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Fioriin2024 samples #1149

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merged 13 commits into from
Mar 28, 2024
Merged

Fioriin2024 samples #1149

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a6fc9a1
Fioriin2024 samples
jfy133 Mar 22, 2024
83f3dd3
Fix C14 DOI
jfy133 Mar 22, 2024
4507c4a
Simply PR template and add instructions for autofill
jfy133 Mar 22, 2024
bc5350e
Merge branch 'master' into Fiorin2024
jfy133 Mar 22, 2024
ab7bf2b
Merge branch 'master' into Fiorin2024
jfy133 Mar 22, 2024
ceaf8d5
Merge branch 'Fiorin2024' of github.com:SPAAM-community/AncientMetage…
jfy133 Mar 22, 2024
2591bff
Add library metadata
jfy133 Mar 25, 2024
3093e39
Merge branch 'master' into Fiorin2024
jfy133 Mar 25, 2024
9d56286
Revert removing trailing zeros
alexhbnr Mar 27, 2024
43f3fad
Add Fiorin2024 samples and fix sample ages
alexhbnr Mar 27, 2024
15ea790
Update polymerase following the supplementary material
alexhbnr Mar 27, 2024
bd7c16d
Update CHANGELOG.md
alexhbnr Mar 27, 2024
41eb1f7
Merge branch 'master' into Fiorin2024
alexhbnr Mar 27, 2024
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7 changes: 1 addition & 6 deletions .github/pull_request_template.md
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Expand Up @@ -11,8 +11,6 @@ For the following list(s):
- [ ] ancientmetagenome-hostassociated ([README](https://github.com/SPAAM-workshop/AncientMetagenomeDir/tree/master/ancientmetagenome-hostassociated))
- [ ] ancientsinglegenome-hostassociated ([README](https://github.com/SPAAM-workshop/AncientMetagenomeDir/tree/master/ancientsinglegenome-hostassociated))

### Publication Information

This is to close <!-- REPLACE this comment (including the < > symbols) with a hashtag and the corresponding issue number here, e.g. #10 -->

### Checklist (New publications)
Expand All @@ -25,11 +23,8 @@ This is to close <!-- REPLACE this comment (including the < > symbols) with a ha
- [ ] Samples are shotgun metagenomes and not amplicon data
- Note: hostassociated-singlegenome may also contain whole-genome enriched data
- [ ] Checked the list follows conventions as described in the corresponding sample type's README file (e.g. using ERS/SRS accession codes for ENA/SRA)?
- [ ] Library metadata has been added
- [ ] **Once sample table validation completed** Library metadata has been added
- Use `@spaam-bot please autofill <table_name> <project_id>` to get a half-filled template! May take a minute or so to get the comment with the file
- Fill in template, and **verify** autofill data correct!
- Once filled in, append(!) the new rows to the end of the corresponding library metadata file
- [ ] Changelog is updated to include the publication under 'Added'?
- [ ] Pull request has passed validation checks (see automated comment from `github-bot`)?
- [ ] Review requested from `@SPAAM-community/ancientmetagenomedir`?
- [ ] (If applicable) Made a separate PR to add new categories to controlled lists (stored under `/assets/enums`, e.g. material or archive)? If so the corresponding PR is here: <!-- REPLACE this comment (including the < > symbols) with that PR -->
1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -12,6 +12,7 @@ and this project follows to [Calendar Versioning](https://calver.org/).
#### Ancient Metagenome: Host Associated

- Nishimura 2024 10.1371/journal.pone.0295924 (added by @alexhbnr)
- Fiorin 2024 10.1038/s41598-024-52422-8 (added by @jfy133)

