diff --git a/CHANGELOG.md b/CHANGELOG.md index 233555a17..4759c5772 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -19,6 +19,7 @@ and this project follows to [Calendar Versioning](https://calver.org/). - Neumann 2023 10.1553/archaeologia107 (added by @DianaSpurite) - Bonczarowska 2023 10.1098/rspb.2023.0622 (added by @DianaSpurite) - Long 2023 10.1371/journal.ppat.1011538 (added by @DianaSpurite) +- Campos 2023 10.1038/s41467-023-39950-z (added by @DianaSpurite) #### Ancient Metagenome: Environmental diff --git a/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv b/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv index a7341d755..c9d5614f7 100644 --- a/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv +++ b/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv @@ -2741,3 +2741,15 @@ Parker2023 2023 10.1371/journal.ppat.1011404 KRA032 ENA PRJEB61096 ERS14884864 K Parker2023 2023 10.1371/journal.ppat.1011404 KRA032 ENA PRJEB61096 ERS14884864 KRA032.A0103 single AmpliTaq Gold DNA none Illumina HiSeq 4000 PAIRED Targeted-Capture 34240226 ERR11202937 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR112/037/ERR11202937/ERR11202937_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR112/037/ERR11202937/ERR11202937_2.fastq.gz 360f8370041b6558afd149593a6a8595;da02c63d5f55963d7ae9c6ab6ea15402 553924381;611677182 Long2023 2023 10.1371/journal.ppat.1011538 Sante Brancorsini SRA PRJNA966239 SRS17532534 LMN01_S415 single AccuPrime Pfx DNA none Illumina HiSeq 1500 PAIRED WGS 26874306 SRR24420453 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR244/053/SRR24420453/SRR24420453_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR244/053/SRR24420453/SRR24420453_2.fastq.gz d7b8d3754d7633e119f0a2769bd821a1;917b0e2ee6ad1bf51904061e7ab8d597 673258837;673103704 Long2023 2023 10.1371/journal.ppat.1011538 Sante Brancorsini SRA PRJNA966239 SRS17532534 LMN01_S301 single AccuPrime Pfx DNA none Illumina HiSeq 1500 PAIRED WGS 1731099 SRR24420454 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR244/054/SRR24420454/SRR24420454_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR244/054/SRR24420454/SRR24420454_2.fastq.gz 7d67f4001c48a53702e280edb68ddde1;e87eeebc190579aa3323845513e5128b 45760293;45221147 +Campos2023 2023 10.1038/s41467-023-39950-z HERB_1845 SRA PRJNA883598 SRS15248955 HERB_1845 double Unknown none NextSeq 500 SINGLE WGS 26083266 SRR21711661 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/061/SRR21721661/SRR21721661.fastq.gz d0a79e7827ddb73b6220ce2a23e40714 701255405 +Campos2023 2023 10.1038/s41467-023-39950-z HERB_1852 SRA PRJNA883598 SRS15248956 HERB_1852 double PfuTurbo Cx Hotstart DNA none NextSeq 500 SINGLE WGS 8020338 SRR21721660 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/060/SRR21721660/SRR21721660.fastq.gz 4e97e0303fbaa346d262e664f8ecd70b 274357796 +Campos2023 2023 10.1038/s41467-023-39950-z HERB_1854 SRA PRJNA883598 SRS15248959 HERB_1854 double PfuTurbo Cx Hotstart DNA none NextSeq 500 SINGLE WGS 6440966 SRR21721657 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/057/SRR21721657/SRR21721657.fastq.gz f4fc3e5526d10841f8500f58ae96651e 230281895 +Campos2023 2023 10.1038/s41467-023-39950-z HERB_1859 SRA PRJNA883598 SRS15248960 HERB_1859 double PfuTurbo Cx Hotstart DNA none NextSeq 500 SINGLE WGS 4752661 SRR21721656 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/056/SRR21721656/SRR21721656.fastq.gz 2bc6b7b859331adf3e7b0b0f5fbdd59b 168302503 +Campos2023 2023 10.1038/s41467-023-39950-z HERB_1865 SRA PRJNA883598 SRS15248961 HERB_1865 double PfuTurbo Cx Hotstart DNA none NextSeq 500 SINGLE WGS 3912063 SRR21721655 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/055/SRR21721655/SRR21721655.fastq.gz 9e1715dfdd60db43bcae63e0861b11c9 151676612 +Campos2023 2023 10.1038/s41467-023-39950-z HERB_1884 SRA PRJNA883598 SRS15248962 HERB_1884 double Unknown none NextSeq 500 SINGLE WGS 14920382 SRR21721654 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/054/SRR21721654/SRR21721654.fastq.gz a63d5b897aafe3754063bdccf8789491 366477920 +Campos2023 2023 10.1038/s41467-023-39950-z HERB_1911 SRA PRJNA883598 SRS15248963 HERB_1911 double Unknown none NextSeq 500 SINGLE WGS 5972972 SRR21721653 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/053/SRR21721653/SRR21721653.fastq.gz e5e1b9df9f3e3a369859cc8d63474a52 195756499 +Campos2023 2023 10.1038/s41467-023-39950-z HERB_1915 SRA PRJNA883598 SRS15248964 HERB_1915 double Unknown none NextSeq 500 SINGLE WGS 7151544 SRR21721652 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/052/SRR21721652/SRR21721652.fastq.gz 892f78532e8e0924aa7fe9a3bff88656 178713143 +Campos2023 2023 10.1038/s41467-023-39950-z HERB_1922 SRA PRJNA883598 SRS15248965 HERB_1922 double PfuTurbo Cx Hotstart DNA none NextSeq 500 SINGLE WGS 17855646 SRR21721651 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/051/SRR21721651/SRR21721651.fastq.gz 154590670a30d3ee14af1d2c0dfdc7fa 583308323 +Campos2023 2023 10.1038/s41467-023-39950-z HERB_1946 SRA PRJNA883598 SRS15248966 HERB_1946 double Unknown none NextSeq 500 SINGLE WGS 10729826 SRR21721650 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/050/SRR21721650/SRR21721650.fastq.gz f31a22f48c35afdba9cfbd2d6f87dd73 311169565 +Campos2023 2023 10.1038/s41467-023-39950-z HERB_1963 SRA PRJNA883598 SRS15248957 HERB_1963 double PfuTurbo Cx Hotstart DNA none NextSeq 500 SINGLE WGS 4107994 SRR21721659 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/059/SRR21721659/SRR21721659.fastq.gz 718980e28d0c4dc91bd52d1efbc9f70a 139054986 +Campos2023 2023 10.1038/s41467-023-39950-z HERB_1974 SRA PRJNA883598 SRS15248958 HERB_1974 double Unknown none NextSeq 500 SINGLE WGS 9256767 SRR21721658 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/SRR217/058/SRR21721658/SRR21721658.fastq.gz e4530fe1bb2ee93f38c728edf4283d3c 199004045 diff --git a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv index fd77195fc..ad741dcb7 100644 --- a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv +++ b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv @@ -605,3 +605,15 @@ Parker2023 2023 10.1371/journal.ppat.1011404 Krakauer Berg, Peißen, Halle (Saal Parker2023 2023 10.1371/journal.ppat.1011404 Krakauer Berg, Peißen, Halle (Saale), Saxony-Anhalt 51.5 12.05 Germany KRA028 Homo sapiens 600 