From a2b0748d1064fee671b619effd957f9c8f388fcb Mon Sep 17 00:00:00 2001 From: GiuliaZ538 <60102859+GiuliaZ538@users.noreply.github.com> Date: Thu, 3 Oct 2024 12:05:59 +0200 Subject: [PATCH 1/7] Update ancientmetagenome-environmental_samples.tsv Zampirolo_et_al_2024, I have added the sample metadata from the publication Zampirolo_et_al_2024 to the sample.tsv file. --- .../ancientmetagenome-environmental_samples.tsv | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv b/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv index 9b4db348e..621211b32 100644 --- a/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv +++ b/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv @@ -701,3 +701,16 @@ 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 floral,faunal,microbial North Wall excavation trench 18 VM2 800 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617135 +Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench 26 VM3 800 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617136 +Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench 64 VM11 3000 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617137 +Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench 107 VM14 3900 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617138 +Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench 116 VM15 4100 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617139 +Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench 134 VM17 5300 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617140 +Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench 151 VM19 6100 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617141 +Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench 185 VM22 6800 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617142 +Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench 196 VM24 7000 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617143 +Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench 222 VM26 9600 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617144 +Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench 236 VM28 9800 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617145 +Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench NA CTRL-2 NA 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617146 +Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench NA LIB-CTRL-1 NA 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617147 From ff92e8810cffc1ed2f3c7c25654d023aea3c1421 Mon Sep 17 00:00:00 2001 From: GiuliaZ538 <60102859+GiuliaZ538@users.noreply.github.com> Date: Thu, 3 Oct 2024 12:09:20 +0200 Subject: [PATCH 2/7] Update ancientmetagenome-environmental_samples.tsv Zampirolo_et_al_2024_fixed a column, updated the dataset. --- ...ncientmetagenome-environmental_samples.tsv | 26 +++++++++---------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv b/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv index 621211b32..b5675a3a0 100644 --- a/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv +++ b/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv @@ -701,16 +701,16 @@ 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 floral,faunal,microbial North Wall excavation trench 18 VM2 800 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617135 -Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench 26 VM3 800 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617136 -Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench 64 VM11 3000 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617137 -Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench 107 VM14 3900 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617138 -Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench 116 VM15 4100 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617139 -Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench 134 VM17 5300 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617140 -Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench 151 VM19 6100 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617141 -Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench 185 VM22 6800 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617142 -Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench 196 VM24 7000 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617143 -Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench 222 VM26 9600 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617144 -Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench 236 VM28 9800 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617145 -Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench NA CTRL-2 NA 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617146 -Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench NA LIB-CTRL-1 NA 10.1016/j.cub.2024.08.047 rock shelter 2019 ENA PRJEB59830 ERS14617147 +Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,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 floral,faunal,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 floral,faunal,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 floral,faunal,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 floral,faunal,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 floral,faunal,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 floral,faunal,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 floral,faunal,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 floral,faunal,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 floral,faunal,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 floral,faunal,microbial North Wall excavation trench 236 VM28 9800 10.1016/j.cub.2024.08.047 rock shelter sediment 2019 ENA PRJEB59830 ERS14617145 +Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench NA CTRL-2 NA 10.1016/j.cub.2024.08.047 rock shelter sediment 2019 ENA PRJEB59830 ERS14617146 +Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench NA LIB-CTRL-1 NA 10.1016/j.cub.2024.08.047 rock shelter sediment 2019 ENA PRJEB59830 ERS14617147 From dfe98df0f9dff4dadf66995714043ce8b7f10bc1 Mon Sep 17 00:00:00 2001 From: GiuliaZ538 <60102859+GiuliaZ538@users.noreply.github.com> Date: Thu, 3 Oct 2024 13:49:56 +0200 Subject: [PATCH 3/7] Update ancientmetagenome-environmental_libraries.tsv Zampirolo_et_al_2024 changes to the library tsv file added metadata from publication --- .../ancientmetagenome-environmental_libraries.tsv | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries.tsv b/ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries.tsv index 2e225e9ad..0b52373ad 100644 --- a/ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries.tsv +++ b/ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries.tsv @@ -811,3 +811,16 @@ 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 X 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 X 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 +Zampirolo2024 2024 10.1016/j.cub.2024.08.047 