From d32d5b90e5a7fe3a1972238b486619a31484f830 Mon Sep 17 00:00:00 2001 From: MagdalenaHC Date: Mon, 7 Oct 2024 13:46:38 +0200 Subject: [PATCH 1/5] Susat2024 --- .../samples/ancientsinglegenome-hostassociated_samples.tsv | 2 ++ 1 file changed, 2 insertions(+) diff --git a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv index f34db1b16..f1fe53bec 100644 --- a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv +++ b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv @@ -717,3 +717,5 @@ White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.720 Kazakhstan B2_B3 White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.720 Kazakhstan B2_B5 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769381 White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.720 Kazakhstan B2_B6 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769382 White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.720 Kazakhstan B2_B7 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769383 +Susat2024 2024 10.1038/s42003-024-06676-7 Warburg 51.488 9.133 Germany Warburg_1 Homo sapiens 5200 10.1038/s42003-024-06676-7 bacteria Yersinia pestis tooth chromosome ENA raw PRJEB49648 ERR13081220 +Susat2024 2024 10.1038/s42003-024-06676-7 Warburg 51.488 9.133 Germany Warburg_2 Homo sapiens 5100 10.1038/s42003-024-06676-7 bacteria Yersinia pestis tooth chromosome ENA raw PRJEB49648 ERR13081216,ERR13081217,ERR13081218,ERR13081219 From 8739f02d4d995ac3ea5436bfdd82a8d3d61e87e8 Mon Sep 17 00:00:00 2001 From: MagdalenaHC Date: Mon, 7 Oct 2024 14:02:51 +0200 Subject: [PATCH 2/5] Susat2024 --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 57c3d31e6..48992ba85 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -17,6 +17,7 @@ and this project follows to [Calendar Versioning](https://calver.org/). #### Ancient Single Genome: Host Associated - White 2021 10.3390/biology10121324 (added by @DianaSpurite, @jfy133, and @alexhbnr) +- Susat 2024 10.1038/s42003-024-06676-7 (added by @MagdalenaHC) #### Ancient Metagenome: Environmental - Added: Zampirolo 2024 10.1016/j.cub.2024.08.047 (added by @GiuliaZ538) From d5c7f1691318646bce7d7cea733a3bbb280ca458 Mon Sep 17 00:00:00 2001 From: MagdalenaHC Date: Mon, 7 Oct 2024 14:25:33 +0200 Subject: [PATCH 3/5] Susat2024 Corrected the Run Accession with the Sample Accession number, as it was wished in the readme documentation. --- .../samples/ancientsinglegenome-hostassociated_samples.tsv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv index f1fe53bec..19455b97c 100644 --- a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv +++ b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv @@ -717,5 +717,5 @@ White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.720 Kazakhstan B2_B3 White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.720 Kazakhstan B2_B5 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769381 White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.720 Kazakhstan B2_B6 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769382 White2021 2021 10.3390/biology10121324 Kuygenzhar 51.103 71.720 Kazakhstan B2_B7 Homo sapiens 200 10.3390/biology10121324 bacteria Porphyromonas gingivalis tooth chromosome ENA raw PRJEB49091 ERS9769383 -Susat2024 2024 10.1038/s42003-024-06676-7 Warburg 51.488 9.133 Germany Warburg_1 Homo sapiens 5200 10.1038/s42003-024-06676-7 bacteria Yersinia pestis tooth chromosome ENA raw PRJEB49648 ERR13081220 -Susat2024 2024 10.1038/s42003-024-06676-7 Warburg 51.488 9.133 Germany Warburg_2 Homo sapiens 5100 10.1038/s42003-024-06676-7 bacteria Yersinia pestis tooth chromosome ENA raw PRJEB49648 ERR13081216,ERR13081217,ERR13081218,ERR13081219 +Susat2024 2024 10.1038/s42003-024-06676-7 Warburg 51.488 9.133 Germany Warburg_1 Homo sapiens 5200 10.1038/s42003-024-06676-7 bacteria Yersinia pestis tooth chromosome ENA raw PRJEB49648 ERS19529513 +Susat2024 2024 10.1038/s42003-024-06676-7 Warburg 51.488 9.133 Germany Warburg_2 Homo sapiens 5100 10.1038/s42003-024-06676-7 bacteria Yersinia pestis tooth chromosome ENA raw PRJEB49648 ERS19529514 From e3ce7448ac7236779aeb65c9a86e955b8c19d51d Mon Sep 17 00:00:00 2001 From: MagdalenaHC Date: Mon, 7 Oct 2024 15:34:14 +0200 Subject: [PATCH 4/5] Susat2024 --- .../ancientsinglegenome-hostassociated_libraries.tsv | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv b/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv