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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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9 changes: 4 additions & 5 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 -->

### PR Workflow
Expand All @@ -36,7 +34,8 @@ 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`)?
- [ ] (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 @@ -13,6 +13,7 @@ and this project follows to [Calendar Versioning](https://calver.org/).

- Nishimura 2024 10.1371/journal.pone.0295924 (added by @alexhbnr)
- Kirdok 2023 10.1038/s41598-023-48762-6 (added by @annaewhite)
- 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 @@ -2484,3 +2484,7 @@ Kirdok2024 2024 10.1038/s41598-023-48762-6 ble008 SRA PRJNA994900 SRS18297826 bl
Kirdok2024 2024 10.1038/s41598-023-48762-6 ble008 SRA PRJNA994900 SRS18297826 ble008-b1e1l5p2 double AmpliTaq Gold DNA none NA Illumina HiSeq X PAIRED WGS 52264823 SRR25280082 ftp.sra.ebi.ac.uk/vol1/fastq/SRR252/082/SRR25280082/SRR25280082.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR252/082/SRR25280082/SRR25280082_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR252/082/SRR25280082/SRR25280082_2.fastq.gz 1efe3d2c79ab223d1988bf735c05cb5d 2209894253;46991596;49895817
Kirdok2024 2024 10.1038/s41598-023-48762-6 ble008 SRA PRJNA994900 SRS18297826 ble008-b1e1l5p2 double AmpliTaq Gold DNA none NA Illumina HiSeq X PAIRED WGS 65330421 SRR25280081 ftp.sra.ebi.ac.uk/vol1/fastq/SRR252/081/SRR25280081/SRR25280081.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR252/081/SRR25280081/SRR25280081_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR252/081/SRR25280081/SRR25280081_2.fastq.gz 9518643cbb0a4e75c8c989209c13ffdd 2772581392;72830775;77022791
Kirdok2024 2024 10.1038/s41598-023-48762-6 ble008 SRA PRJNA994900 SRS18297826 ble008-b1e2l1p1 double AmpliTaq Gold DNA none NA Illumina HiSeq X PAIRED WGS 50058906 SRR25280080 ftp.sra.ebi.ac.uk/vol1/fastq/SRR252/080/SRR25280080/SRR25280080.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR252/080/SRR25280080/SRR25280080_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR252/080/SRR25280080/SRR25280080_2.fastq.gz fb9a0a91efd12fb098ae5763c774f1e3 2393856382;80774306;82268992
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 @@ -1418,3 +1418,7 @@ Nishimura2024 2024 10.1371/journal.pone.0295924 Torihama 35.557 135.898 Japan TH
Kirdok2024 2024 10.1038/s41598-023-48762-6 Huseby Klev 58.16 11.48 Sweden ble004 Homo sapiens 9700 10.1038/s41598-023-48762-6 oral birch pitch SRA PRJNA994900 SRS18297824
Kirdok2024 2024 10.1038/s41598-023-48762-6 Huseby Klev 58.16 11.48 Sweden ble007 Homo sapiens 9700 10.1038/s41598-023-48762-6 oral birch pitch SRA PRJNA994900 SRS18297825
Kirdok2024 2024 10.1038/s41598-023-48762-6 Huseby Klev 58.16 11.48 Sweden ble008 Homo sapiens 9700 10.1038/s41598-023-48762-6 oral birch pitch SRA PRJNA994900 SRS18297826
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
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