From 52ca68bae89a833362e286cc2e02ee0b001332f3 Mon Sep 17 00:00:00 2001 From: hsf378 <54803911+YuejiaoHuang@users.noreply.github.com> Date: Thu, 13 Jun 2024 15:58:13 +0200 Subject: [PATCH 01/12] Update ancientsinglegenome-hostassociated_samples.tsv need clarify whether we should use "UR17x29" as the sample name (as referenced in the Lebrasseur2024 paper) or "UR17x29_Rus_m1853" (as mentioned in the previously published paper 10.1038/s41586-021-04018-9)? --- .../samples/ancientsinglegenome-hostassociated_samples.tsv | 1 + 1 file changed, 1 insertion(+) diff --git a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv index 3ccee6d07..3cf88606f 100644 --- a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv +++ b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv @@ -666,3 +666,4 @@ Rozwalak2024 2024 10.1038/s41467-023-44370-0 Cueva de los Muertos Chiquitos (Zap Jackson2024 2024 10.1093/molbev/msae017 Killuragh 52.6 -8.33 Ireland KGH2-F Homo sapiens 3800 10.1093/molbev/msae017 bacteria Tannerella forsythia tooth chromosome ENA raw,reference_aligned PRJEB64128 ERS15977755 Jackson2024 2024 10.1093/molbev/msae017 Killuragh 52.6 -8.33 Ireland KGH2-B Homo sapiens 3800 10.1093/molbev/msae017 bacteria Streptococcus mutans tooth chromosome ENA raw,reference_aligned PRJEB64128 ERS15977754 Jackson2024 2024 10.1093/molbev/msae017 Killuragh 52.6 -8.33 Ireland KGH1-E Homo sapiens 3800 10.1093/molbev/msae017 bacteria Tannerella forsythia tooth chromosome ENA raw,reference_aligned PRJEB64128 ERS15977753 +Lebrasseur2024 2024 10.1093/ve/vead087 Kamennyi Ambar 5 52.833 60.367 Russia UR17x29_Rus_m1853 Equus caballus 3800 10.1093/ve/vead087 virus Equine Herpesvirus 4 bone chromosome ENA raw PRJEB44430 ERS7256200 From ce1ce7f1d1603a6ddc93fe13c3812581220dc8f5 Mon Sep 17 00:00:00 2001 From: hsf378 <54803911+YuejiaoHuang@users.noreply.github.com> Date: Thu, 13 Jun 2024 16:14:19 +0200 Subject: [PATCH 02/12] Update CHANGELOG.md in Lebrasseur2024 --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index fcb39d183..cd43722ad 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,6 +13,8 @@ and this project follows to [Calendar Versioning](https://calver.org/). #### Ancient Single Genome: Host Associated +- Lebrasseur 2024 10.1093/ve/vead087(added by @YuejiaoHuang) + #### Ancient Metagenome: Environmental ### Changed From fc5244a32f5c46a0d1f5ae74457b315a1b91ffd2 Mon Sep 17 00:00:00 2001 From: hsf378 <54803911+YuejiaoHuang@users.noreply.github.com> Date: Thu, 13 Jun 2024 16:31:18 +0200 Subject: [PATCH 03/12] Update singlegenome_species.json --- assets/enums/singlegenome_species.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/assets/enums/singlegenome_species.json b/assets/enums/singlegenome_species.json index 91862eb74..15e4d7157 100644 --- a/assets/enums/singlegenome_species.json +++ b/assets/enums/singlegenome_species.json @@ -51,6 +51,7 @@ "Xanthomonas citri pv. citri", "Clostridium tetani", "Mushuvirus mushu", - "Streptococcus mutans" + "Streptococcus mutans", + "Equine Herpesvirus 4" ] } From 76283e3a87297cdafc5fa00c209b0497c3a0aec8 Mon Sep 17 00:00:00 2001 From: hsf378 <54803911+YuejiaoHuang@users.noreply.github.com> Date: Thu, 13 Jun 2024 16:34:44 +0200 Subject: [PATCH 04/12] Update sample_host.json --- assets/enums/sample_host.