index 91cb58bc3..7ca770c87 100644 --- a/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv +++ b/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv @@ -3111,3 +3111,8 @@ White2021 2021 10.3390/biology10121324 B2_B6 ENA PRJEB49091 ERS9769382 L024 doub White2021 2021 10.3390/biology10121324 B2_B6 ENA PRJEB49091 ERS9769382 L024-B double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS 108865268 ERR13663675 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR136/075/ERR13663675/ERR13663675_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR136/075/ERR13663675/ERR13663675_2.fastq.gz 9f698e07345a859feb34cb4e99a55d11;d7d70554b02c6f5dc7952fd2485c163c 2589844121;2788114713 White2021 2021 10.3390/biology10121324 B2_B7 ENA PRJEB49091 ERS9769383 L025-B double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS 81293780 ERR13663677 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR136/077/ERR13663677/ERR13663677_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR136/077/ERR13663677/ERR13663677_2.fastq.gz 00eb8d335bfedd6a0569e708bb5be5f8;3b34fc20b2c7a012ce5d25d177d55dc8 2074741912;2130629421 White2021 2021 10.3390/biology10121324 B2_B7 ENA PRJEB49091 ERS9769383 L025 double AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED WGS 179780446 ERR13663678 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR136/078/ERR13663678/ERR13663678_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR136/078/ERR13663678/ERR13663678_2.fastq.gz 47149ec413c0a14645b7a838fc088507;1372803ee3d494b1876b82982c69d10c 4575913200;4879999751 +Susat2024 2024 10.1038/s42003-024-06676-7 Warburg_1 ENA PRJEB49648 ERS19529513 KH201292 double AccuPrime Pfx DNA half-udg Illumina NovaSeq 6000 SINGLE WGS 407857327 ERR13081220 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR130/020/ERR13081220/ERR13081220.fastq.gz 5175e567917874e58afc0ba7d0842df2 10971181148 +Susat2024 2024 10.1038/s42003-024-06676-7 Warburg_2 ENA PRJEB49648 ERS19529514 KH200218_1 double AccuPrime Pfx DNA half-udg Illumina NovaSeq 6000 SINGLE WGS 825408927 ERR13081216 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR130/016/ERR13081216/ERR13081216.fastq.gz 6cc72b1013107335a732b1de3c42315b 32378107839 +Susat2024 2024 10.1038/s42003-024-06676-7 Warburg_2 ENA PRJEB49648 ERS19529514 KH200218_2 double AccuPrime Pfx DNA half-udg Illumina NovaSeq 6000 SINGLE WGS 779197269 ERR13081217 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR130/017/ERR13081217/ERR13081217.fastq.gz e3716b3fcc0dc508355bac4066e98440 30780770975 +Susat2024 2024 10.1038/s42003-024-06676-7 Warburg_2 ENA PRJEB49648 ERS19529514 KH200218_3 double AccuPrime Pfx DNA half-udg Illumina NovaSeq 6000 SINGLE WGS 331237067 ERR13081218 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR130/018/ERR13081218/ERR13081218.fastq.gz 859d36af02ca9bc64a77a6198d647339 13693431199 +Susat2024 2024 10.1038/s42003-024-06676-7 Warburg_2 ENA PRJEB49648 ERS19529514 KH200218_4 double AccuPrime Pfx DNA half-udg Illumina NovaSeq 6000 SINGLE WGS 264407276 ERR13081219 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR130/019/ERR13081219/ERR13081219.fastq.gz e24316d796fcb34c2594f4aef1dc1a85 10868287934 From 43a1e637a36871dff1bb09a4ceebeeb5d77111f8 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 11 Dec 2024 13:44:52 +0100 Subject: [PATCH 5/5] Move changelgo entry into the correct place --- CHANGELOG.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index df8601d14..c3d935cc8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,11 +13,13 @@ and this project follows to [Calendar Versioning](https://calver.org/). #### Ancient Single Genome: Host Associated +- Susat 2024 10.1038/s42003-024-06676-7 (added by @MagdalenaHC) + #### Ancient Metagenome: Environmental ### Changed -- Bonczarowska2023: Fixed library type (actually half-UDG, despite paper reporting non-UDG) 10.1098/rspb.2023.0622 (fixed by @marcel-keller) +- Bonczarowska2023: Fixed library type (actually half-UDG, despite paper reporting non-UDG) 10.1098/rspb.2023.0622 (fixed by @marcel-keller) ### Removed @@ -33,7 +35,6 @@ and this project follows to [Calendar Versioning](https://calver.org/). #### Ancient Single Genome: Host Associated - White 2021 10.3390/biology10121324 (added by @DianaSpurite, @jfy133, and @alexhbnr) -- Susat 2024 10.1038/s42003-024-06676-7 (added by @MagdalenaHC) #### Ancient Metagenome: Environmental