diff --git a/CHANGELOG.md b/CHANGELOG.md index ffe65591a..71a2ec92b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,8 @@ and this project follows to [Calendar Versioning](https://calver.org/). #### Ancient Metagenome: Host Associated +- Madison 2023 10.1371/journal.pone.0291540 (added by @DianaSpurite) + #### Ancient Single Genome: Host Associated #### Ancient Metagenome: Environmental diff --git a/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv b/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv index 13b5b998e..bef6f5ae3 100644 --- a/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv +++ b/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv @@ -2399,3 +2399,14 @@ Klapper2023 2023 10.1126/science.adf5300 ZAF001.A ENA PRJEB55583 ERS3774445 ZAF0 Klapper2023 2023 10.1126/science.adf5300 ZAF001.A ENA PRJEB55583 ERS3774445 ZAF001.A0102 double PfuTurbo Cx Hotstart DNA half-udg NA NextSeq 500 PAIRED WGS 22694900 ERR10114865 ftp.sra.ebi.ac.uk/vol1/fastq/ERR101/065/ERR10114865/ERR10114865_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR101/065/ERR10114865/ERR10114865_2.fastq.gz e33fa537e5eaeaefa85547b861eda112;a309c625cf35d98e55930273da139aab 398424687;407961114 Fontani2023 2023 10.1038/s41598-023-39250-y SLBT ENA PRJEB58818 ERS14581258 SLBT single AmpliTaq Gold DNA none NA HiSeq X Ten PAIRED WGS 15391964 ERR10841228 ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/028/ERR10841228/ERR10841228_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/028/ERR10841228/ERR10841228_2.fastq.gz 0d2b63b6027225877f959b2fc00a6547;4ca0f51553da0d83a3ef39a66e7b006c 614385371;498604634 Fontani2023 2023 10.1038/s41598-023-39250-y SLB ENA PRJEB58818 ERS14410560 SLB single AmpliTaq Gold DNA none NA HiSeq X Ten PAIRED WGS 1023235990 ERR10841194 ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/094/ERR10841194/ERR10841194_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/094/ERR10841194/ERR10841194_2.fastq.gz 0674a2dec35470f7b5528adc23013763;9a57bd71240f38fcbbb0557129377948 33577438838;37974211170 +Madison2023 2023 10.1371/journal.pone.0291540 2564 SRA PRJNA836960 SRS12960506 MPM-2564 double Q5 Hot Start High-Fidelity DNA none NA Illumina NovaSeq 6000 PAIRED WGS 9108413 SRR19160147 ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/047/SRR19160147/SRR19160147_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/047/SRR19160147/SRR19160147_2.fastq.gz 174da4cb664b28b9c7136b2d6e8d2a7c;74efb591ef5e31256fde88c29e56205b 495214261;514052538 +Madison2023 2023 10.1371/journal.pone.0291540 1151 SRA PRJNA836960 SRS12960469 INHS-1151 double Q5 Hot Start High-Fidelity DNA none NA Illumina NovaSeq 6000 PAIRED WGS 10074735 SRR19160184 ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/084/SRR19160184/SRR19160184_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/084/SRR19160184/SRR19160184_2.fastq.gz 7cca1cf0693e6bc32bf20e305efe4532;1419121b9a18e6c1fe575a27ce73cf73 509442539;523102942 +Madison2023 2023 10.1371/journal.pone.0291540 1491 SRA PRJNA836960 SRS12960459 UIUC-1491 double Q5 Hot Start High-Fidelity DNA none NA Illumina NovaSeq 6000 PAIRED WGS 13760971 SRR19160194 ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/094/SRR19160194/SRR19160194_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/094/SRR19160194/SRR19160194_2.fastq.gz