From deabe34980ba34a226cd0adf9b1295e38a9e528f Mon Sep 17 00:00:00 2001 From: DavideBozzi <60131768+DavideBozzi@users.noreply.github.com> Date: Wed, 2 Oct 2024 14:52:45 +0200 Subject: [PATCH 01/20] Update ancientmetagenome-hostassociated_samples.tsv Adding sample info for Bozzi2024 and Hansen2017 --- ...cientmetagenome-hostassociated_samples.tsv | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) diff --git a/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv b/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv index 72c69176e..bd202bc92 100644 --- a/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv +++ b/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv @@ -1469,3 +1469,73 @@ Austin2024 2024 10.1038/s41598-024-64818-7 St. Louis and Missouri 38.65 -90.26 U Austin2024 2024 10.1038/s41598-024-64818-7 St. Louis and Missouri 38.65 -90.26 USA ARP 27 S Homo sapiens 100 10.1038/s41598-024-64818-7 oral dental calculus SRA PRJNA1056444 SRS19976921 Austin2024 2024 10.1038/s41598-024-64818-7 St. Louis and Missouri 38.65 -90.26 USA ARP 28 S Homo sapiens 100 10.1038/s41598-024-64818-7 oral dental calculus SRA PRJNA1056444 SRS19976912 Austin2024 2024 10.1038/s41598-024-64818-7 St. Louis and Missouri 38.65 -90.26 USA ARP 29 S Homo sapiens 100 10.1038/s41598-024-64818-7 oral dental calculus SRA PRJNA1056444 SRS19976942 +Bozzi2024 2024 10.1038/s41598-023-40246-x Mutum -19.82 -41.44 Brazil MN0003 Homo sapiens 100 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16595011 +Bozzi2024 2024 10.1038/s41598-023-40246-x Rio Doce -20.24 -42.9 Brazil MN0008 Homo sapiens 100 10.1101/2022.01.27.477466 skeletal tissue bone ENA PRJEB67998 ERS16595020 +Bozzi2024 2024 10.1038/s41598-023-40246-x Rio Mucuri -17.51 -41.34 Brazil MN0009 Homo sapiens 200 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16595017 +Bozzi2024 2024 10.1038/s41598-023-40246-x Itamacuari -18.03 -41.68 Brazil MN00010 Homo sapiens 100 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16594997 +Bozzi2024 2024 10.1038/s41598-023-40246-x Mutum -19.82 -41.44 Brazil MN00013 Homo sapiens 100 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16595018 +Bozzi2024 2024 10.1038/s41598-023-40246-x Itapimirim -20 -40 Brazil MN00016 Homo sapiens 400 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16595006 +Bozzi2024 2024 10.1038/s41598-023-40246-x Mutum -19.82 -41.44 Brazil MN00021 Homo sapiens 100 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16595013 +Bozzi2024 2024 10.1038/s41598-023-40246-x Mutum -19.82 -41.44 Brazil MN00022 Homo sapiens 100 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16595004 +Bozzi2024 2024 10.1038/s41598-023-40246-x Rio Mucuri -17.51 -41.34 Brazil MN00023 Homo sapiens 100 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16595003 +Bozzi2024 2024 10.1038/s41598-023-40246-x Mutum -19.82 -41.44 Brazil MN00039 Homo sapiens 100 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16595002 +Bozzi2024 2024 10.1038/s41598-023-40246-x Mutum -19.82 -41.44 Brazil MN00045 Homo sapiens 200 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16595007 +Bozzi2024 2024 10.1038/s41598-023-40246-x Mucuri (Itambacuari) -18.03 -41.68 Brazil MN00056 Homo sapiens 100 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16595019 +Bozzi2024 2024 10.1038/s41598-023-40246-x Rio Doce -20.24 -42.9 Brazil MN00064 Homo sapiens 200 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16595009 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown -13 -50 Brazil MN00067 Homo sapiens 100 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16595014 +Bozzi2024 2024 10.1038/s41598-023-40246-x Mutum -19.82 -41.44 Brazil MN00068 Homo sapiens 100 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16595005 +Bozzi2024 2024 10.1038/s41598-023-40246-x Rio Mucuri -17.51 -41.34 Brazil MN00069 Homo sapiens 100 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16595000 +Bozzi2024 2024 10.1038/s41598-023-40246-x Rio Prado -16.61 -40.57 Brazil MN00346 Homo sapiens 100 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16595015 +Bozzi2024 2024 10.1038/s41598-023-40246-x Laguna -28.48 -48.78 Brazil MN01701 Homo sapiens 1800 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16594998 +Bozzi2024 2024 10.1038/s41598-023-40246-x Serra de Babilonia -18 -44 Brazil MN1943 Homo sapiens 900 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16595001 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M10_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485688 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M10_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485690 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M2_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485694 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M2_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485696 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M3_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485698 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M4_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485700 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M5_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485705 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M7_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485709 