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/assets/enums/sample_host.json b/assets/enums/sample_host.json index 8e8cd8995..f488f928a 100644 --- a/assets/enums/sample_host.json +++ b/assets/enums/sample_host.json @@ -33,6 +33,7 @@ "Bovidae", "Citrus aurantiifolia", "Citrus medica", - "Lithobates pipiens" + "Lithobates pipiens", + "Equus caballus" ] } From 018b755ba776d9e33ac503a4a1c97fc4fc013dcb Mon Sep 17 00:00:00 2001 From: hsf378 <54803911+YuejiaoHuang@users.noreply.github.com> Date: Mon, 17 Jun 2024 10:43:20 +0200 Subject: [PATCH 05/12] Update ancientsinglegenome-hostassociated_samples.tsv --- .../samples/ancientsinglegenome-hostassociated_samples.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv index 3cf88606f..6beb5a3ed 100644 --- a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv +++ b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv @@ -666,4 +666,4 @@ Rozwalak2024 2024 10.1038/s41467-023-44370-0 Cueva de los Muertos Chiquitos (Zap Jackson2024 2024 10.1093/molbev/msae017 Killuragh 52.6 -8.33 Ireland KGH2-F Homo sapiens 3800 10.1093/molbev/msae017 bacteria Tannerella forsythia tooth chromosome ENA raw,reference_aligned PRJEB64128 ERS15977755 Jackson2024 2024 10.1093/molbev/msae017 Killuragh 52.6 -8.33 Ireland KGH2-B Homo sapiens 3800 10.1093/molbev/msae017 bacteria Streptococcus mutans tooth chromosome ENA raw,reference_aligned PRJEB64128 ERS15977754 Jackson2024 2024 10.1093/molbev/msae017 Killuragh 52.6 -8.33 Ireland KGH1-E Homo sapiens 3800 10.1093/molbev/msae017 bacteria Tannerella forsythia tooth chromosome ENA raw,reference_aligned PRJEB64128 ERS15977753 -Lebrasseur2024 2024 10.1093/ve/vead087 Kamennyi Ambar 5 52.833 60.367 Russia UR17x29_Rus_m1853 Equus caballus 3800 10.1093/ve/vead087 virus Equine Herpesvirus 4 bone chromosome ENA raw PRJEB44430 ERS7256200 +Lebrasseur2024 2024 10.1093/ve/vead087 Kamennyi Ambar 5 52.833 60.367 Russia UR17x29 Equus caballus 3800 10.1093/ve/vead087 virus Equine Herpesvirus 4 bone chromosome ENA raw PRJEB44430 ERS7256200 From 238a03dd40a38ae04ef18b091e53f906d1ff9ab9 Mon Sep 17 00:00:00 2001 From: hsf378 <54803911+YuejiaoHuang@users.noreply.github.com> Date: Mon, 17 Jun 2024 11:07:44 +0200 Subject: [PATCH 06/12] Update singlegenome_species.json --- assets/enums/singlegenome_species.json | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/assets/enums/singlegenome_species.json b/assets/enums/singlegenome_species.json index 15e4d7157..91862eb74 100644 --- a/assets/enums/singlegenome_species.json +++ b/assets/enums/singlegenome_species.json @@ -51,7 +51,6 @@ "Xanthomonas citri pv. citri", "Clostridium tetani", "Mushuvirus mushu", - "Streptococcus mutans", - "Equine Herpesvirus 4" + "Streptococcus mutans" ] } From d0a964a1ee95231ca64361e34dc52c31f8ef8e3d Mon Sep 17 00:00:00 2001 From: hsf378 <54803911+YuejiaoHuang@users.noreply.github.com> Date: Mon, 17 Jun 2024 11:08:20 +0200 Subject: [PATCH 07/12] Update sample_host.json --- assets/enums/sample_host.json | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/assets/enums/sample_host.json b/assets/enums/sample_host.json index f488f928a..8e8cd8995 100644 --- a/assets/enums/sample_host.json +++ b/assets/enums/sample_host.json @@ -33,7 +33,6 @@ "Bovidae", "Citrus aurantiifolia", "Citrus medica", - "Lithobates pipiens", - "Equus caballus" + "Lithobates pipiens" ] } From db03f88b6f73463aa9c7639d834497b45d7dd61c Mon Sep 17 00:00:00 2001 From: hsf378 <54803911+YuejiaoHuang@users.noreply.github.com> Date: Mon, 17 Jun 2024 13:48:31 +0200 Subject: [PATCH 08/12] Update ancientsinglegenome-hostassociated_samples.tsv --- .../samples/ancientsinglegenome-hostassociated_samples.