse2/ce_aliases.txt"
+ },
+ "type" : "RefNameAliasAdapter"
+ }
+ },
+ "name" : "c_elegans_PRJNA13758",
"sequence" : {
"displays" : [
{
- "type" : "LinearReferenceSequenceDisplay",
- "displayId" : "c_elegans.PRJNA13758-1645387701624-LinearReferenceSequenceDisplay"
+ "displayId" : "c_elegans.PRJNA13758-1645387701624-LinearReferenceSequenceDisplay",
+ "type" : "LinearReferenceSequenceDisplay"
}
],
"type" : "ReferenceSequenceTrack",
+ "trackId" : "c_elegans_PRJNA13758-1645387701624",
"adapter" : {
- "type" : "BgzipFastaAdapter",
+ "fastaLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA13758.WS278.genomic.fa.gz"
+ },
"faiLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA13758.WS278.genomic.fa.gz.fai"
},
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA13758.WS278.genomic.fa.gz",
- "locationType" : "UriLocation"
- },
"gziLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA13758.WS278.genomic.fa.gz.gzi"
- }
- },
- "trackId" : "c_elegans_PRJNA13758-1645387701624"
- },
- "name" : "c_elegans_PRJNA13758",
- "refNameAliases" : {
- "adapter" : {
- "type" : "RefNameAliasAdapter",
- "location" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/test/jbrowse2/ce_aliases.txt"
- }
+ },
+ "type" : "BgzipFastaAdapter"
}
- }
+ },
+ "displayName" : "C. elegans N2"
},
{
- "name" : "c_elegans_PRJNA275000",
+ "displayName" : "c_elegans_PRJNA275000",
"sequence" : {
- "trackId" : "c_elegans_PRJNA275000-1646426635733",
"adapter" : {
"type" : "BgzipFastaAdapter",
"gziLocation" : {
@@ -61941,14 +60654,15 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA275000.WS284.genomic.fa.gz.gzi"
},
"faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA275000.WS284.genomic.fa.gz.fai"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA275000.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
},
"fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA275000.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_elegans.PRJNA275000.WS284.genomic.fa.gz"
}
},
+ "trackId" : "c_elegans_PRJNA275000-1646426635733",
"type" : "ReferenceSequenceTrack",
"displays" : [
{
@@ -61957,180 +60671,180 @@
}
]
},
- "displayName" : "c_elegans_PRJNA275000"
+ "name" : "c_elegans_PRJNA275000"
},
{
"displayName" : "c_inopinata_PRJDB5687",
"sequence" : {
"type" : "ReferenceSequenceTrack",
+ "displays" : [
+ {
+ "displayId" : "c_inopinata_PRJDB5687-LinearReferenceSequenceDisplay",
+ "type" : "LinearReferenceSequenceDisplay"
+ }
+ ],
"adapter" : {
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_inopinata.PRJDB5687.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
+ },
+ "fastaLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_inopinata.PRJDB5687.WS284.genomic.fa.gz"
+ },
"type" : "BgzipFastaAdapter",
"gziLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_inopinata.PRJDB5687.WS284.genomic.fa.gz.gzi"
- },
- "faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_inopinata.PRJDB5687.WS284.genomic.fa.gz.fai"
- },
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_inopinata.PRJDB5687.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
}
},
- "trackId" : "c_inopinata_PRJDB5687-1646426635733",
- "displays" : [
- {
- "type" : "LinearReferenceSequenceDisplay",
- "displayId" : "c_inopinata_PRJDB5687-LinearReferenceSequenceDisplay"
- }
- ]
+ "trackId" : "c_inopinata_PRJDB5687-1646426635733"
},
"name" : "c_inopinata_PRJDB5687"
},
{
"name" : "c_japonica_PRJNA12591",
"sequence" : {
+ "displays" : [
+ {
+ "displayId" : "c_japonica_PRJNA12591-LinearReferenceSequenceDisplay",
+ "type" : "LinearReferenceSequenceDisplay"
+ }
+ ],
+ "type" : "ReferenceSequenceTrack",
+ "trackId" : "c_japonica_PRJNA12591-1646426635733",
"adapter" : {
- "type" : "BgzipFastaAdapter",
- "gziLocation" : {
+ "fastaLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz"
},
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
- "fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz"
- }
- },
- "type" : "ReferenceSequenceTrack",
- "trackId" : "c_japonica_PRJNA12591-1646426635733",
- "displays" : [
- {
- "displayId" : "c_japonica_PRJNA12591-LinearReferenceSequenceDisplay",
- "type" : "LinearReferenceSequenceDisplay"
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_japonica.PRJNA12591.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
}
- ]
+ }
},
"displayName" : "c_japonica_PRJNA12591"
},
{
+ "displayName" : "c_latens_PRJNA248912",
