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Zampirolo et al. 2024 #1194

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a2b0748
Update ancientmetagenome-environmental_samples.tsv
GiuliaZ538 Oct 3, 2024
ff92e88
Update ancientmetagenome-environmental_samples.tsv
GiuliaZ538 Oct 3, 2024
dfe98df
Update ancientmetagenome-environmental_libraries.tsv
GiuliaZ538 Oct 3, 2024
2e23507
Update CHANGELOG.md Zampirolo2024
GiuliaZ538 Oct 3, 2024
25b37be
Change order of elements of primary_study_focus
alexhbnr Oct 3, 2024
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Merge branch 'master' into Zampirolo-et-al.-2024
alexhbnr Oct 4, 2024
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Fix username
alexhbnr Oct 4, 2024
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Remove neg controls and correct instrument model to match the paper
alexhbnr Oct 4, 2024
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -12,13 +12,14 @@ and this project follows to [Calendar Versioning](https://calver.org/).
#### Ancient Metagenome: Host Associated

- Austin 2024 10.1038/s41598-024-64818-7 (added by @alexhbnr and @jfy133)
- Bozzi 2024 10.1038/s41598-023-40246-x (added by @DavideBozzi and @alexhbn)
- Bozzi 2024 10.1038/s41598-023-40246-x (added by @DavideBozzi and @alexhbnr)

#### Ancient Single Genome: Host Associated

- White 2021 10.3390/biology10121324 (added by @DianaSpurite, @jfy133, and @alexhbnr)