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M8_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485712 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V10_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485718 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V11_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485719 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V1_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485721 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V1_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485722 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V2_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485724 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V4_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485727 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V6_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485732 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V7_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485734 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V9_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485738 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M10_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485689 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M1_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485691 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M1_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485693 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M5_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485704 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M6_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485708 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M8_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485714 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M9_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485715 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V2_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485723 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V3_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485726 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V4_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485728 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V5_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485729 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V6_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485731 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V7_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485733 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V8_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485735 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V8_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485736 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M1_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485692 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M2_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485695 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M3_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485697 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M3_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485699 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M4_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485701 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M4_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485702 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M5_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485703 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M6_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485706 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M6_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485707 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M7_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485710 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M7_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485711 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M8_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485713 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M9_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485716 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V10_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485717 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V11_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485720 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V3_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485725 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V5_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485730 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V9_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485737 From df396da8815e507031d0e395b2f6223b8d36694d Mon Sep 17 00:00:00 2001 From: DavideBozzi <60131768+DavideBozzi@users.noreply.github.com> Date: Wed, 2 Oct 2024 14:54:38 +0200 Subject: [PATCH 02/20] Update ancientmetagenome-hostassociated_libraries.tsv Add library info for Bozzi2024 and Hansen2017 --- ...entmetagenome-hostassociated_libraries.tsv | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) diff --git a/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv b/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv index e68b0c279..fa49e55d7 100644 --- a/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv +++ b/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv @@ -2599,3 +2599,73 @@ Austin2024 2024 10.1038/s41598-024-64818-7 ARP 21 S SRA PRJNA1056444 SRS19976919 Austin2024 2024 10.1038/s41598-024-64818-7 ARP 31 S SRA PRJNA1056444 SRS19976918 ARP31S_shotgun double KAPA HiFi Uracil+ half-udg NA NextSeq 500 PAIRED WGS 96719984 SRR27336798 ftp.sra.ebi.ac.uk/vol1/fastq/SRR273/098/SRR27336798/SRR27336798_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR273/098/SRR27336798/SRR27336798_2.fastq.gz b88b1d8e4afd3b15ed74b491e1036e4b;6ae95f827831eeb1ce02e91a0e31babc 3651086684;3545748908 Austin2024 2024 10.1038/s41598-024-64818-7 ARP 13 T SRA PRJNA1056444 SRS19976914 ARP13T_shotgun double KAPA HiFi Uracil+ half-udg NA NextSeq 500 SINGLE WGS 7421314 SRR27336802 ftp.sra.ebi.ac.uk/vol1/fastq/SRR273/002/SRR27336802/SRR27336802.fastq.gz 5810e74da314eabe751ecec2030edd0c 202442256 Austin2024 2024 10.1038/s41598-024-64818-7 ARP 34 S SRA PRJNA1056444 SRS19976911 ARP34S_shotgun double KAPA HiFi Uracil+ half-udg NA NextSeq 500 SINGLE WGS 9941233 SRR27336805 ftp.sra.ebi.ac.uk/vol1/fastq/SRR273/005/SRR27336805/SRR27336805.fastq.gz 6b803041313b9c4ecc29a83ee05dd7f3 255778837 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN0003 ENA PRJEB67998 ERS16595011 MN0003 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 127033674 ERR12206690 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/090/ERR12206690/ERR12206690.fastq.gz b85993652682384691f1a230e36c7e04 5242518069 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN0008 ENA PRJEB67998 ERS16595020 MN0008 double Phusion High-Fidelity DNA Polymerases USER-treatment NA Illumina HiSeq 2500 SINGLE WGS 569521377 ERR12206699 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/099/ERR12206699/ERR12206699.fastq.gz 5e16418d71a85137714dfc8212c30193 21881693637 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN0009 ENA PRJEB67998 ERS16595017 MN0009 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 381236503 ERR12206696 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/096/ERR12206696/ERR12206696.fastq.gz 29c9ed2afe93be03c90398a1e7e287fd 14714457403 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00010 ENA PRJEB67998 ERS16594997 MN00010 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 55475228 ERR12206676 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/076/ERR12206676/ERR12206676.fastq.gz 3d66ff055110d2430ddba575572b2b56 2138238746 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00013 ENA PRJEB67998 ERS16595018 MN00013 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 586099025 ERR12206697 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/097/ERR12206697/ERR12206697.fastq.gz df56276d1a5e4baf89d61ca73299e83f 24700734284 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00016 ENA PRJEB67998 ERS16595006 MN00016 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 51356321 ERR12206685 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/085/ERR12206685/ERR12206685.fastq.gz 1389a73b452064e168b17138bb75d30d 2279369624 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00021 ENA PRJEB67998 ERS16595013 MN00021 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 349386012 ERR12206692 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/092/ERR12206692/ERR12206692.fastq.gz d06a85c33c96f3505969a8f786e61afb 15598000000 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00022 ENA PRJEB67998 ERS16595004 MN00022 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 36160802 ERR12206683 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/083/ERR12206683/ERR12206683.fastq.gz e95c733e8f877540383d92bf62b60933 1976554190 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00023 ENA PRJEB67998 ERS16595003 MN00023 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 354185366 ERR12206682 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/082/ERR12206682/ERR12206682.fastq.gz 0f4ba70128fe5d2ee6fcd729ed348504 13679208317 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00039 ENA PRJEB67998 ERS16595002 MN00039 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 77223283 ERR12206681 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/081/ERR12206681/ERR12206681.fastq.gz 4ebdd66804d888bbe734a868a0581bac 3433882741 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00045 ENA PRJEB67998 ERS16595007 MN00045 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 86895628 ERR12206686 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/086/ERR12206686/ERR12206686.fastq.gz 1bc2faeae6ee7569b7831c3f6e0ae884 4664264133 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00056 ENA PRJEB67998 ERS16595019 MN00056 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 376352081 ERR12206698 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/098/ERR12206698/ERR12206698.fastq.gz 33c54926028dfbae1c92ccab07bf4e84 15905541599 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00064 ENA PRJEB67998 ERS16595009 MN00064 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 99467321 ERR12206688 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/088/ERR12206688/ERR12206688.fastq.gz 