f7cba18f4a736db18570a584163df0c2;ce22ce5d8860aae559e8c329e1668443 636117790;736413548 +Madison2023 2023 10.1371/journal.pone.0291540 1489 SRA PRJNA836960 SRS12960503 UIUC-1489 double Q5 Hot Start High-Fidelity DNA none NA Illumina NovaSeq 6000 PAIRED WGS 22345028 SRR19160150 ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/050/SRR19160150/SRR19160150_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/050/SRR19160150/SRR19160150_2.fastq.gz 17aa22d70c14508603422efd9f771924;75ad9d67cb05c286436923dd3dfc1bf3 1274014703;1331072780 +Madison2023 2023 10.1371/journal.pone.0291540 7405 SRA PRJNA836960 SRS12960478 INHS-7405 double Q5 Hot Start High-Fidelity DNA none NA Illumina NovaSeq 6000 PAIRED WGS 20082540 SRR19160175 ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/075/SRR19160175/SRR19160175_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/075/SRR19160175/SRR19160175_2.fastq.gz 2dfcf42ec22014e19606aa97915a2a0f;edaa63871ecfc5366306706bb7d172d1 1098644794;1142593542 +Madison2023 2023 10.1371/journal.pone.0291540 1490 SRA PRJNA836960 SRS12960473 UIUC-1490 double Q5 Hot Start High-Fidelity DNA none NA Illumina NovaSeq 6000 PAIRED WGS 29571665 SRR19160180 ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/080/SRR19160180/SRR19160180_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/080/SRR19160180/SRR19160180_2.fastq.gz 4770523d940820af7dbd4c0942891563;e11661a818afaadd01f9bfd980191306 1259944643;1299585715 +Madison2023 2023 10.1371/journal.pone.0291540 4572 SRA PRJNA836960 SRS12960447 MPM-4572 double Q5 Hot Start High-Fidelity DNA none NA Illumina NovaSeq 6000 PAIRED WGS 29748544 SRR19160206 ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/006/SRR19160206/SRR19160206_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/006/SRR19160206/SRR19160206_2.fastq.gz 9bd61fd2724448af14c356d08e0c2ea9;cad4f4278254e1470316394c5a5fe517 1534352326;1517571826 +Madison2023 2023 10.1371/journal.pone.0291540 14914 SRA PRJNA836960 SRS12960422 INHS-14914 double Q5 Hot Start High-Fidelity DNA none NA Illumina NovaSeq 6000 PAIRED WGS 27332784 SRR19160231 ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/031/SRR19160231/SRR19160231_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/031/SRR19160231/SRR19160231_2.fastq.gz 2764c0c8aa70ea8148ae82fd381fba86;42fb717b030a80b552f289fb79a844e8 1466272446;1506170419 +Madison2023 2023 10.1371/journal.pone.0291540 3007 SRA PRJNA836960 SRS12960492 UIUC-3007 double Q5 Hot Start High-Fidelity DNA none NA Illumina NovaSeq 6000 PAIRED WGS 18791680 SRR19160161 ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/061/SRR19160161/SRR19160161_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/061/SRR19160161/SRR19160161_2.fastq.gz 2360dd0d5cb5ee99f0991fb20c8e28ef;5a770368fcad34732e09016727d7e3b9 816761872;839593765 +Madison2023 2023 10.1371/journal.pone.0291540 2194 SRA PRJNA836960 SRS12960479 INHS-2194 double Q5 Hot Start High-Fidelity DNA none NA Illumina NovaSeq 6000 PAIRED WGS 25643283 SRR19160174 ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/074/SRR19160174/SRR19160174_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/074/SRR19160174/SRR19160174_2.fastq.gz 365144a66329a56a42d7ad8030a8f05f;ca20fc4b3a6ae857126650591558e6b9 1401616407;1467729754 +Madison2023 2023 10.1371/journal.pone.0291540 1700 