#### Ancient Single Genome: Host Associated

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4 changes: 4 additions & 0 deletions ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv
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Expand Up @@ -2414,3 +2414,7 @@ Nishimura2024 2024 10.1371/journal.pone.0295924 TH62 DDBJ PRJDB15258 DRS361428 T
Nishimura2024 2024 10.1371/journal.pone.0295924 TH58 DDBJ PRJDB15258 DRS361172 TH58 double Q5 Hot Start High-Fidelity DNA none NA Illumina NovaSeq 6000 PAIRED WGS 716702703 DRR525849 ftp.sra.ebi.ac.uk/vol1/fastq/DRR525/DRR525849/DRR525849_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR525/DRR525849/DRR525849_2.fastq.gz 020c909fa101c6930412f39b2f68ea30;50c9c6a1e29fac5a0224b4eefa300ede 29657479008;29352434704
Nishimura2024 2024 10.1371/journal.pone.0295924 TH74 DDBJ PRJDB15258 DRS361450 TH74 double Q5 Hot Start High-Fidelity DNA none NA Illumina NovaSeq 6000 PAIRED WGS 442910397 DRR525851 ftp.sra.ebi.ac.uk/vol1/fastq/DRR525/DRR525851/DRR525851_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR525/DRR525851/DRR525851_2.fastq.gz 354980633d2c292a4a2caa5383c9ff1f;484099e646c08b42bb760f983143c49b 17964963775;17725707445
Nishimura2024 2024 10.1371/journal.pone.0295924 TH55 DDBJ PRJDB15258 DRS361563 TH55 double Q5 Hot Start High-Fidelity DNA none NA Illumina NovaSeq 6000 PAIRED WGS 770783108 DRR525848 ftp.sra.ebi.ac.uk/vol1/fastq/DRR525/DRR525848/DRR525848_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/DRR525/DRR525848/DRR525848_2.fastq.gz 4c064fa9c675b5b6d54a94de99ae5abc;57ace6b8737fd24d72e9b619614f6018 36029292326;33687517751
Fiorin2024 2024 10.1038/s41598-024-52422-8 P18 ENA PRJEB67363 ERS16464521 DC-AE_10 double PfuTurbo Cx Hotstart DNA none NA Illumina HiSeq X PAIRED WGS 25699726 ERR12115115 ftp.sra.ebi.ac.uk/vol1/fastq/ERR121/015/ERR12115115/ERR12115115_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR121/015/ERR12115115/ERR12115115_2.fastq.gz c7b16255657f02b6c8ab45b3fb93d509;a15b1de896d26a28d856e9a104e74265 806734163;784835478
Fiorin2024 2024 10.1038/s41598-024-52422-8 P68 ENA PRJEB67363 ERS16464520 DC-AE_9 double PfuTurbo Cx Hotstart DNA none NA Illumina HiSeq X PAIRED WGS 33962022 ERR12115114 ftp.sra.ebi.ac.uk/vol1/fastq/ERR121/014/ERR12115114/ERR12115114_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR121/014/ERR12115114/ERR12115114_2.fastq.gz 821372f3c4d767098a619713e857d8cc;a4e78a6375b52d3faf94ea5312ac39a5 1018886070;1048915555
Fiorin2024 2024 10.1038/s41598-024-52422-8 P45 ENA PRJEB67363 ERS16464519 DC-AA_2 double PfuTurbo Cx Hotstart DNA none NA Illumina HiSeq X PAIRED WGS 44872334 ERR12115113 ftp.sra.ebi.ac.uk/vol1/fastq/ERR121/013/ERR12115113/ERR12115113_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR121/013/ERR12115113/ERR12115113_2.fastq.gz d3c59d642b1b6b0bf4884105fa060eb4;a2328acfc96e1f6ef2a314e21fae622b 1478354571;1619082110
Fiorin2024 2024 10.1038/s41598-024-52422-8 P112 ENA PRJEB67363 ERS16464522 DC-AE_11 double PfuTurbo Cx Hotstart DNA none NA Illumina HiSeq X PAIRED WGS 42434054 ERR12115116 ftp.sra.ebi.ac.uk/vol1/fastq/ERR121/016/ERR12115116/ERR12115116_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR121/016/ERR12115116/ERR12115116_2.fastq.gz 7d13708ed0c692b4aac63c79af8de5f3;073b3943793611fe9c30c58b6869f87e 1254782524;1309498120
4 changes: 4 additions & 0 deletions ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv
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Expand Up @@ -1415,3 +1415,7 @@ Nishimura2024 2024 10.1371/journal.pone.0295924 Torihama 35.557 135.898 Japan TH
Nishimura2024 2024 10.1371/journal.pone.0295924 Torihama 35.557 135.898 Japan TH58 Homo sapiens 6400 10.1371/journal.pone.0295924 gut palaeofaeces DDBJ PRJDB15258 DRS361172
Nishimura2024 2024 10.1371/journal.pone.0295924 Torihama 35.557 135.898 Japan TH74 Homo sapiens 6400 10.1371/journal.pone.0295924 gut palaeofaeces DDBJ PRJDB15258 DRS361450
Nishimura2024 2024 10.1371/journal.pone.0295924 Torihama 35.557 135.898 Japan TH55 Homo sapiens 6400 10.1371/journal.pone.0295924 gut palaeofaeces DDBJ PRJDB15258 DRS361563
Fiorin2024 2024 10.1038/s41598-024-52422-8 St Leonard's Leper Hospital 52.576 -0.254 United Kingdom P18 Homo sapiens 900 10.5284/1046113 oral dental calculus ENA PRJEB67363 ERS16464521
Fiorin2024 2024 10.1038/s41598-024-52422-8 St Leonard's Leper Hospital 52.576 -0.254 United Kingdom P68 Homo sapiens 900 10.5284/1046113 oral dental calculus ENA PRJEB67363 ERS16464520
Fiorin2024 2024 10.1038/s41598-024-52422-8 St Leonard's Leper Hospital 52.576 -0.254 United Kingdom P45 Homo sapiens 900 10.5284/1046113 oral dental calculus ENA PRJEB67363 ERS16464519
Fiorin2024 2024 10.1038/s41598-024-52422-8 St Leonard's Leper Hospital 52.576 -0.254 United Kingdom P112 Homo sapiens 900 10.5284/1046113 oral dental calculus ENA PRJEB67363 ERS16464522