1182c36389309495f6cb9a6ab2103f12 5008316959 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00067 ENA PRJEB67998 ERS16595014 MN00067 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 372359007 ERR12206693 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/093/ERR12206693/ERR12206693.fastq.gz ffa640a3436f00c9531e76c5f63aba85 15364141727 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00068 ENA PRJEB67998 ERS16595005 MN00068 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 34774516 ERR12206684 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/084/ERR12206684/ERR12206684.fastq.gz a2d5742ace17d374eb23c901e2006b88 1766856188 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00069 ENA PRJEB67998 ERS16595000 MN00069 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 16296410 ERR12206679 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/079/ERR12206679/ERR12206679.fastq.gz 92f08e6406dadeb895245000662072c0 695960358 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00346 ENA PRJEB67998 ERS16595015 MN00346 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 472422899 ERR12206694 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/094/ERR12206694/ERR12206694.fastq.gz 2c8627452380d03246da17e6e5814a65 20230959642 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN01701 ENA PRJEB67998 ERS16594998 MN01701 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 293566149 ERR12206677 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/077/ERR12206677/ERR12206677.fastq.gz 8d0623dc04e10d0779358bf8178c365d 9768291581 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN1943 ENA PRJEB67998 ERS16595001 MN1943 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 26332773 ERR12206680 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/080/ERR12206680/ERR12206680.fastq.gz 83ba586fa804c20aac7a3299a755cc62 1002741128 +Hansen2017 2017 10.1371/journal.pone.0170940 M10_P ENA PRJEB18722 ERS1485688 M10_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 1969191 ERR1777519 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777519/ERR1777519.fastq.gz 4806e5a4b8f976079c187cc5efa2dae8 84218155 +Hansen2017 2017 10.1371/journal.pone.0170940 M10_T ENA PRJEB18722 ERS1485690 M10_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 2576499 ERR1777521 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/001/ERR1777521/ERR1777521.fastq.gz d306ddeb663b2da381609d4d19babc89 103453734 +Hansen2017 2017 10.1371/journal.pone.0170940 M2_P ENA PRJEB18722 ERS1485694 M2_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777525 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/005/ERR1777525/ERR1777525.fastq.gz 0a564cf7af305b294c0d3ac1ec8a23f3 137404389 +Hansen2017 2017 10.1371/journal.pone.0170940 M2_T ENA PRJEB18722 ERS1485696 M2_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777527 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/007/ERR1777527/ERR1777527.fastq.gz 591c2709393088585eacf2ca100a5632 155308768 +Hansen2017 2017 10.1371/journal.pone.0170940 M3_S ENA PRJEB18722 ERS1485698 M3_S double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777529 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777529/ERR1777529.fastq.gz 56fe5bf53162d5609eade9db3bcd88d4 149295352 +Hansen2017 2017 10.1371/journal.pone.0170940 M4_P ENA PRJEB18722 ERS1485700 M4_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777531 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/001/ERR1777531/ERR1777531.fastq.gz b117c7a2f196bd76b75efd2609baf351 134749769 +Hansen2017 2017 10.1371/journal.pone.0170940 M5_T ENA PRJEB18722 ERS1485705 M5_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777536 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/006/ERR1777536/ERR1777536.fastq.gz 330b5384d2070963786c5174eec7ba33 147975496 +Hansen2017 2017 10.1371/journal.pone.0170940 M7_P ENA PRJEB18722 ERS1485709 M7_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777540 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/000/ERR1777540/ERR1777540.fastq.gz 4004a0d5dfddfaf019c0983ae362806c 140440673 +Hansen2017 2017 10.1371/journal.pone.0170940 M8_P ENA PRJEB18722 ERS1485712 M8_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777543 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/003/ERR1777543/ERR1777543.fastq.gz b88af542eca4128b0ca9e4f153886302 140951663 +Hansen2017 2017 10.1371/journal.pone.0170940 V10_T ENA PRJEB18722 ERS1485718 V10_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777549 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777549/ERR1777549.fastq.gz baf2a30be4627947f55be0039aea6003 192503916 +Hansen2017 2017 10.1371/journal.pone.0170940 V11_P ENA PRJEB18722 ERS1485719 V11_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777550 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/000/ERR1777550/ERR1777550.fastq.gz 6c89a1e6b74b6db84a967b1d7a3e5e09 169750850 +Hansen2017 2017 10.1371/journal.pone.0170940 V1_P ENA PRJEB18722 ERS1485721 V1_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777552 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/002/ERR1777552/ERR1777552.fastq.gz ea6c4ebfb9639f25397874e6b59810e4 170946497 +Hansen2017 2017 10.1371/journal.pone.0170940 V1_T ENA PRJEB18722 ERS1485722 V1_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777553 