"sequence" : {
+ "type" : "ReferenceSequenceTrack",
"displays" : [
{
"displayId" : "c_latens_PRJNA248912-LinearReferenceSequenceDisplay",
"type" : "LinearReferenceSequenceDisplay"
}
],
- "type" : "ReferenceSequenceTrack",
"adapter" : {
- "type" : "BgzipFastaAdapter",
- "gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_latens.PRJNA248912.WS284.genomic.fa.gz.gzi"
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_latens.PRJNA248912.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
},
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_latens.PRJNA248912.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
- "fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_latens.PRJNA248912.WS284.genomic.fa.gz"
- }
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_latens.PRJNA248912.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BgzipFastaAdapter"
},
"trackId" : "c_latens_PRJNA248912-1646426635733"
},
- "displayName" : "c_latens_PRJNA248912",
"name" : "c_latens_PRJNA248912"
},
{
+ "displayName" : "c_nigoni_PRJNA384657",
+ "name" : "c_nigoni_PRJNA384657",
"sequence" : {
- "trackId" : "c_nigoni_PRJNA384657-1646426635733",
"adapter" : {
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_nigoni.PRJNA384657.WS284.genomic.fa.gz.gzi",
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_nigoni.PRJNA384657.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
"faiLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_nigoni.PRJNA384657.WS284.genomic.fa.gz.fai"
},
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_nigoni.PRJNA384657.WS284.genomic.fa.gz",
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_nigoni.PRJNA384657.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
- },
- "type" : "BgzipFastaAdapter"
+ }
},
+ "trackId" : "c_nigoni_PRJNA384657-1646426635733",
"type" : "ReferenceSequenceTrack",
"displays" : [
{
- "displayId" : "c_nigoni_PRJNA384657-LinearReferenceSequenceDisplay",
- "type" : "LinearReferenceSequenceDisplay"
+ "type" : "LinearReferenceSequenceDisplay",
+ "displayId" : "c_nigoni_PRJNA384657-LinearReferenceSequenceDisplay"
}
]
- },
- "displayName" : "c_nigoni_PRJNA384657",
- "name" : "c_nigoni_PRJNA384657"
+ }
},
{
+ "displayName" : "c_panamensis_PRJEB28259",
+ "name" : "c_panamensis_PRJEB28259",
"sequence" : {
"displays" : [
{
- "type" : "LinearReferenceSequenceDisplay",
- "displayId" : "c_panamensis_PRJEB28259-LinearReferenceSequenceDisplay"
+ "displayId" : "c_panamensis_PRJEB28259-LinearReferenceSequenceDisplay",
+ "type" : "LinearReferenceSequenceDisplay"
}
],
+ "type" : "ReferenceSequenceTrack",
+ "trackId" : "c_panamensis_PRJEB28259-1646426635733",
"adapter" : {
- "type" : "BgzipFastaAdapter",
"gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
- },
- "faiLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz.fai"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz.gzi"
},
+ "type" : "BgzipFastaAdapter",
"fastaLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz"
+ },
+ "faiLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_panamensis.PRJEB28259.WS284.genomic.fa.gz.fai"
}
- },
- "type" : "ReferenceSequenceTrack",
- "trackId" : "c_panamensis_PRJEB28259-1646426635733"
- },
- "displayName" : "c_panamensis_PRJEB28259",
- "name" : "c_panamensis_PRJEB28259"
+ }
+ }
},
{
+ "displayName" : "c_parvicauda_PRJEB12595",
"sequence" : {
- "displays" : [
- {
- "type" : "LinearReferenceSequenceDisplay",
- "displayId" : "c_parvicauda_PRJEB12595-LinearReferenceSequenceDisplay"
- }
- ],
+ "trackId" : "c_parvicauda_PRJEB12595-1646426635733",
"adapter" : {
- "type" : "BgzipFastaAdapter",
"gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_parvicauda.PRJEB12595.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ },
+ "type" : "BgzipFastaAdapter",
+ "faiLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_parvicauda.PRJEB12595.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_parvicauda.PRJEB12595.WS284.genomic.fa.gz.fai"
},
"fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_parvicauda.PRJEB12595.WS284.genomic.fa.gz"
- },
- "faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_parvicauda.PRJEB12595.WS284.genomic.fa.gz.fai"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_parvicauda.PRJEB12595.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
}
},
- "type" : "ReferenceSequenceTrack",