10.1371/journal.ppat.1011404 bacteria Yersinia pestis skeleton chromosome ENA raw PRJEB61096 ERS14884863 Parker2023 2023 10.1371/journal.ppat.1011404 Krakauer Berg, Peißen, Halle (Saale), Saxony-Anhalt 51.5 12.05 Germany KRA032 Homo sapiens 600 10.1371/journal.ppat.1011404 bacteria Yersinia pestis skeleton chromosome ENA raw PRJEB61096 ERS14884864 Long2023 2023 10.1371/journal.ppat.1011538 Convento del Beato Sante, Mombaroccio, Pesaro e Urbino 43.789 12.861 Italy Sante Brancorsini Homo sapiens 600 10.1371/journal.ppat.1011538 bacteria Brucella melitensis kidney stone chromosome SRA raw PRJNA966239 SRS17532534 +Campos2023 2023 10.1038/s41467-023-39950-z Java -7.23 109.72 Indonesia HERB_1845 Citrus aurantiifolia 200 10.1038/s41467-023-39950-z bacteria Xanthomonas citri pv. citri leaf chromosome SRA raw PRJNA883598 SRS15248955 +Campos2023 2023 10.1038/s41467-023-39950-z Khasi hills 25.58 91.63 India HERB_1852 Citrus medica 100 10.1038/s41467-023-39950-z bacteria Xanthomonas citri pv. citri leaf chromosome SRA raw PRJNA883598 SRS15248956 +Campos2023 2023 10.1038/s41467-023-39950-z Java -7.23 109.72 Indonesia HERB_1854 Citrus aurantiifolia 100 10.1038/s41467-023-39950-z bacteria Xanthomonas citri pv. citri leaf chromosome SRA raw PRJNA883598 SRS15248959 +Campos2023 2023 10.1038/s41467-023-39950-z Bangladesh 24 90 Bangladesh HERB_1859 Citrus medica 100 10.1038/s41467-023-39950-z bacteria Xanthomonas citri pv. citri leaf chromosome SRA raw PRJNA883598 SRS15248960 +Campos2023 2023 10.1038/s41467-023-39950-z India 22 79 India HERB_1865 Citrus medica 100 10.1038/s41467-023-39950-z bacteria Xanthomonas citri pv. citri leaf chromosome SRA raw PRJNA883598 SRS15248961 +Campos2023 2023 10.1038/s41467-023-39950-z Luzon 16.5 122.2 Philippines HERB_1884 Citrus medica 100 10.1038/s41467-023-39950-z bacteria Xanthomonas citri pv. citri leaf chromosome SRA raw PRJNA883598 SRS15248962 +Campos2023 2023 10.1038/s41467-023-39950-z Java -7.23 109.72 Indonesia HERB_1911 Citrus aurantiifolia 100 10.1038/s41467-023-39950-z bacteria Xanthomonas citri pv. citri leaf chromosome SRA raw PRJNA883598 SRS15248963 +Campos2023 2023 10.1038/s41467-023-39950-z Philippines 15 120 Philippines HERB_1915 Citrus sp. 100 10.1038/s41467-023-39950-z bacteria Xanthomonas citri pv. citri leaf chromosome SRA raw PRJNA883598 SRS15248964 +Campos2023 2023 10.1038/s41467-023-39950-z Yunnan 24.55 101.45 China HERB_1922 Citrus medica 100 10.1038/s41467-023-39950-z bacteria Xanthomonas citri pv. citri leaf chromosome SRA raw PRJNA883598 SRS15248965 +Campos2023 2023 10.1038/s41467-023-39950-z Tlofofo 13.33 144.73 Guam HERB_1946 Citrus sp. 100 10.1038/s41467-023-39950-z bacteria Xanthomonas citri pv. citri leaf chromosome SRA raw PRJNA883598 SRS15248966 +Campos2023 2023 10.1038/s41467-023-39950-z Sanichare 26.67 88.02 Nepal HERB_1963 Citrus medica 100 10.1038/s41467-023-39950-z bacteria Xanthomonas citri pv. citri leaf chromosome SRA raw PRJNA883598 SRS15248957 +Campos2023 2023 10.1038/s41467-023-39950-z Mauritius -20.3 57.6 Mauritius HERB_1974 Citrus sp. 100 10.1038/s41467-023-39950-z bacteria Xanthomonas citri pv. citri leaf chromosome SRA raw PRJNA883598 SRS15248958