CTRL-2 ENA PRJEB59830 ERS14617146 CTRL-2/SedaCTRL-CZ-16 double KAPA HiFi Uracil+ none NA Illumina NovaSeq X PAIRED WGS 2637916 ERR10878164 ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/064/ERR10878164/ERR10878164_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/064/ERR10878164/ERR10878164_2.fastq.gz b283eff799cb236aa37e84fd1e35b937;69df48e803b5cb0512cbff6b0ba99e8f 64789583;73683732 +Zampirolo2024 2024 10.1016/j.cub.2024.08.047 LIB-CTRL-1 ENA PRJEB59830 ERS14617147 LIB-CTRL-1/SedaCTRL-LIB-CZ-17 double KAPA HiFi Uracil+ none NA Illumina NovaSeq X PAIRED WGS 431062 ERR10878165 ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/065/ERR10878165/ERR10878165_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/065/ERR10878165/ERR10878165_2.fastq.gz 4df5da4cff904a7c440601cb5f9e6860;ad741bb4649f4930a8365a67e058d2d1 9543900;8624688 From 2e23507fc7e176d0330636686ed2f8400ec3477d Mon Sep 17 00:00:00 2001 From: GiuliaZ538 <60102859+GiuliaZ538@users.noreply.github.com> Date: Thu, 3 Oct 2024 13:58:27 +0200 Subject: [PATCH 4/7] Update CHANGELOG.md Zampirolo2024 Added publication metadata to changelog.md for Zampirolo et al 2024 --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 80bc72297..e378dd1ac 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,6 +18,7 @@ and this project follows to [Calendar Versioning](https://calver.org/). - 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 From 25b37be360ee561b175bbfeb8672fada3440b056 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alex=20H=C3=BCbner?= Date: Thu, 3 Oct 2024 17:28:22 +0200 Subject: [PATCH 5/7] Change order of elements of primary_study_focus To fit enums. --- ...ncientmetagenome-environmental_samples.tsv | 26 +++++++++---------- 1 file changed, 13 insertions(+), 13 deletions(-) diff --git a/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv b/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv index b5675a3a0..d2d0ab3d4 100644 --- a/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv +++ b/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv @@ -701,16 +701,16 @@ 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 floral,faunal,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 floral,faunal,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 floral,faunal,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 floral,faunal,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 floral,faunal,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 floral,faunal,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 floral,faunal,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 floral,faunal,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 floral,faunal,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 floral,faunal,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 floral,faunal,microbial North Wall excavation trench 236 VM28 9800 10.1016/j.cub.2024.08.047 rock shelter sediment 2019 ENA PRJEB59830 ERS14617145 -Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench NA CTRL-2 NA 10.1016/j.cub.2024.08.047 rock shelter sediment 2019 ENA PRJEB59830 ERS14617146 -Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia floral,faunal,microbial North Wall excavation trench NA LIB-CTRL-1 NA 10.1016/j.cub.2024.08.047 rock shelter sediment 2019 ENA PRJEB59830 ERS14617147 +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 +Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia faunal,floral,microbial North Wall excavation trench NA CTRL-2 NA 10.1016/j.cub.2024.08.047 rock shelter sediment 2019 ENA PRJEB59830 ERS14617146 +Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia faunal,floral,microbial North Wall excavation trench NA LIB-CTRL-1 NA 10.1016/j.cub.2024.08.047 rock shelter sediment 2019 ENA PRJEB59830 ERS14617147 From feb4c46f0ae8ef1e2874ae1b6a13c6b3a5a519dd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alex=20H=C3=BCbner?= Date: Fri, 4 Oct 2024 14:53:53 +0200 Subject: [PATCH 6/7] Fix username --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 66ae3ae60..57c3d31e6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,7 +12,7 @@ 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 From 0bd59fdfadb1a69e29545d02c119ae60d5c52aa8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alex=20H=C3=BCbner?= Date: Fri, 4 Oct 2024 16:29:03 +0200 Subject: [PATCH 7/7] Remove neg controls and correct instrument model to match the paper --- .../libraries/ancientmetagenome-environmental_libraries.tsv | 6 ++---- .../samples/ancientmetagenome-environmental_samples.tsv | 2 -- 2 files changed, 2 insertions(+), 6 deletions(-) diff --git a/ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries.tsv b/ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries.tsv index 0b52373ad..d0e05e783 100644 --- a/ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries.tsv +++ b/ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_libraries.tsv @@ -820,7 +820,5 @@ Zampirolo2024 2024 10.1016/j.cub.2024.08.047 VM17 ENA PRJEB59830 ERS14617140 VM1 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 X 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 X 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 -Zampirolo2024 2024 10.1016/j.cub.2024.08.047 CTRL-2 ENA PRJEB59830 ERS14617146 CTRL-2/SedaCTRL-CZ-16 double KAPA HiFi Uracil+ none NA Illumina NovaSeq X PAIRED WGS 2637916 ERR10878164 ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/064/ERR10878164/ERR10878164_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/064/ERR10878164/ERR10878164_2.fastq.gz b283eff799cb236aa37e84fd1e35b937;69df48e803b5cb0512cbff6b0ba99e8f 64789583;73683732 -Zampirolo2024 2024 10.1016/j.cub.2024.08.047 LIB-CTRL-1 ENA PRJEB59830 ERS14617147 LIB-CTRL-1/SedaCTRL-LIB-CZ-17 double KAPA HiFi Uracil+ none NA Illumina NovaSeq X PAIRED WGS 431062 ERR10878165 ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/065/ERR10878165/ERR10878165_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/065/ERR10878165/ERR10878165_2.fastq.gz 4df5da4cff904a7c440601cb5f9e6860;ad741bb4649f4930a8365a67e058d2d1 9543900;8624688 +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 diff --git a/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv b/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv index d2d0ab3d4..b9ac50682 100644 --- a/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv +++ b/ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples.tsv @@ -712,5 +712,3 @@ Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czec 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 -Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia faunal,floral,microbial North Wall excavation trench NA CTRL-2 NA 10.1016/j.cub.2024.08.047 rock shelter sediment 2019 ENA PRJEB59830 ERS14617146 -Zampirolo2024 2024 10.1016/j.cub.2024.08.047 Velký Mamut'ák 50.518 15.071 Czechia faunal,floral,microbial North Wall excavation trench NA LIB-CTRL-1 NA 10.1016/j.cub.2024.08.047 rock shelter sediment 2019 ENA PRJEB59830 ERS14617147