- "trackId" : "c_parvicauda_PRJEB12595-1646426635733"
+ "displays" : [
+ {
+ "displayId" : "c_parvicauda_PRJEB12595-LinearReferenceSequenceDisplay",
+ "type" : "LinearReferenceSequenceDisplay"
+ }
+ ],
+ "type" : "ReferenceSequenceTrack"
},
- "displayName" : "c_parvicauda_PRJEB12595",
"name" : "c_parvicauda_PRJEB12595"
},
{
@@ -62138,21 +60852,21 @@
"sequence" : {
"displays" : [
{
- "type" : "LinearReferenceSequenceDisplay",
- "displayId" : "c_quiockensis_PRJEB11354-LinearReferenceSequenceDisplay"
+ "displayId" : "c_quiockensis_PRJEB11354-LinearReferenceSequenceDisplay",
+ "type" : "LinearReferenceSequenceDisplay"
}
],
- "trackId" : "c_quiockensis_PRJEB11354-1646426635733",
"type" : "ReferenceSequenceTrack",
+ "trackId" : "c_quiockensis_PRJEB11354-1646426635733",
"adapter" : {
- "type" : "BgzipFastaAdapter",
"gziLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_quiockensis.PRJEB11354.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
},
+ "type" : "BgzipFastaAdapter",
"faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_quiockensis.PRJEB11354.WS284.genomic.fa.gz.fai"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_quiockensis.PRJEB11354.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
},
"fastaLocation" : {
"locationType" : "UriLocation",
@@ -62163,10 +60877,14 @@
"name" : "c_quiockensis_PRJEB11354"
},
{
- "name" : "c_remanei_PRJNA53967",
- "displayName" : "c_remanei_PRJNA53967",
"sequence" : {
- "trackId" : "c_remanei_PRJNA53967-1646426635733",
+ "type" : "ReferenceSequenceTrack",
+ "displays" : [
+ {
+ "displayId" : "c_remanei_PRJNA53967-LinearReferenceSequenceDisplay",
+ "type" : "LinearReferenceSequenceDisplay"
+ }
+ ],
"adapter" : {
"type" : "BgzipFastaAdapter",
"gziLocation" : {
@@ -62174,57 +60892,51 @@
"locationType" : "UriLocation"
},
"faiLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA53967.WS284.genomic.fa.gz.fai"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA53967.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
},
"fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA53967.WS284.genomic.fa.gz"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA53967.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
}
},
- "type" : "ReferenceSequenceTrack",
- "displays" : [
- {
- "displayId" : "c_remanei_PRJNA53967-LinearReferenceSequenceDisplay",
- "type" : "LinearReferenceSequenceDisplay"
- }
- ]
- }
+ "trackId" : "c_remanei_PRJNA53967-1646426635733"
+ },
+ "name" : "c_remanei_PRJNA53967",
+ "displayName" : "c_remanei_PRJNA53967"
},
{
+ "displayName" : "c_remanei_PRJNA577507",
"sequence" : {
- "trackId" : "c_remanei_PRJNA577507-1646426635733",
"adapter" : {
- "type" : "BgzipFastaAdapter",
"faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA577507.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA577507.WS284.genomic.fa.gz.fai"
},
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA577507.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_remanei.PRJNA577507.WS284.genomic.fa.gz.gzi"
}
},
+ "trackId" : "c_remanei_PRJNA577507-1646426635733",
"type" : "ReferenceSequenceTrack",
"displays" : [
{
- "displayId" : "c_remanei_PRJNA577507-LinearReferenceSequenceDisplay",
- "type" : "LinearReferenceSequenceDisplay"
+ "type" : "LinearReferenceSequenceDisplay",
+ "displayId" : "c_remanei_PRJNA577507-LinearReferenceSequenceDisplay"
}
]
},
- "displayName" : "c_remanei_PRJNA577507",
"name" : "c_remanei_PRJNA577507"
},
{
"name" : "c_sinica_PRJNA194557",
- "displayName" : "c_sinica_PRJNA194557",
"sequence" : {
- "type" : "ReferenceSequenceTrack",
"adapter" : {
"type" : "BgzipFastaAdapter",
"gziLocation" : {
@@ -62241,75 +60953,78 @@
}
},
"trackId" : "c_sinica_PRJNA194557-1646426635733",
+ "type" : "ReferenceSequenceTrack",
"displays" : [
{
"displayId" : "c_sinica_PRJNA194557-LinearReferenceSequenceDisplay",
"type" : "LinearReferenceSequenceDisplay"
}
]
- }
+ },
+ "displayName" : "c_sinica_PRJNA194557"
},
{
- "name" : "c_sulstoni_PRJEB12601",
- "displayName" : "c_sulstoni_PRJEB12601",
"sequence" : {
"adapter" : {
+ "type" : "BgzipFastaAdapter",
"gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
+ },
+ "fastaLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz"
},
"faiLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz.fai"
- },
- "fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_sulstoni.PRJEB12601.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