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv index 6beb5a3ed..967945b16 100644 --- a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv +++ b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv @@ -666,4 +666,4 @@ Rozwalak2024 2024 10.1038/s41467-023-44370-0 Cueva de los Muertos Chiquitos (Zap Jackson2024 2024 10.1093/molbev/msae017 Killuragh 52.6 -8.33 Ireland KGH2-F Homo sapiens 3800 10.1093/molbev/msae017 bacteria Tannerella forsythia tooth chromosome ENA raw,reference_aligned PRJEB64128 ERS15977755 Jackson2024 2024 10.1093/molbev/msae017 Killuragh 52.6 -8.33 Ireland KGH2-B Homo sapiens 3800 10.1093/molbev/msae017 bacteria Streptococcus mutans tooth chromosome ENA raw,reference_aligned PRJEB64128 ERS15977754 Jackson2024 2024 10.1093/molbev/msae017 Killuragh 52.6 -8.33 Ireland KGH1-E Homo sapiens 3800 10.1093/molbev/msae017 bacteria Tannerella forsythia tooth chromosome ENA raw,reference_aligned PRJEB64128 ERS15977753 -Lebrasseur2024 2024 10.1093/ve/vead087 Kamennyi Ambar 5 52.833 60.367 Russia UR17x29 Equus caballus 3800 10.1093/ve/vead087 virus Equine Herpesvirus 4 bone chromosome ENA raw PRJEB44430 ERS7256200 +Lebrasseur2024 2024 10.1093/ve/vead087 Kamennyi Ambar 5 52.833 60.367 Russia UR17x29 Equus caballus 3800 10.1093/ve/vead087 virus Equid herpesvirus 4 bone chromosome ENA raw PRJEB44430 ERS7256200 From ed8ee08a2570992439e89c3680b426ea1213d890 Mon Sep 17 00:00:00 2001 From: hsf378 <54803911+YuejiaoHuang@users.noreply.github.com> Date: Mon, 17 Jun 2024 15:25:35 +0200 Subject: [PATCH 09/12] Update ancientsinglegenome-hostassociated_libraries.tsv --- .../ancientsinglegenome-hostassociated_libraries.tsv | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv b/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv index df37ac669..7378a2c40 100644 --- a/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv +++ b/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv @@ -3046,4 +3046,14 @@ Jackson2024 2024 10.1093/molbev/msae017 KGH1-E ENA PRJEB64128 ERS15977753 KGH1-E Jackson2024 2024 10.1093/molbev/msae017 KGH1-E ENA PRJEB64128 ERS15977753 KGH1-E-WEX1-UDG1-80_6-PCR1-Nova16-L002 double AccuPrime Pfx DNA full-udg Illumina NovaSeq 6000 PAIRED WGS 11252586 ERR11660424 fastq_hostremoved ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/024/ERR11660424/ERR11660424_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/024/ERR11660424/ERR11660424_2.fastq.gz adfb95f2f75fb41bda1406f3641cf4ed;047e0a7fae662f4f8787ceeef670163b 182599851;179187636 Jackson2024 2024 10.1093/molbev/msae017 KGH1-E ENA PRJEB64128 ERS15977753 KGH1-E-WEX1-UDG1-80_6-PCR1-Nova19-L002 double AccuPrime Pfx DNA full-udg Illumina NovaSeq 6000 PAIRED WGS 1032062 ERR11660425 fastq_hostremoved ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/025/ERR11660425/ERR11660425_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/025/ERR11660425/ERR11660425_2.fastq.gz 3fcc2117242154932b6382ab9f8ab2a4;4ea24d58af027a524a20f4808e4ac1ea 27517633;28773829 Jackson2024 2024 10.1093/molbev/msae017 KGH1-E ENA PRJEB64128 ERS15977753 KGH1-E-WEX1-UDG1-81_6-PCR1-Nova16-L001 double AccuPrime Pfx DNA full-udg Illumina NovaSeq 6000 PAIRED WGS 11184792 ERR11660426 