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Merge pull request #1176 from SPAAM-community/Urban2024
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Urban2024
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@aidaanva
aidaanva authored Jun 26, 2024
2 parents 6ed679b + a85d8a9 commit 03e0569
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -13,6 +13,8 @@ and this project follows to [Calendar Versioning](https://calver.org/).

#### Ancient Single Genome: Host Associated

- Urban 2024 10.1016/j.cub.2024.04.006 (added by @aidaanva)

#### Ancient Metagenome: Environmental

### Changed
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21 changes: 20 additions & 1 deletion ...entsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv
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Expand Up @@ -3046,4 +3046,23 @@ 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
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
Urban2024 2024 10.1016/j.cub.2024.04.006 MMW_H50_1 SRA PRJNA1021938 SRS20486703 MMW_H50_1_cap double PfuTurbo Cx Hotstart DNA none NextSeq 500 PAIRED Targeted-Capture 3329459 SRR28001574 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/074/SRR28001574/SRR28001574_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/074/SRR28001574/SRR28001574_2.fastq.gz 2dde567228b8cb4e49449f361b8d9ca1;fd6a9a5fda73797c1af3becb2efbff53 156467184;159121792
Urban2024 2024 10.1016/j.cub.2024.04.006 MMW_H50_1 SRA PRJNA1021938 SRS20486703 MMW_H50_1_sg double PfuTurbo Cx Hotstart DNA none NextSeq 500 PAIRED WGS 3613368 SRR28001551 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/051/SRR28001551/SRR28001551_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/051/SRR28001551/SRR28001551_2.fastq.gz b4802915a7ee94318e0934904bb83f3d;0ba9f6ce56fc624ab42296c4997b2c0 169044170;176617490
Urban2024 2024 10.1016/j.cub.2024.04.006 MMW_H80_1 SRA PRJNA1021938 SRS20486681 MMW_H80_1_cap double PfuTurbo Cx Hotstart DNA none NextSeq 500 PAIRED Targeted-Capture 7566799 SRR28001572 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/072/SRR28001572/SRR28001572_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/072/SRR28001572/SRR28001572_2.fastq.gz 5a040f140b2f8b900d778bc8cd2df68f;5c7ad27382077a5ea9810e8b00757194 350808159;362817661
Urban2024 2024 10.1016/j.cub.2024.04.006 MMW_H80_1 SRA PRJNA1021938 SRS20486681 MMW_H80_1_sg double PfuTurbo Cx Hotstart DNA none NextSeq 500 PAIRED WGS 3482302 SRR28001598 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/098/SRR28001598/SRR28001598_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/098/SRR28001598/SRR28001598_2.fastq.gz 6e1fec40d1b00b9849f790de212fbaef;4cc9847db4a82bcb5bd3e3c66e042f56 162147728;171102778
Urban2024 2024 10.1016/j.cub.2024.04.006 MMW_H94_1 SRA PRJNA1021938 SRS20486688 MMW_H94_1_cap double PfuTurbo Cx Hotstart DNA none NextSeq 500 PAIRED Targeted-Capture 1782739 SRR28001571 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/071/SRR28001571/SRR28001571_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/071/SRR28001571/SRR28001571_2.fastq.gz 50c5247c2ce1379020d984c96a21d26a;512f593af4db02058317019e74ebbca5 83975345;85935256
Urban2024 2024 10.1016/j.cub.2024.04.006 MMW_H94_1 SRA PRJNA1021938 SRS20486688 MMW_H94_1_sg double PfuTurbo Cx Hotstart DNA none NextSeq 500 PAIRED WGS 3529513 SRR28001591 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/091/SRR28001591/SRR28001591_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/091/SRR28001591/SRR28001591_2.fastq.gz 696354cf94aa4a9f084606d76b2ffa3c;8609b8c0bb99b3171b4a7135a0dfb71c 162033285;169966357
Urban2024 2024 10.1016/j.cub.2024.04.006 SGW_S3_1 SRA PRJNA1021938 SRS20486690 SGW_S3_1_Lib1_capKAPA double PfuTurbo Cx Hotstart DNA none NextSeq 500 SINGLE Targeted-Capture 8823598 SRR28001561 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/061/SRR28001561/SRR28001561.fastq.gz 2e5d9ad74ef2ae38529e0de37a327112 395881457