- },
- "type" : "BgzipFastaAdapter"
+ }
},
- "type" : "ReferenceSequenceTrack",
"trackId" : "c_sulstoni_PRJEB12601-1646426635733",
+ "type" : "ReferenceSequenceTrack",
"displays" : [
{
"type" : "LinearReferenceSequenceDisplay",
"displayId" : "c_sulstoni_PRJEB12601-LinearReferenceSequenceDisplay"
}
]
- }
+ },
+ "name" : "c_sulstoni_PRJEB12601",
+ "displayName" : "c_sulstoni_PRJEB12601"
},
{
- "name" : "c_tribulationis_PRJEB12608",
- "displayName" : "c_tribulationis_PRJEB12608",
"sequence" : {
+ "type" : "ReferenceSequenceTrack",
+ "displays" : [
+ {
+ "displayId" : "c_tribulationis_PRJEB12608-LinearReferenceSequenceDisplay",
+ "type" : "LinearReferenceSequenceDisplay"
+ }
+ ],
"adapter" : {
- "gziLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tribulationis.PRJEB12608.WS284.genomic.fa.gz.gzi"
- },
"fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tribulationis.PRJEB12608.WS284.genomic.fa.gz"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tribulationis.PRJEB12608.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
},
"faiLocation" : {
"locationType" : "UriLocation",
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tribulationis.PRJEB12608.WS284.genomic.fa.gz.fai"
},
- "type" : "BgzipFastaAdapter"
- },
- "type" : "ReferenceSequenceTrack",
- "trackId" : "c_tribulationis_PRJEB12608-1646426635733",
- "displays" : [
- {
- "displayId" : "c_tribulationis_PRJEB12608-LinearReferenceSequenceDisplay",
- "type" : "LinearReferenceSequenceDisplay"
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tribulationis.PRJEB12608.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
}
- ]
- }
+ },
+ "trackId" : "c_tribulationis_PRJEB12608-1646426635733"
+ },
+ "name" : "c_tribulationis_PRJEB12608",
+ "displayName" : "c_tribulationis_PRJEB12608"
},
{
"displayName" : "c_tropicalis_PRJNA53597",
"sequence" : {
+ "type" : "ReferenceSequenceTrack",
"displays" : [
{
"displayId" : "c_tropicalis_PRJNA53597-LinearReferenceSequenceDisplay",
@@ -62317,21 +61032,20 @@
}
],
"adapter" : {
- "fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tropicalis.PRJNA53597.WS284.genomic.fa.gz"
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tropicalis.PRJNA53597.WS284.genomic.fa.gz.gzi",
+ "locationType" : "UriLocation"
},
+ "type" : "BgzipFastaAdapter",
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tropicalis.PRJNA53597.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tropicalis.PRJNA53597.WS284.genomic.fa.gz.gzi",
+ "fastaLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_tropicalis.PRJNA53597.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
- },
- "type" : "BgzipFastaAdapter"
+ }
},
- "type" : "ReferenceSequenceTrack",
"trackId" : "c_tropicalis_PRJNA53597-1646426635733"
},
"name" : "c_tropicalis_PRJNA53597"
@@ -62339,18 +61053,11 @@
{
"name" : "c_uteleia_PRJEB12600",
"sequence" : {
- "displays" : [
- {
- "type" : "LinearReferenceSequenceDisplay",
- "displayId" : "c_uteleia_PRJEB12600-LinearReferenceSequenceDisplay"
- }
- ],
"trackId" : "c_uteleia_PRJEB12600-1646426635733",
- "type" : "ReferenceSequenceTrack",
"adapter" : {
"fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_uteleia.PRJEB12600.WS284.genomic.fa.gz"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_uteleia.PRJEB12600.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
},
"faiLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_uteleia.PRJEB12600.WS284.genomic.fa.gz.fai",
@@ -62361,241 +61068,560 @@
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_uteleia.PRJEB12600.WS284.genomic.fa.gz.gzi"
},
"type" : "BgzipFastaAdapter"
- }
- },
- "displayName" : "c_uteleia_PRJEB12600"
- },
- {
- "displayName" : "c_waitukubuli_PRJEB12602",
- "sequence" : {
+ },
"displays" : [
{
- "displayId" : "c_waitukubuli_PRJEB12602-LinearReferenceSequenceDisplay",
+ "displayId" : "c_uteleia_PRJEB12600-LinearReferenceSequenceDisplay",
"type" : "LinearReferenceSequenceDisplay"
}
],
- "type" : "ReferenceSequenceTrack",
+ "type" : "ReferenceSequenceTrack"
+ },
+ "displayName" : "c_uteleia_PRJEB12600"
+ },
+ {
+ "name" : "c_waitukubuli_PRJEB12602",
+ "sequence" : {
+ "trackId" : "c_waitukubuli_PRJEB12602-1646426635733",
"adapter" : {
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
+ "faiLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz.fai"