fastq_hostremoved ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/026/ERR11660426/ERR11660426_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/026/ERR11660426/ERR11660426_2.fastq.gz 904aedeb6b30dbb6ca88b733cd73dfa4;395ca80600fa9a4823c26ed61605d7ba 183165865;178901785 -Jackson2024 2024 10.1093/molbev/msae017 KGH1-E ENA PRJEB64128 ERS15977753 KGH1-E-WEX1-UDG1-81_6-PCR1-Nova16-L002 double AccuPrime Pfx DNA full-udg Illumina NovaSeq 6000 PAIRED WGS 11168602 ERR11660427 fastq_hostremoved ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/027/ERR11660427/ERR11660427_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/027/ERR11660427/ERR11660427_2.fastq.gz 378c0a501f4ab156d9c2c384dab9b5ac;84db574b20d5254da215cf8fdf458118 181992370;178329735 \ No newline at end of file +Jackson2024 2024 10.1093/molbev/msae017 KGH1-E ENA PRJEB64128 ERS15977753 KGH1-E-WEX1-UDG1-81_6-PCR1-Nova16-L002 double AccuPrime Pfx DNA full-udg Illumina NovaSeq 6000 PAIRED WGS 11168602 ERR11660427 fastq_hostremoved ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/027/ERR11660427/ERR11660427_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/027/ERR11660427/ERR11660427_2.fastq.gz 378c0a501f4ab156d9c2c384dab9b5ac;84db574b20d5254da215cf8fdf458118 181992370;178329735 +Lebrasseur2024 2024 10.1093/ve/vead087 UR17x29 ENA PRJEB44430 ERS7256200 L5 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 SINGLE WGS 145317698 ERR6466112 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR646/002/ERR6466112/ERR6466112.fastq.gz e4e00eb66e236b20020f6d12323ff24d 5064443689 +Lebrasseur2024 2024 10.1093/ve/vead087 UR17x29 ENA PRJEB44430 ERS7256200 L3 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 SINGLE WGS 164415447 ERR6466110 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR646/000/ERR6466110/ERR6466110.fastq.gz 3387cbb54cd5593384586c3f70787405 6026604046 +Lebrasseur2024 2024 10.1093/ve/vead087 UR17x29 ENA PRJEB44430 ERS7256200 L1 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 SINGLE WGS 9413628 ERR6466108 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR646/008/ERR6466108/ERR6466108.fastq.gz 082fa661d3351c0fac22e2e922dc3795 342573885 +Lebrasseur2024 2024 10.1093/ve/vead087 UR17x29 ENA PRJEB44430 ERS7256200 L2 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 SINGLE WGS 123717709 ERR6466109 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR646/009/ERR6466109/ERR6466109.fastq.gz 267fe0d4b684a1cf765ae560abdfbbc3 4352735230 +Lebrasseur2024 2024 10.1093/ve/vead087 UR17x29 ENA PRJEB44430 ERS7256200 L4 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 SINGLE WGS 141415855 ERR6466111 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR646/001/ERR6466111/ERR6466111.fastq.gz 7bed95eb12f3d17c93fd6d47c5edfd04 4974034411 +Lebrasseur2024 2024 10.1093/ve/vead087 UR17x29 ENA PRJEB44430 ERS7256200 L1 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 PAIRED WGS 3101154 ERR6473065 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/005/ERR6473065/ERR6473065_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/005/ERR6473065/ERR6473065_2.fastq.gz 7b6cbb9068af3c5fafa1faf82216a44e;f67789231731ef401cf661dfa566225c 77977673;83680852 +Lebrasseur2024 2024 10.1093/ve/vead087 UR17x29 ENA PRJEB44430 ERS7256200 L2 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 PAIRED WGS 49007344 ERR6473066 