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/003/ERR1777553/ERR1777553.fastq.gz ab551a25f258138d8f8e70e62ad6a77f 170873100 +Hansen2017 2017 10.1371/journal.pone.0170940 V2_T ENA PRJEB18722 ERS1485724 V2_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777555 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/005/ERR1777555/ERR1777555.fastq.gz 1cb8e7191b76df89efa7a9d3df02a61a 192882043 +Hansen2017 2017 10.1371/journal.pone.0170940 V4_P ENA PRJEB18722 ERS1485727 V4_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777558 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/008/ERR1777558/ERR1777558.fastq.gz 4c0077c666d9fcfec1cde2a6a127c2d9 174703955 +Hansen2017 2017 10.1371/journal.pone.0170940 V6_T ENA PRJEB18722 ERS1485732 V6_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777563 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/003/ERR1777563/ERR1777563.fastq.gz 4b6552901c8152b3687f1afeb96d2141 149161358 +Hansen2017 2017 10.1371/journal.pone.0170940 V7_T ENA PRJEB18722 ERS1485734 V7_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777565 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/005/ERR1777565/ERR1777565.fastq.gz a9c428c080a0fccfc31ccaf4f2a7d3b0 165288978 +Hansen2017 2017 10.1371/journal.pone.0170940 V9_T ENA PRJEB18722 ERS1485738 V9_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777569 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777569/ERR1777569.fastq.gz c36d5312e9792aed265b69fe9192f9b7 220684796 +Hansen2017 2017 10.1371/journal.pone.0170940 M10_S ENA PRJEB18722 ERS1485689 M10_S double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 3403464 ERR1777520 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/000/ERR1777520/ERR1777520.fastq.gz 8e29052a204658d15a0d8871fd79f6ea 106424195 +Hansen2017 2017 10.1371/journal.pone.0170940 M1_P ENA PRJEB18722 ERS1485691 M1_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777522 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/002/ERR1777522/ERR1777522.fastq.gz 5fa41875bcd8e08bc1241c9e3d0a2490 132291555 +Hansen2017 2017 10.1371/journal.pone.0170940 M1_T ENA PRJEB18722 ERS1485693 M1_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777524 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/004/ERR1777524/ERR1777524.fastq.gz dd3c5abb1eed6923aad43381a0180ab9 144483331 +Hansen2017 2017 10.1371/journal.pone.0170940 M5_S ENA PRJEB18722 ERS1485704 M5_S double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 2887515 ERR1777535 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/005/ERR1777535/ERR1777535.fastq.gz 9cdcddd9c3b0c04630b655b3fee861b4 124268668 +Hansen2017 2017 10.1371/journal.pone.0170940 M6_T ENA PRJEB18722 ERS1485708 M6_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777539 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777539/ERR1777539.fastq.gz 6886d401499fb6ec3ff0403d9eaff5e7 131451664 +Hansen2017 2017 10.1371/journal.pone.0170940 M8_T ENA PRJEB18722 ERS1485714 M8_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777545 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/005/ERR1777545/ERR1777545.fastq.gz af5c8404925e7088f7710834e3802bcc 142873018 +Hansen2017 2017 10.1371/journal.pone.0170940 M9_P ENA PRJEB18722 ERS1485715 M9_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777546 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/006/ERR1777546/ERR1777546.fastq.gz 3b19e91c9f3ccf603bb89f4e2242ed02 149505252 +Hansen2017 2017 10.1371/journal.pone.0170940 V2_P ENA PRJEB18722 ERS1485723 V2_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777554 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/004/ERR1777554/ERR1777554.fastq.gz 828c3f8bbdc85cbc7ac90e9409823691 169553191 +Hansen2017 2017 10.1371/journal.pone.0170940 V3_T ENA PRJEB18722 ERS1485726 V3_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777557 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/007/ERR1777557/ERR1777557.fastq.gz 68166f49bcb2163f98152b2ec2bf83ef 203184689 +Hansen2017 2017 10.1371/journal.pone.0170940 V4_T ENA PRJEB18722 ERS1485728 V4_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777559 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777559/ERR1777559.fastq.gz 5f6f4302ffa1a131c7bd2253677afd08 147997278 +Hansen2017 2017 10.1371/journal.pone.0170940 V5_P ENA PRJEB18722 ERS1485729 V5_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777560 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/000/ERR1777560/ERR1777560.fastq.gz 87b68a0421abe1c01fe98acb3489f643 175230588 +Hansen2017 2017 10.1371/journal.pone.0170940 V6_P ENA PRJEB18722 ERS1485731 V6_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777562 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/002/ERR1777562/ERR1777562.fastq.gz 90149a71159da13d63a58ea53166d1c1 172934284 +Hansen2017 2017 10.1371/journal.pone.0170940 V7_P ENA PRJEB18722 ERS1485733 V7_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777564 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/004/ERR1777564/ERR1777564.fastq.gz 183a3f0758c42f251aee5bc6f0338f0b 178326323 +Hansen2017 2017 10.1371/journal.pone.0170940 V8_P ENA PRJEB18722 ERS1485735 V8_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777566 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/006/ERR1777566/ERR1777566.fastq.gz a7678244e70413365b9e9107f13284e9 172335078 +Hansen2017 2017 10.1371/journal.pone.0170940 