},
"fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz"
},
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_waitukubuli.PRJEB12602.WS284.genomic.fa.gz.gzi"
},
"type" : "BgzipFastaAdapter"
},
- "trackId" : "c_waitukubuli_PRJEB12602-1646426635733"
+ "displays" : [
+ {
+ "displayId" : "c_waitukubuli_PRJEB12602-LinearReferenceSequenceDisplay",
+ "type" : "LinearReferenceSequenceDisplay"
+ }
+ ],
+ "type" : "ReferenceSequenceTrack"
},
- "name" : "c_waitukubuli_PRJEB12602"
+ "displayName" : "c_waitukubuli_PRJEB12602"
},
{
- "name" : "c_zanzibari_PRJEB12596",
"sequence" : {
+ "type" : "ReferenceSequenceTrack",
"displays" : [
{
- "displayId" : "c_zanzibari_PRJEB12596-LinearReferenceSequenceDisplay",
- "type" : "LinearReferenceSequenceDisplay"
+ "type" : "LinearReferenceSequenceDisplay",
+ "displayId" : "c_zanzibari_PRJEB12596-LinearReferenceSequenceDisplay"
}
],
"adapter" : {
- "gziLocation" : {
+ "faiLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz.fai"
},
"fastaLocation" : {
"uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz.fai",
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/c_zanzibari.PRJEB12596.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
- },
- "type" : "BgzipFastaAdapter"
+ }
},
- "type" : "ReferenceSequenceTrack",
"trackId" : "c_zanzibari_PRJEB12596-1646426635733"
},
+ "name" : "c_zanzibari_PRJEB12596",
"displayName" : "c_zanzibari_PRJEB12596"
},
{
"displayName" : "o_tipulae_PRJEB15512",
+ "name" : "o_tipulae_PRJEB15512",
"sequence" : {
- "type" : "ReferenceSequenceTrack",
"adapter" : {
"faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz.fai"
},
"fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
},
"gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_tipulae.PRJEB15512.WS284.genomic.fa.gz.gzi"
},
"type" : "BgzipFastaAdapter"
},
"trackId" : "o_tipulae_PRJEB15512-1646426635733",
- "displays" : [
- {
- "displayId" : "o_tipulae_PRJEB15512-LinearReferenceSequenceDisplay",
- "type" : "LinearReferenceSequenceDisplay"
- }
- ]
- },
- "name" : "o_tipulae_PRJEB15512"
- },
- {
- "name" : "o_volvulus_PRJEB513",
- "displayName" : "o_volvulus_PRJEB513",
- "sequence" : {
"type" : "ReferenceSequenceTrack",
- "adapter" : {
- "type" : "BgzipFastaAdapter",
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_volvulus.PRJEB513.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
- },
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_volvulus.PRJEB513.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
- },
- "fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_volvulus.PRJEB513.WS284.genomic.fa.gz"
- }
- },
- "trackId" : "o_volvulus_PRJEB513-1646426635733",
"displays" : [
{
- "displayId" : "o_volvulus_PRJEB513-LinearReferenceSequenceDisplay",
- "type" : "LinearReferenceSequenceDisplay"
+ "type" : "LinearReferenceSequenceDisplay",
+ "displayId" : "o_tipulae_PRJEB15512-LinearReferenceSequenceDisplay"
}
]
}
},
{
- "name" : "p_pacificus_PRJNA12644",
- "displayName" : "p_pacificus_PRJNA12644",
"sequence" : {
+ "type" : "ReferenceSequenceTrack",
"displays" : [
{
- "displayId" : "p_pacificus_PRJNA12644-LinearReferenceSequenceDisplay",
- "type" : "LinearReferenceSequenceDisplay"
+ "type" : "LinearReferenceSequenceDisplay",
+ "displayId" : "o_volvulus_PRJEB513-LinearReferenceSequenceDisplay"
}
],
- "trackId" : "p_pacificus_PRJNA12644-1646426635733",
- "type" : "ReferenceSequenceTrack",
"adapter" : {
- "type" : "BgzipFastaAdapter",
- "gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_pacificus.PRJNA12644.WS284.genomic.fa.gz.gzi",
- "locationType" : "UriLocation"
+ "faiLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_volvulus.PRJEB513.WS284.genomic.fa.gz.fai"
},
"fastaLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_pacificus.PRJNA12644.WS284.genomic.fa.gz"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_volvulus.PRJEB513.WS284.genomic.fa.gz"
},
- "faiLocation" : {
+ "type" : "BgzipFastaAdapter",
+ "gziLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_pacificus.PRJNA12644.WS284.genomic.fa.gz.fai"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/o_volvulus.PRJEB513.WS284.genomic.fa.gz.gzi"
}
- }
- }
+ },
+ "trackId" : "o_volvulus_PRJEB513-1646426635733"
+ },
+ "name" : "o_volvulus_PRJEB513",
+ "displayName" : "o_volvulus_PRJEB513"
},
{
- "displayName" : "p_redivivus_PRJNA186477",