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/006/ERR6473066/ERR6473066_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/006/ERR6473066/ERR6473066_2.fastq.gz 84126b9524670a49de73e08d92a5d7d5;bd08bdc3adc3d20c79f0b2a1301cebb4 1105788532;1193498427 +Lebrasseur2024 2024 10.1093/ve/vead087 UR17x29 ENA PRJEB44430 ERS7256200 L3 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 PAIRED WGS 63260952 ERR6473067 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/007/ERR6473067/ERR6473067_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/007/ERR6473067/ERR6473067_2.fastq.gz fa232c63845324f7904e0784108d8aa2;061da989e01c5d7bf5810feade6bc369 1451846939;1561372230 +Lebrasseur2024 2024 10.1093/ve/vead087 UR17x29 ENA PRJEB44430 ERS7256200 L5 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 PAIRED WGS 47844024 ERR6473069 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/009/ERR6473069/ERR6473069_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/009/ERR6473069/ERR6473069_2.fastq.gz 0d6871e8ee4d55d6f91c631b0c2b8cfa;de5a88e9f3cd9d0bc8a65de75996e255 1080256598;1159144498 +Lebrasseur2024 2024 10.1093/ve/vead087 UR17x29 ENA PRJEB44430 ERS7256200 L4 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 PAIRED WGS 53079796 ERR6473068 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/008/ERR6473068/ERR6473068_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/008/ERR6473068/ERR6473068_2.fastq.gz 2efcc3e20d92cc45884723d6e34e72a6;7770973368ece8abd4ddfecc1e9c89bb 1196561912;1286080555 From f41978ab8de4856ac9091ac508d07cbc4137eba4 Mon Sep 17 00:00:00 2001 From: hsf378 <54803911+YuejiaoHuang@users.noreply.github.com> Date: Tue, 9 Jul 2024 19:29:32 +0200 Subject: [PATCH 10/12] Update ancientsinglegenome-hostassociated_libraries.tsv --- .../ancientsinglegenome-hostassociated_libraries.tsv | 5 ----- 1 file changed, 5 deletions(-) diff --git a/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv b/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv index 7378a2c40..b459a502d 100644 --- a/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv +++ b/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv @@ -3052,8 +3052,3 @@ Lebrasseur2024 2024 10.1093/ve/vead087 UR17x29 ENA PRJEB44430 ERS7256200 L3 doub Lebrasseur2024 2024 10.1093/ve/vead087 UR17x29 ENA PRJEB44430 ERS7256200 L1 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 SINGLE WGS 9413628 ERR6466108 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR646/008/ERR6466108/ERR6466108.fastq.gz 082fa661d3351c0fac22e2e922dc3795 342573885 Lebrasseur2024 2024 10.1093/ve/vead087 UR17x29 ENA PRJEB44430 ERS7256200 L2 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 SINGLE WGS 123717709 ERR6466109 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR646/009/ERR6466109/ERR6466109.fastq.gz 267fe0d4b684a1cf765ae560abdfbbc3 4352735230 Lebrasseur2024 2024 10.1093/ve/vead087 UR17x29 ENA PRJEB44430 ERS7256200 L4 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 SINGLE WGS 141415855 ERR6466111 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR646/001/ERR6466111/ERR6466111.fastq.gz 7bed95eb12f3d17c93fd6d47c5edfd04 4974034411 -Lebrasseur2024 2024 10.1093/ve/vead087 UR17x29 ENA PRJEB44430 ERS7256200 L1 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 PAIRED WGS 3101154 ERR6473065 