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Madison2023 #1123

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Dec 1, 2023
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Madison2023 #1123

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8cd97a3
Update ancientmetagenome-hostassociated_samples.tsv
DianaSpurite Oct 9, 2023
864d65f
Update ancientmetagenome-hostassociated_libraries.tsv
DianaSpurite Oct 9, 2023
6f9e2a6
Update CHANGELOG.md
DianaSpurite Oct 9, 2023
1c348c7
Update ancientmetagenome-hostassociated_samples.tsv
DianaSpurite Oct 9, 2023
dfd3cec
Update ancientmetagenome-hostassociated_samples.tsv
DianaSpurite Nov 30, 2023
0547c22
Add missing two samples and round lat and long
alexhbnr Nov 30, 2023
2e171e6
Add two missing samples and add lib polymerase
alexhbnr Nov 30, 2023
d086f49
Merge branch 'Madison2023' of github.com:SPAAM-community/AncientMetag…
alexhbnr Nov 30, 2023
8459e31
Remove the two youngest samples after discussing with Diana and James
alexhbnr Dec 1, 2023
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -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
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11 changes: 11 additions & 0 deletions ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv
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Expand Up @@ -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
11 changes: 11 additions & 0 deletions ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv
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Expand Up @@ -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