#### Ancient Metagenome: Environmental
- Added: Zampirolo 2024 10.1016/j.cub.2024.08.047 (added by @GiuliaZ538)

### Changed

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11 changes: 11 additions & 0 deletions ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries.tsv
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Expand Up @@ -811,3 +811,14 @@ Liu2024 2024 10.1126/sciadv.adn8490 ESL077 ENA PRJEB74036 ERS18499367 200327_A00
Liu2024 2024 10.1126/sciadv.adn8490 ESL078 ENA PRJEB74036 ERS18499368 210409_A00902_B_L1-2_APMG-28-8 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 82609702 ERR12814474 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/074/ERR12814474/ERR12814474_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/074/ERR12814474/ERR12814474_2.fastq.gz 5dab614f4198cbedb3542d0b88330ef6;c2628f6e6a055a191bdac3f29f5e05be 2390002791;2534714308
Liu2024 2024 10.1126/sciadv.adn8490 ESL079 ENA PRJEB74036 ERS18499369 210409_A00902_B_L1-2_APMG-28-7 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 134931132 ERR12814475 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/075/ERR12814475/ERR12814475_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/075/ERR12814475/ERR12814475_2.fastq.gz 7e120573673c7a1783005f7ad911a5ff;1ea4590ef271b2e74017f1e92404d770 4090579685;3924358144
Liu2024 2024 10.1126/sciadv.adn8490 ESL001 ENA PRJEB74036 ERS18499370 200327_A00902_B_L1-2_APMG-10-22 single AccuPrime Pfx DNA none NA Illumina NovaSeq 6000 PAIRED WGS 85518486 ERR12814476 ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/076/ERR12814476/ERR12814476_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR128/076/ERR12814476/ERR12814476_2.fastq.gz 2a5e7c3250bcdfcf9e815571c6efca1c;c5a94cd6c3b2236dbf477960b3bc8dde 2277648738;2617729740
Zampirolo2024 2024 10.1016/j.cub.2024.08.047 VM2 ENA PRJEB59830 ERS14617135 VM2/SedaVM2 double KAPA HiFi Uracil+ none NA Illumina HiSeq 4000 SINGLE WGS 26089750 ERR10878152 ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/052/ERR10878152/ERR10878152.fastq.gz c1e838afd1314ef5a80ef60344662943 796070627
Zampirolo2024 2024 10.1016/j.cub.2024.08.047 VM3 ENA PRJEB59830 ERS14617136 VM3/SedaVM3 double KAPA HiFi Uracil+ none NA Illumina HiSeq 4000 SINGLE WGS 55013661 ERR10878153 ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/053/ERR10878153/ERR10878153.fastq.gz 9617733c3a010982961a11e71e77c7bb 1828721344
Zampirolo2024 2024 10.1016/j.cub.2024.08.047 VM11 ENA PRJEB59830 ERS14617137 VM11/SedaVM11 double KAPA HiFi Uracil+ none NA Illumina HiSeq 4000 SINGLE WGS 26094794 ERR10878154 ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/054/ERR10878154/ERR10878154.fastq.gz 3af8a33732bc72684e7b94931b9c0285 846315529
Zampirolo2024 2024 10.1016/j.cub.2024.08.047 VM14 ENA PRJEB59830 ERS14617138 VM14/SedaVM14 double KAPA HiFi Uracil+ none NA Illumina HiSeq 4000 SINGLE WGS 41709344 ERR10878155 ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/055/ERR10878155/ERR10878155.fastq.gz 91c404dc5a068616bfa07d4c1ef2f2bd 1349293515
Zampirolo2024 2024 10.1016/j.cub.2024.08.047 VM15 ENA PRJEB59830 ERS14617139 VM15/SedaVM15 double KAPA HiFi Uracil+ none NA Illumina HiSeq 4000 SINGLE WGS 28165755 ERR10878156 ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/056/ERR10878156/ERR10878156.fastq.gz 3d7ac95dbfb6b405b329a56f821dc0d1 1141845854
Zampirolo2024 2024 10.1016/j.cub.2024.08.047 VM17 ENA PRJEB59830 ERS14617140 VM17/SedaVM17 double KAPA HiFi Uracil+ none NA Illumina HiSeq 4000 SINGLE WGS 74503889 ERR10878157 ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/057/ERR10878157/ERR10878157.fastq.gz e41ef23800e417ca574e52d29a544091 2799383121
Zampirolo2024 2024 10.1016/j.cub.2024.08.047 VM19 ENA PRJEB59830 ERS14617141 VM19/SedaVM19 double KAPA HiFi Uracil+ none NA Illumina HiSeq 4000 SINGLE WGS 45753766 ERR10878158 ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/058/ERR10878158/ERR10878158.fastq.gz a33eb324eaacc1d95b039782686e21c6 1562314048
Zampirolo2024 2024 10.1016/j.cub.2024.08.047 VM22 ENA PRJEB59830 ERS14617142 VM22/SedaVM22 double KAPA HiFi Uracil+ none NA Illumina HiSeq 4000 SINGLE WGS 21588084 ERR10878159 ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/059/ERR10878159/ERR10878159.fastq.gz f3163a72460c74b0b68efd86353f31a5 688511443
Zampirolo2024 2024 10.1016/j.cub.2024.08.047 VM24 ENA PRJEB59830 ERS14617143 VM24/SedaVM24 double KAPA HiFi Uracil+ none NA Illumina HiSeq 4000 SINGLE WGS 41233122 ERR10878160 ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/060/ERR10878160/ERR10878160.fastq.gz 4ffc1d776594654a6da21eb7fdcf4dd3 1355770150
Zampirolo2024 2024 10.1016/j.cub.2024.08.047 VM26 ENA PRJEB59830 ERS14617144 VM26/SedaVM26 double KAPA HiFi Uracil+ none NA Illumina NovaSeq 6000 PAIRED WGS 13260540 ERR10878162 ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/062/ERR10878162/ERR10878162_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/062/ERR10878162/ERR10878162_2.fastq.gz aa6a7e6bd013e867070d439082793c7c;b735dfaca779affb718c251a800b9131 323763782;361608906
Zampirolo2024 2024 10.1016/j.cub.2024.08.047 VM28 ENA PRJEB59830 ERS14617145 VM28/SedaVM28 double KAPA HiFi Uracil+ none NA Illumina NovaSeq 6000 PAIRED WGS 36876202 ERR10878163 ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/063/ERR10878163/ERR10878163_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/063/ERR10878163/ERR10878163_2.fastq.gz b81b50ea8a3ab61e3ab3fb80dfc6d9ce;5a893ad1006ca2551af05041ab6352d1 959964334;893177531
11 changes: 11 additions & 0 deletions ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv
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Expand Up @@ -701,3 +701,14 @@ Liu2024 2024 10.1126/sciadv.adn8490 Lake Naleng 31.10 99.75 China faunal,floral
Liu2024 2024 10.1126/sciadv.adn8490 Lake Naleng 31.10 99.75 China faunal,floral,microbial 04_NC 58 ESL077 700 10.1007/s00334-009-0219-5 lake lake sediment 2021 ENA PRJEB74036 ERS18499368
Liu2024 2024 10.1126/sciadv.adn8490 Lake Naleng 31.10 99.75 China faunal,floral,microbial 04_NC 38 ESL078 500 10.1007/s00334-009-0219-5 lake lake sediment 2021 ENA PRJEB74036 ERS18499369
Liu2024 2024 10.1126/sciadv.adn8490 Lake Naleng 31.10 99.75 China faunal,floral,microbial 04_NC 14 ESL079 100 10.1007/s00334-009-0219-5 lake lake sediment 2021 ENA PRJEB74036 ERS18499370
Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia faunal,floral,microbial North Wall excavation trench 18 VM2 800 10.1016/j.cub.2024.08.047 rock shelter sediment 2019 ENA PRJEB59830 ERS14617135
Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia faunal,floral,microbial North Wall excavation trench 26 VM3 800 10.1016/j.cub.2024.08.047 rock shelter sediment 2019 ENA PRJEB59830 ERS14617136
Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia faunal,floral,microbial North Wall excavation trench 64 VM11 3000 10.1016/j.cub.2024.08.047 rock shelter sediment 2019 ENA PRJEB59830 ERS14617137
Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia faunal,floral,microbial North Wall excavation trench 107 VM14 3900 10.1016/j.cub.2024.08.047 rock shelter sediment 2019 ENA PRJEB59830 ERS14617138
Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia faunal,floral,microbial North Wall excavation trench 116 VM15 4100 10.1016/j.cub.2024.08.047 rock shelter sediment 2019 ENA PRJEB59830 ERS14617139
Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia faunal,floral,microbial North Wall excavation trench 134 VM17 5300 10.1016/j.cub.2024.08.047 rock shelter sediment 2019 ENA PRJEB59830 ERS14617140
Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia faunal,floral,microbial North Wall excavation trench 151 VM19 6100 10.1016/j.cub.2024.08.047 rock shelter sediment 2019 ENA PRJEB59830 ERS14617141
Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia faunal,floral,microbial North Wall excavation trench 185 VM22 6800 10.1016/j.cub.2024.08.047 rock shelter sediment 2019 ENA PRJEB59830 ERS14617142
Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia faunal,floral,microbial North Wall excavation trench 196 VM24 7000 10.1016/j.cub.2024.08.047 rock shelter sediment 2019 ENA PRJEB59830 ERS14617143
Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia faunal,floral,microbial North Wall excavation trench 222 VM26 9600 10.1016/j.cub.2024.08.047 rock shelter sediment 2019 ENA PRJEB59830 ERS14617144
Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia faunal,floral,microbial North Wall excavation trench 236 VM28 9800 10.1016/j.cub.2024.08.047 rock shelter sediment 2019 ENA PRJEB59830 ERS14617145
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