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/005/ERR6473065/ERR6473065_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/005/ERR6473065/ERR6473065_2.fastq.gz 7b6cbb9068af3c5fafa1faf82216a44e;f67789231731ef401cf661dfa566225c 77977673;83680852 -Lebrasseur2024 2024 10.1093/ve/vead087 UR17x29 ENA PRJEB44430 ERS7256200 L2 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 PAIRED WGS 49007344 ERR6473066 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/006/ERR6473066/ERR6473066_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/006/ERR6473066/ERR6473066_2.fastq.gz 84126b9524670a49de73e08d92a5d7d5;bd08bdc3adc3d20c79f0b2a1301cebb4 1105788532;1193498427 -Lebrasseur2024 2024 10.1093/ve/vead087 UR17x29 ENA PRJEB44430 ERS7256200 L3 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 PAIRED WGS 63260952 ERR6473067 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/007/ERR6473067/ERR6473067_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/007/ERR6473067/ERR6473067_2.fastq.gz fa232c63845324f7904e0784108d8aa2;061da989e01c5d7bf5810feade6bc369 1451846939;1561372230 -Lebrasseur2024 2024 10.1093/ve/vead087 UR17x29 ENA PRJEB44430 ERS7256200 L5 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 PAIRED WGS 47844024 ERR6473069 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/009/ERR6473069/ERR6473069_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/009/ERR6473069/ERR6473069_2.fastq.gz 0d6871e8ee4d55d6f91c631b0c2b8cfa;de5a88e9f3cd9d0bc8a65de75996e255 1080256598;1159144498 -Lebrasseur2024 2024 10.1093/ve/vead087 UR17x29 ENA PRJEB44430 ERS7256200 L4 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 PAIRED WGS 53079796 ERR6473068 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/008/ERR6473068/ERR6473068_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR647/008/ERR6473068/ERR6473068_2.fastq.gz 2efcc3e20d92cc45884723d6e34e72a6;7770973368ece8abd4ddfecc1e9c89bb 1196561912;1286080555 From 245e5d1e363cb1ece98764d4f0e06cb728862db1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alex=20H=C3=BCbner?= Date: Sun, 14 Jul 2024 15:12:31 +0200 Subject: [PATCH 11/12] Change sample age DOI to the original publication --- .../samples/ancientsinglegenome-hostassociated_samples.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv index 967945b16..3e970cb45 100644 --- a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv +++ b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv @@ -666,4 +666,4 @@ Rozwalak2024 2024 10.1038/s41467-023-44370-0 Cueva de los Muertos Chiquitos (Zap Jackson2024 2024 10.1093/molbev/msae017 Killuragh 52.6 -8.33 Ireland KGH2-F Homo sapiens 3800 10.1093/molbev/msae017 bacteria Tannerella forsythia tooth chromosome ENA raw,reference_aligned PRJEB64128 ERS15977755 Jackson2024 2024 10.1093/molbev/msae017 Killuragh 52.6 -8.33 Ireland KGH2-B Homo sapiens 3800 10.1093/molbev/msae017 bacteria Streptococcus mutans tooth chromosome ENA raw,reference_aligned PRJEB64128 ERS15977754 Jackson2024 2024 10.1093/molbev/msae017 Killuragh 52.6 -8.33 Ireland KGH1-E Homo sapiens 3800 10.1093/molbev/msae017 bacteria Tannerella forsythia tooth chromosome ENA raw,reference_aligned PRJEB64128 ERS15977753 -Lebrasseur2024 2024 10.1093/ve/vead087 Kamennyi Ambar 5 52.833 60.367 Russia UR17x29 Equus caballus 3800 10.1093/ve/vead087 virus Equid herpesvirus 4 bone chromosome ENA raw PRJEB44430 ERS7256200 +Lebrasseur2024 2024 10.1093/ve/vead087 Kamennyi Ambar 5 52.833 60.367 Russia UR17x29 Equus caballus 3800 10.1038/s41586-021-04018-9 virus Equid herpesvirus 4 bone chromosome ENA raw PRJEB44430 ERS7256200 From 5aee0a56c61824745f1ef8709d3c28ecd0c296d0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alex=20H=C3=BCbner?