+ "displayName" : "p_pacificus_PRJNA12644",
+ "name" : "p_pacificus_PRJNA12644",
"sequence" : {
- "type" : "ReferenceSequenceTrack",
"adapter" : {
- "type" : "BgzipFastaAdapter",
"gziLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz.gzi"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_pacificus.PRJNA12644.WS284.genomic.fa.gz.gzi"
},
+ "type" : "BgzipFastaAdapter",
"faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz.fai",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_pacificus.PRJNA12644.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
},
"fastaLocation" : {
- "locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_pacificus.PRJNA12644.WS284.genomic.fa.gz",
+ "locationType" : "UriLocation"
}
},
- "trackId" : "p_redivivus_PRJNA186477-1646426635733",
+ "trackId" : "p_pacificus_PRJNA12644-1646426635733",
+ "type" : "ReferenceSequenceTrack",
"displays" : [
{
"type" : "LinearReferenceSequenceDisplay",
- "displayId" : "p_redivivus_PRJNA186477-LinearReferenceSequenceDisplay"
+ "displayId" : "p_pacificus_PRJNA12644-LinearReferenceSequenceDisplay"
}
]
- },
- "name" : "p_redivivus_PRJNA186477"
+ }
},
{
+ "displayName" : "p_redivivus_PRJNA186477",
+ "name" : "p_redivivus_PRJNA186477",
"sequence" : {
- "displays" : [
- {
- "displayId" : "s_ratti_PRJEB125-LinearReferenceSequenceDisplay",
- "type" : "LinearReferenceSequenceDisplay"
- }
- ],
+ "trackId" : "p_redivivus_PRJNA186477-1646426635733",
"adapter" : {
- "faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/s_ratti.PRJEB125.WS284.genomic.fa.gz.fai",
- "locationType" : "UriLocation"
- },
"fastaLocation" : {
"locationType" : "UriLocation",
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/s_ratti.PRJEB125.WS284.genomic.fa.gz"
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz"
+ },
+ "faiLocation" : {
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz.fai",
+ "locationType" : "UriLocation"
},
"gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/s_ratti.PRJEB125.WS284.genomic.fa.gz.gzi",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/p_redivivus.PRJNA186477.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
},
"type" : "BgzipFastaAdapter"
},
- "type" : "ReferenceSequenceTrack",
- "trackId" : "s_ratti_PRJEB125-1646426635733"
- },
- "displayName" : "s_ratti_PRJEB125",
- "name" : "s_ratti_PRJEB125"
+ "displays" : [
+ {
+ "type" : "LinearReferenceSequenceDisplay",
+ "displayId" : "p_redivivus_PRJNA186477-LinearReferenceSequenceDisplay"
+ }
+ ],
+ "type" : "ReferenceSequenceTrack"
+ }
},
{
- "name" : "t_muris_PRJEB126",
- "displayName" : "t_muris_PRJEB126",
+ "displayName" : "s_ratti_PRJEB125",
"sequence" : {
"displays" : [
{
- "displayId" : "t_muris_PRJEB126-LinearReferenceSequenceDisplay",
- "type" : "LinearReferenceSequenceDisplay"
+ "type" : "LinearReferenceSequenceDisplay",
+ "displayId" : "s_ratti_PRJEB125-LinearReferenceSequenceDisplay"
}
],
"type" : "ReferenceSequenceTrack",
+ "trackId" : "s_ratti_PRJEB125-1646426635733",
"adapter" : {
"gziLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz.gzi",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/s_ratti.PRJEB125.WS284.genomic.fa.gz.gzi",
"locationType" : "UriLocation"
},
+ "type" : "BgzipFastaAdapter",
"fastaLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/s_ratti.PRJEB125.WS284.genomic.fa.gz",
"locationType" : "UriLocation"
},
"faiLocation" : {
- "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz.fai",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/s_ratti.PRJEB125.WS284.genomic.fa.gz.fai",
"locationType" : "UriLocation"
+ }
+ }
+ },
+ "name" : "s_ratti_PRJEB125"
+ },
+ {
+ "sequence" : {
+ "trackId" : "t_muris_PRJEB126-1646426635733",
+ "adapter" : {
+ "fastaLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz"
+ },
+ "faiLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz.fai"
+ },
+ "gziLocation" : {
+ "locationType" : "UriLocation",
+ "uri" : "https://s3.amazonaws.com/wormbase-modencode/fasta/current/t_muris.PRJEB126.WS284.genomic.fa.gz.gzi"
},
"type" : "BgzipFastaAdapter"
},
- "trackId" : "t_muris_PRJEB126-1646426635733"
+ "displays" : [
+ {
+ "displayId" : "t_muris_PRJEB126-LinearReferenceSequenceDisplay",
+ "type" : "LinearReferenceSequenceDisplay"
+ }
+ ],
+ "type" : "ReferenceSequenceTrack"
+ },
+ "name" : "t_muris_PRJEB126",
+ "displayName" : "t_muris_PRJEB126"
+ }
+ ],
+ "aggregateTextSearchAdapters" : [