SRA PRJNA836960 SRS12960402 INHS-1700 double Q5 Hot Start High-Fidelity DNA none NA Illumina NovaSeq 6000 PAIRED WGS 18119300 SRR19160251 ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/051/SRR19160251/SRR19160251_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR191/051/SRR19160251/SRR19160251_2.fastq.gz 166c7b4c6a75ab795f589f7fe611160f;a874390b236e7ce8e799d2315fa6f840 993118143;1028287751 diff --git a/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv b/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv index f86e096d9..516d69aee 100644 --- a/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv +++ b/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv @@ -1400,3 +1400,14 @@ Honap2023 2023 10.1002/ajpa.24735 WRP 9 Site NA NA USA WAMP18 Homo sapiens 700 1 Honap2023 2023 10.1002/ajpa.24735 Selzer site NA NA USA WAMP34 Homo sapiens 700 10.1002/ajpa.24735 oral dental calculus ENA PRJNA885571 SRS15300804 Fontani2023 2023 10.1038/s41598-023-39250-y Grotta di Pietra Sant’Angelo (San Lorenzo Bellizzi) 39.89 16.33 Italy SLBT Homo sapiens 6100 10.1038/s41598-023-39250-y oral dental calculus ENA PRJEB58818 ERS14581258 Fontani2023 2023 10.1038/s41598-023-39250-y Grotta di Pietra Sant’Angelo (San Lorenzo Bellizzi) 39.89 16.33 Italy SLB Homo sapiens 6100 10.1038/s41598-023-39250-y oral tooth ENA PRJEB58818 ERS14410560 +Madison2023 2023 10.1371/journal.pone.0291540 Antioch 42.478 -88.096 USA 7405 Lithobates pipiens 100 10.1371/journal.pone.0291540 gut intestine SRA PRJNA836960 SRS13029047 +Madison2023 2023 10.1371/journal.pone.0291540 Beaver Dam 43.464 -88.853 USA 1489 Lithobates pipiens 100 10.1371/journal.pone.0291540 gut intestine SRA PRJNA836960 SRS12960503 +Madison2023 2023 10.1371/journal.pone.0291540 Beaver Dam 43.464 -88.853 USA 1490 Lithobates pipiens 100 10.1371/journal.pone.0291540 gut intestine SRA PRJNA836960 SRS13029045 +Madison2023 2023 10.1371/journal.pone.0291540 Beaver Dam 43.464 -88.853 USA 1491 Lithobates pipiens 100 10.1371/journal.pone.0291540 gut intestine SRA PRJNA836960 SRS13029056 +Madison2023 2023 10.1371/journal.pone.0291540 Bluff Creek 42.799 -88.682 USA 4572 Lithobates pipiens 100 10.1371/journal.pone.0291540 gut intestine SRA PRJNA836960 SRS12960447 +Madison2023 2023 10.1371/journal.pone.0291540 Buffalo Slough 44.433 -91.787 USA 14914 Lithobates pipiens 100 10.1371/journal.pone.0291540 gut intestine SRA PRJNA836960 SRS13029062 +Madison2023 2023 10.1371/journal.pone.0291540 Chemung 42.416 -88.665 USA 2194 Lithobates pipiens 100 10.1371/journal.pone.0291540 gut intestine SRA PRJNA836960 SRS12960479 +Madison2023 2023 10.1371/journal.pone.0291540 Harrison township 42.384 -89.194 USA 3007 Lithobates pipiens 100 10.1371/journal.pone.0291540 gut intestine SRA PRJNA836960 SRS13029053 +Madison2023 2023 10.1371/journal.pone.0291540 Lake Pistakee 42.386 -88.209 USA 1700 Lithobates pipiens 100 10.1371/journal.pone.0291540 gut intestine SRA PRJNA836960 SRS12960402 +Madison2023 2023 10.1371/journal.pone.0291540 Marengo, Kishwaukee Riv. 42.250 -88.606 USA 1151 Lithobates pipiens 100 10.1371/journal.pone.0291540 gut intestine SRA PRJNA836960 SRS13029051 +Madison2023 2023 10.1371/journal.pone.0291540 Pell lake 42.541 -88.358 USA 2564 Lithobates pipiens 100 10.1371/journal.pone.0291540 gut intestine SRA PRJNA836960 SRS13029052