= Date: Sun, 14 Jul 2024 15:27:30 +0200 Subject: [PATCH 12/12] Update the original data DOI --- .../ancientsinglegenome-hostassociated_libraries.tsv | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv b/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv index b459a502d..64b44fbe6 100644 --- a/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv +++ b/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv @@ -3047,8 +3047,8 @@ Jackson2024 2024 10.1093/molbev/msae017 KGH1-E ENA PRJEB64128 ERS15977753 KGH1-E Jackson2024 2024 10.1093/molbev/msae017 KGH1-E ENA PRJEB64128 ERS15977753 KGH1-E-WEX1-UDG1-80_6-PCR1-Nova19-L002 double AccuPrime Pfx DNA full-udg Illumina NovaSeq 6000 PAIRED WGS 1032062 ERR11660425 fastq_hostremoved 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ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/027/ERR11660427/ERR11660427_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR116/027/ERR11660427/ERR11660427_2.fastq.gz 378c0a501f4ab156d9c2c384dab9b5ac;84db574b20d5254da215cf8fdf458118 181992370;178329735 -Lebrasseur2024 2024 10.1093/ve/vead087 UR17x29 ENA PRJEB44430 ERS7256200 L5 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 SINGLE WGS 145317698 ERR6466112 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR646/002/ERR6466112/ERR6466112.fastq.gz e4e00eb66e236b20020f6d12323ff24d 5064443689 -Lebrasseur2024 2024 10.1093/ve/vead087 UR17x29 ENA PRJEB44430 ERS7256200 L3 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 SINGLE WGS 164415447 ERR6466110 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR646/000/ERR6466110/ERR6466110.fastq.gz 3387cbb54cd5593384586c3f70787405 6026604046 -Lebrasseur2024 2024 10.1093/ve/vead087 UR17x29 ENA PRJEB44430 ERS7256200 L1 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 SINGLE WGS 9413628 ERR6466108 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR646/008/ERR6466108/ERR6466108.fastq.gz 082fa661d3351c0fac22e2e922dc3795 342573885 -Lebrasseur2024 2024 10.1093/ve/vead087 UR17x29 ENA PRJEB44430 ERS7256200 L2 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 SINGLE WGS 123717709 ERR6466109 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR646/009/ERR6466109/ERR6466109.fastq.gz 267fe0d4b684a1cf765ae560abdfbbc3 4352735230 -Lebrasseur2024 2024 10.1093/ve/vead087 UR17x29 ENA PRJEB44430 ERS7256200 L4 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 SINGLE WGS 141415855 ERR6466111 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR646/001/ERR6466111/ERR6466111.fastq.gz 7bed95eb12f3d17c93fd6d47c5edfd04 4974034411 +Lebrasseur2024 2024 10.1038/s41586-021-04018-9 UR17x29 ENA PRJEB44430 ERS7256200 L5 double AccuPrime Pfx DNA half-udg Illumina HiSeq 4000 SINGLE WGS 145317698 ERR6466112 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR646/002/ERR6466112/ERR6466112.fastq.gz e4e00eb66e236b20020f6d12323ff24d 5064443689 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half-udg Illumina HiSeq 4000 SINGLE WGS 141415855 ERR6466111 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR646/001/ERR6466111/ERR6466111.fastq.gz 7bed95eb12f3d17c93fd6d47c5edfd04 4974034411