+ {
+ "textSearchAdapterId" : "b_malayi_PRJNA10729_generate-names-index",
+ "assemblyNames" : [
+ "b_malayi_PRJNA10729"
+ ],
+ "type" : "JBrowse1TextSearchAdapter",
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/b_malayi_PRJNA10729/names/"
+ }
+ },
+ {
+ "type" : "JBrowse1TextSearchAdapter",
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_angaria_PRJNA51225/names/"
+ },
+ "assemblyNames" : [
+ "c_angaria_PRJNA51225"
+ ],
+ "textSearchAdapterId" : "c_angaria_PRJNA51225_generate-names-index"
+ },
+ {
+ "textSearchAdapterId" : "c_becei_PRJEB28243_generate-names-index",
+ "assemblyNames" : [
+ "c_becei_PRJEB28243"
+ ],
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_becei_PRJEB28243/names/"
+ },
+ "type" : "JBrowse1TextSearchAdapter"
+ },
+ {
+ "assemblyNames" : [
+ "c_bovis_PRJEB34497"
+ ],
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_bovis_PRJEB34497/names/"
+ },
+ "type" : "JBrowse1TextSearchAdapter",
+ "textSearchAdapterId" : "c_bovis_PRJEB34497_generate-names-index"
+ },
+ {
+ "textSearchAdapterId" : "c_brenneri_PRJNA20035_generate-names-index",
+ "type" : "JBrowse1TextSearchAdapter",
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_brenneri_PRJNA20035/names/"
+ },
+ "assemblyNames" : [
+ "c_brenneri_PRJNA20035"
+ ]
+ },
+ {
+ "textSearchAdapterId" : "c_briggsae_PRJNA10731_generate-names-index",
+ "type" : "JBrowse1TextSearchAdapter",
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_briggsae_PRJNA10731/names/"
+ },
+ "assemblyNames" : [
+ "c_briggsae_PRJNA10731"
+ ]
+ },
+ {
+ "textSearchAdapterId" : "c_elegans_PRJEB28388_generate-names-index",
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJEB28388/names/"
+ },
+ "type" : "JBrowse1TextSearchAdapter",
+ "assemblyNames" : [
+ "c_elegans_PRJEB28388"
+ ]
+ },
+ {
+ "textSearchAdapterId" : "c_elegans_PRJNA13758_generate-names-index",
+ "assemblyNames" : [
+ "c_elegans_PRJNA13758"
+ ],
+ "type" : "JBrowse1TextSearchAdapter",
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA13758/names/"
+ }
+ },
+ {
+ "textSearchAdapterId" : "c_elegans_PRJNA275000_generate-names-index",
+ "assemblyNames" : [
+ "c_elegans_PRJNA275000"
+ ],
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_elegans_PRJNA275000/names/"
+ },
+ "type" : "JBrowse1TextSearchAdapter"
+ },
+ {
+ "textSearchAdapterId" : "c_inopinata_PRJDB5687_generate-names-index",
+ "assemblyNames" : [
+ "c_inopinata_PRJDB5687"
+ ],
+ "type" : "JBrowse1TextSearchAdapter",
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_inopinata_PRJDB5687/names/"
+ }
+ },
+ {
+ "textSearchAdapterId" : "c_japonica_PRJNA12591_generate-names-index",
+ "assemblyNames" : [
+ "c_japonica_PRJNA12591"
+ ],
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_japonica_PRJNA12591/names/"
+ },
+ "type" : "JBrowse1TextSearchAdapter"
+ },
+ {
+ "textSearchAdapterId" : "c_latens_PRJNA248912_generate-names-index",
+ "assemblyNames" : [
+ "c_latens_PRJNA248912"
+ ],
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_latens_PRJNA248912/names/"
+ },
+ "type" : "JBrowse1TextSearchAdapter"
+ },
+ {
+ "textSearchAdapterId" : "c_nigoni_PRJNA384657_generate-names-index",
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_nigoni_PRJNA384657/names/"
+ },
+ "type" : "JBrowse1TextSearchAdapter",
+ "assemblyNames" : [
+ "c_nigoni_PRJNA384657"
+ ]
+ },
+ {
+ "textSearchAdapterId" : "c_panamensis_PRJEB28259_generate-names-index",
+ "assemblyNames" : [
+ "c_panamensis_PRJEB28259"
+ ],
+ "type" : "JBrowse1TextSearchAdapter",
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_panamensis_PRJEB28259/names/"
+ }
+ },
+ {
+ "textSearchAdapterId" : "c_parvicauda_PRJEB12595_generate-names-index",
+ "assemblyNames" : [
+ "c_parvicauda_PRJEB12595"
+ ],
+ "type" : "JBrowse1TextSearchAdapter",
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_parvicauda_PRJEB12595/names/"
}
+ },
+ {
+ "textSearchAdapterId" : "c_quiockensis_PRJEB11354_generate-names-index",
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_quiockensis_PRJEB11354/names/"
+ },
+ "type" : "JBrowse1TextSearchAdapter",
+ "assemblyNames" : [
+ "c_quiockensis_PRJEB11354"
+ ]
+ },
+ {
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA53967/names/"
+ },
+ "type" : "JBrowse1TextSearchAdapter",
+ "assemblyNames" : [
+ "c_remanei_PRJNA53967"
+ ],
+ "textSearchAdapterId" : "c_remanei_PRJNA53967_generate-names-index"