Urban2024 2024 10.1016/j.cub.2024.04.006 SGW_S3_1 SRA PRJNA1021938 SRS20486690 SGW_S3_1_Lib1_capMyBaits_Run1 double PfuTurbo Cx Hotstart DNA none NextSeq 500 PAIRED Targeted-Capture 7339169 SRR28001570 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/070/SRR28001570/SRR28001570_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/070/SRR28001570/SRR28001570_2.fastq.gz 57a7557b0f9b7b708685d20647c1aeca;e4e3b0cf1e5ca8056eabb08743d452f3 336089684;363686496
Urban2024 2024 10.1016/j.cub.2024.04.006 SGW_S3_1 SRA PRJNA1021938 SRS20486690 SGW_S3_1_Lib1_capMyBaits_Run2 double PfuTurbo Cx Hotstart DNA none NextSeq 500 PAIRED Targeted-Capture 13883156 SRR28001568 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/068/SRR28001568/SRR28001568_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/068/SRR28001568/SRR28001568_2.fastq.gz 1c9c505d7d564c21c304390f15ae4e0c;334e7c75668a27dc2eca91f65444e9f8 608641869;654087235
Urban2024 2024 10.1016/j.cub.2024.04.006 SGW_S3_1 SRA PRJNA1021938 SRS20486690 SGW_S3_1_Lib1_capMyBaits_Run3 double PfuTurbo Cx Hotstart DNA none NextSeq 500 PAIRED Targeted-Capture 3237493 SRR28001566 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/066/SRR28001566/SRR28001566_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/066/SRR28001566/SRR28001566_2.fastq.gz 1321a2e0be625a062e5969f47c108676;9a5ae164bf0f384c888216cff238f867 132230475;143538989
Urban2024 2024 10.1016/j.cub.2024.04.006 SGW_S3_1 SRA PRJNA1021938 SRS20486690 SGW_S3_1_Lib1_capMyBaits_Run4 double PfuTurbo Cx Hotstart DNA none NextSeq 500 PAIRED Targeted-Capture 3317272 SRR28001564 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/064/SRR28001564/SRR28001564_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/064/SRR28001564/SRR28001564_2.fastq.gz e23a49764bc751360a919dae08de14c5;862cc45fb142f1a5536861a2bfc4fa02 137664283;154045731
Urban2024 2024 10.1016/j.cub.2024.04.006 SGW_S3_1 SRA PRJNA1021938 SRS20486690 SGW_S3_1_Lib1_sg_Run1 double PfuTurbo Cx Hotstart DNA none NextSeq 500 PAIRED WGS 4246407 SRR28001589 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/089/SRR28001589/SRR28001589_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/089/SRR28001589/SRR28001589_2.fastq.gz 939f80e713295caebc3be5bed71e19c3;8335066159b39fd4374779e8da15b7e8 196998487;209697605
Urban2024 2024 10.1016/j.cub.2024.04.006 SGW_S3_1 SRA PRJNA1021938 SRS20486690 SGW_S3_1_Lib1_sg_Run2 double PfuTurbo Cx Hotstart DNA none NextSeq 500 PAIRED WGS 10104162 SRR28001587 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/087/SRR28001587/SRR28001587_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/087/SRR28001587/SRR28001587_2.fastq.gz 9f2bdfada83f9bcd8c072f1a9f894c28;467b3f87c412782a9e5827d372d48b73 434877638;459606127
Urban2024 2024 10.1016/j.cub.2024.04.006 SGW_S3_1 SRA PRJNA1021938 SRS20486690 SGW_S3_1_Lib2_capKAPA double PfuTurbo Cx Hotstart DNA none NextSeq 500 SINGLE Targeted-Capture 28493511 SRR28001560 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/060/SRR28001560/SRR28001560.fastq.gz 3028f1a70f4d7197cc64351f870052f0 1252220085
Urban2024 2024 10.1016/j.cub.2024.04.006 SGW_S3_1 SRA PRJNA1021938 SRS20486690 SGW_S3_1_Lib2_capMyBaits_Run1 double PfuTurbo Cx Hotstart DNA none NextSeq 500 PAIRED Targeted-Capture 73721739 SRR28001569 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/069/SRR28001569/SRR28001569_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/069/SRR28001569/SRR28001569_2.fastq.gz c570960b677437696b43e4e63e787f8d;0c479ac1e0c7ae3b7024115c5124a227 3178845451;3426341754
Urban2024 2024 10.1016/j.cub.2024.04.006 SGW_S3_1 SRA PRJNA1021938 SRS20486690 SGW_S3_1_Lib2_capMyBaits_Run2 double PfuTurbo Cx Hotstart DNA none NextSeq 500 PAIRED Targeted-Capture 51916693 SRR28001567 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/067/SRR28001567/SRR28001567_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/067/SRR28001567/SRR28001567_2.fastq.gz f731005acab81baf6e218b8a2f68f207;b2c61e2354fb6088ccbae84dd38e63ca 2269898961;2342544905
Urban2024 2024 10.1016/j.cub.2024.04.006 SGW_S3_1 SRA PRJNA1021938 SRS20486690 SGW_S3_1_Lib2_capMyBaits_Run3 double PfuTurbo Cx Hotstart DNA none NextSeq 500 PAIRED Targeted-Capture 14696554 SRR28001565 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/065/SRR28001565/SRR28001565_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/065/SRR28001565/SRR28001565_2.fastq.gz 4fe2246a40d429d70cb741c9373e2c57;4ed0a6f047bc14ac85daaa7b397c1c76 584446190;621416780