+ },
+ {
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_remanei_PRJNA577507/names/"
+ },
+ "type" : "JBrowse1TextSearchAdapter",
+ "assemblyNames" : [
+ "c_remanei_PRJNA577507"
+ ],
+ "textSearchAdapterId" : "c_remanei_PRJNA577507_generate-names-index"
+ },
+ {
+ "textSearchAdapterId" : "c_sinica_PRJNA194557_generate-names-index",
+ "assemblyNames" : [
+ "c_sinica_PRJNA194557"
+ ],
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sinica_PRJNA194557/names/"
+ },
+ "type" : "JBrowse1TextSearchAdapter"
+ },
+ {
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_sulstoni_PRJEB12601/names/"
+ },
+ "type" : "JBrowse1TextSearchAdapter",
+ "assemblyNames" : [
+ "c_sulstoni_PRJEB12601"
+ ],
+ "textSearchAdapterId" : "c_sulstoni_PRJEB12601_generate-names-index"
+ },
+ {
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tribulationis_PRJEB12608/names/"
+ },
+ "type" : "JBrowse1TextSearchAdapter",
+ "assemblyNames" : [
+ "c_tribulationis_PRJEB12608"
+ ],
+ "textSearchAdapterId" : "c_tribulationis_PRJEB12608_generate-names-index"
+ },
+ {
+ "textSearchAdapterId" : "c_tropicalis_PRJNA53597_generate-names-index",
+ "assemblyNames" : [
+ "c_tropicalis_PRJNA53597"
+ ],
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_tropicalis_PRJNA53597/names/"
+ },
+ "type" : "JBrowse1TextSearchAdapter"
+ },
+ {
+ "textSearchAdapterId" : "c_uteleia_PRJEB12600_generate-names-index",
+ "assemblyNames" : [
+ "c_uteleia_PRJEB12600"
+ ],
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_uteleia_PRJEB12600/names/"
+ },
+ "type" : "JBrowse1TextSearchAdapter"
+ },
+ {
+ "assemblyNames" : [
+ "c_waitukubuli_PRJEB12602"
+ ],
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_waitukubuli_PRJEB12602/names/"
+ },
+ "type" : "JBrowse1TextSearchAdapter",
+ "textSearchAdapterId" : "c_waitukubuli_PRJEB12602_generate-names-index"
+ },
+ {
+ "assemblyNames" : [
+ "c_zanzibari_PRJEB12596"
+ ],
+ "type" : "JBrowse1TextSearchAdapter",
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/c_zanzibari_PRJEB12596/names/"
+ },
+ "textSearchAdapterId" : "c_zanzibari_PRJEB12596_generate-names-index"
+ },
+ {
+ "type" : "JBrowse1TextSearchAdapter",
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_tipulae_PRJEB15512/names/"
+ },
+ "assemblyNames" : [
+ "o_tipulae_PRJEB15512"
+ ],
+ "textSearchAdapterId" : "o_tipulae_PRJEB15512_generate-names-index"
+ },
+ {
+ "assemblyNames" : [
+ "o_volvulus_PRJEB513"
+ ],
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/o_volvulus_PRJEB513/names/"
+ },
+ "type" : "JBrowse1TextSearchAdapter",
+ "textSearchAdapterId" : "o_volvulus_PRJEB513_generate-names-index"
+ },
+ {
+ "assemblyNames" : [
+ "p_pacificus_PRJNA12644"
+ ],
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_pacificus_PRJNA12644/names/"
+ },
+ "type" : "JBrowse1TextSearchAdapter",
+ "textSearchAdapterId" : "p_pacificus_PRJNA12644_generate-names-index"
+ },
+ {
+ "assemblyNames" : [
+ "p_redivivus_PRJNA186477"
+ ],
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/p_redivivus_PRJNA186477/names/"
+ },
+ "type" : "JBrowse1TextSearchAdapter",
+ "textSearchAdapterId" : "p_redivivus_PRJNA186477_generate-names-index"
+ },
+ {
+ "assemblyNames" : [
+ "s_ratti_PRJEB125"
+ ],
+ "type" : "JBrowse1TextSearchAdapter",
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/s_ratti_PRJEB125/names/"
+ },
+ "textSearchAdapterId" : "s_ratti_PRJEB125_generate-names-index"
+ },
+ {
+ "type" : "JBrowse1TextSearchAdapter",
+ "namesIndexLocation" : {
+ "uri" : "https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS295/t_muris_PRJEB126/names/"
+ },
+ "assemblyNames" : [
+ "t_muris_PRJEB126"
+ ],
+ "textSearchAdapterId" : "t_muris_PRJEB126_generate-names-index"
}
],
"plugins" : [
@@ -62606,10 +61632,10 @@
"name" : "HexJexlPlugin"
},
{
+ "name" : "VariantColorPlugin",
"umdLoc" : {
"uri" : "variantColor_plugin.js"
- },
- "name" : "VariantColorPlugin"
+ }
},
{
"name" : "JBrowseSiteSpecificHelp",
@@ -62617,21 +61643,5 @@
"uri" : "plugins/JBrowseSiteSpecificHelp/jbrowse-site-specific-help.umd.development.js"
}
}
- ],
- "configuration" : {
- "logoPath" : {
- "locationType" : "UriLocation",
- "uri" : "logo_wormbase_gradient-150px.png"
- },
- "theme" : {
- "palette" : {
- "tertiary" : {
- "main" : "#9da9b6"
- },
- "secondary" : {
- "main" : "#29405F"
- }
- }
- }
- }
+ ]
}