Urban2024 2024 10.1016/j.cub.2024.04.006 SGW_S3_1 SRA PRJNA1021938 SRS20486690 SGW_S3_1_Lib2_capMyBaits_Run4 double PfuTurbo Cx Hotstart DNA none NextSeq 500 PAIRED Targeted-Capture 14336952 SRR28001563 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/063/SRR28001563/SRR28001563_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/063/SRR28001563/SRR28001563_2.fastq.gz 0c00297d41d8bf0c828226b3cafab542;095e90091cb5d9769ed9f538136275ef 581835802;630491193
Urban2024 2024 10.1016/j.cub.2024.04.006 SGW_S3_1 SRA PRJNA1021938 SRS20486690 SGW_S3_1_Lib2_sg_Run1 double PfuTurbo Cx Hotstart DNA none NextSeq 500 PAIRED WGS 1604157 SRR28001588 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/088/SRR28001588/SRR28001588_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR280/088/SRR28001588/SRR28001588_2.fastq.gz ca969148cd913848121ae2a4de4e2125;9ea93852575548bfc1536b06e840850c 70368500;72656572
6 changes: 5 additions & 1 deletion ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv
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Expand Up @@ -641,7 +641,7 @@ Hodgkins2023 2023 10.1038/s41467-023-41174-0 l’Observance in Marseille 43.296
Hodgkins2023 2023 10.1038/s41467-023-41174-0 Saints Màrtirs Just i Pastor, Barcelona 41.387 2.168 Spain Barcelona-3031-Tooth Homo sapiens 1400 10.1016/j.chom.2016.05.012 bacteria Clostridium tetani tooth chromosome ENA raw PRJEB13664 ERS1124787
Hodgkins2023 2023 10.1038/s41467-023-41174-0 Saint-Laurent-de-la-Cabrerisse 43.084 2.7 France SLC-France-Tooth Homo sapiens 1300 10.1073/pnas.1812865115 bacteria Clostridium tetani tooth chromosome ENA raw PRJEB24499 ERS2865271
Hodgkins2023 2023 10.1038/s41467-023-41174-0 Karlova, Tartu 58.371 26.732 Estonia Karolva-Tooth Homo sapiens 4200 10.1098/rspb.2019.1528 bacteria Clostridium tetani tooth chromosome ENA raw PRJEB32786 ERS3568107
Hodgkins2023 2023 10.1038/s41467-023-41174-0 Abusir el-Meleq, Middle Egypt 29.9 31.2 Egypt Abusir1655-Tooth Homo sapiens 3100 10.1038/ncomms15694 bacteria Clostridium tetani tooth chromosome ENA raw PRJEB33848 ERS3635957
Hodgkins2023 2023 10.1038/s41467-023-41174-0 Abusir el-Meleq, Middle Egypt 29.9 31.2 Egypt Abusir1655-Tooth Homo sapiens 3100 10.1038/ncomms15694 bacteria Clostridium tetani tooth chromosome ENA raw PRJEB33848 ERS3635957
Hodgkins2023 2023 10.1038/s41467-023-41174-0 Abusir el-Meleq, Middle Egypt 29.9 31.2 Egypt Abusir1595-Tooth Homo sapiens 2900 10.1038/ncomms15694 bacteria Clostridium tetani tooth chromosome ENA raw PRJEB33848 ERS3635963
Hodgkins2023 2023 10.1038/s41467-023-41174-0 Abusir el-Meleq, Middle Egypt 29.9 31.2 Egypt Abusir1668-Tooth Homo sapiens 2200 10.1038/ncomms15694 bacteria Clostridium tetani tooth chromosome ENA raw PRJEB33848 ERS3635986,ERS3636003
Hodgkins2023 2023 10.1038/s41467-023-41174-0 Abusir el-Meleq, Middle Egypt 29.9 31.2 Egypt Abusir1671-Tooth Homo sapiens 2100 10.1038/ncomms15694 bacteria Clostridium tetani tooth chromosome ENA raw PRJEB33848 ERS3636004
Expand All @@ -666,3 +666,7 @@ 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
Urban2024 2024 10.1016/j.cub.2024.04.006 St. Mary Magdalene leprosarium, Winchester 51.059 -1.308 United Kingdom MMW_H50_1 Homo sapiens 600 10.1016/j.cub.2024.04.006 bacteria Mycobacterium leprae tooth chromosome SRA raw PRJNA1021938 SRS20486703
Urban2024 2024 10.1016/j.cub.2024.04.006 St. Mary Magdalene leprosarium, Winchester 51.059 -1.308 United Kingdom MMW_H80_1 Homo sapiens 900 10.1016/j.cub.2024.04.006 bacteria Mycobacterium leprae tooth chromosome SRA raw PRJNA1021938 SRS20486681
Urban2024 2024 10.1016/j.cub.2024.04.006 St. Mary Magdalene leprosarium, Winchester 51.059 -1.308 United Kingdom MMW_H94_1 Homo sapiens 700 10.1016/j.cub.2024.04.006 bacteria Mycobacterium leprae tooth chromosome SRA raw PRJNA1021938 SRS20486688
Urban2024 2024 10.1016/j.cub.2024.04.006 Staple Gardens, Winchester 51.064 -1.317 United Kingdom SGW_S3_1 Sciurus vulgaris 1000 10.1016/j.cub.2024.04.006 bacteria Mycobacterium leprae bone chromosome SRA raw PRJNA1021938 SRS20486690

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