V8_T ENA PRJEB18722 ERS1485736 V8_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777567 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/007/ERR1777567/ERR1777567.fastq.gz 033565fd19dc4c838ab3cd8b311872c2 188294390 +Hansen2017 2017 10.1371/journal.pone.0170940 M1_S ENA PRJEB18722 ERS1485692 M1_S double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777523 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/003/ERR1777523/ERR1777523.fastq.gz eb2a615170d1a2a6263580811d5da4ab 137155726 +Hansen2017 2017 10.1371/journal.pone.0170940 M2_S ENA PRJEB18722 ERS1485695 M2_S double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777526 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/006/ERR1777526/ERR1777526.fastq.gz 6504d629aa9a0f34c289d88aadf41b30 144693552 +Hansen2017 2017 10.1371/journal.pone.0170940 M3_P ENA PRJEB18722 ERS1485697 M3_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777528 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/008/ERR1777528/ERR1777528.fastq.gz 7d924557ebaf13380982f3df57bd0057 149981713 +Hansen2017 2017 10.1371/journal.pone.0170940 M3_T ENA PRJEB18722 ERS1485699 M3_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777530 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/000/ERR1777530/ERR1777530.fastq.gz e7bafa9b2480a5c4618169a07d35a8bc 157682427 +Hansen2017 2017 10.1371/journal.pone.0170940 M4_S ENA PRJEB18722 ERS1485701 M4_S double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777532 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/002/ERR1777532/ERR1777532.fastq.gz 3ca620f094a71532a0d93b47b1ade66b 150987147 +Hansen2017 2017 10.1371/journal.pone.0170940 M4_T ENA PRJEB18722 ERS1485702 M4_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777533 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/003/ERR1777533/ERR1777533.fastq.gz 447fc4a8fcdc33e97cfff84be444d518 158897813 +Hansen2017 2017 10.1371/journal.pone.0170940 M5_P ENA PRJEB18722 ERS1485703 M5_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 2066219 ERR1777534 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/004/ERR1777534/ERR1777534.fastq.gz df060ed5d72f1340a40a6de2bf72560f 79137145 +Hansen2017 2017 10.1371/journal.pone.0170940 M6_P ENA PRJEB18722 ERS1485706 M6_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777537 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/007/ERR1777537/ERR1777537.fastq.gz 2eee13f7882ea2f5d70f2c4db996ee90 148547656 +Hansen2017 2017 10.1371/journal.pone.0170940 M6_S ENA PRJEB18722 ERS1485707 M6_S double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 3971984 ERR1777538 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/008/ERR1777538/ERR1777538.fastq.gz 202d21202a5e67b1ed098e3d96750fe8 137421999 +Hansen2017 2017 10.1371/journal.pone.0170940 M7_S ENA PRJEB18722 ERS1485710 M7_S double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 3944221 ERR1777541 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/001/ERR1777541/ERR1777541.fastq.gz 0b9d34c928ac5942ce614b704d7efef0 140398815 +Hansen2017 2017 10.1371/journal.pone.0170940 M7_T ENA PRJEB18722 ERS1485711 M7_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777542 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/002/ERR1777542/ERR1777542.fastq.gz ac5585d7534f0e8d9a4a2bb7323f161b 152708452 +Hansen2017 2017 10.1371/journal.pone.0170940 M8_S ENA PRJEB18722 ERS1485713 M8_S double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 2141948 ERR1777544 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/004/ERR1777544/ERR1777544.fastq.gz 7ce712e6524cc296928d96d1b9f8dbd0 70911496 +Hansen2017 2017 10.1371/journal.pone.0170940 M9_T ENA PRJEB18722 ERS1485716 M9_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777547 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/007/ERR1777547/ERR1777547.fastq.gz 5b89fe79668860fde638c44ab762d7b4 135379904 +Hansen2017 2017 10.1371/journal.pone.0170940 V10_P ENA PRJEB18722 ERS1485717 V10_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777548 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/008/ERR1777548/ERR1777548.fastq.gz 28822b97bc84ff1bfc663082df8c810b 170609451 +Hansen2017 2017 10.1371/journal.pone.0170940 V11_T ENA PRJEB18722 ERS1485720 V11_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777551 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/001/ERR1777551/ERR1777551.fastq.gz cd2f00158fea3bc7476428d9fc159e0d 188022380 +Hansen2017 2017 10.1371/journal.pone.0170940 V3_P ENA PRJEB18722 ERS1485725 V3_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777556 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/006/ERR1777556/ERR1777556.fastq.gz 262b72279b0e4778786907e8b23a80c9 174539467 +Hansen2017 2017 10.1371/journal.pone.0170940 V5_T ENA PRJEB18722 ERS1485730 V5_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777561 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/001/ERR1777561/ERR1777561.fastq.gz 42c22f3b88feeaf5d84c8e493783c245 156582293 +Hansen2017 2017 10.1371/journal.pone.0170940 V9_P ENA PRJEB18722 ERS1485737 V9_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777568 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/008/ERR1777568/ERR1777568.fastq.gz 10396cb2aad632e275194c2f9cccd636 174445223 From 33591184ad942d293328cc4c2de4e4f37219fd68 Mon Sep 17 00:00:00 2001 From: DavideBozzi <60131768+DavideBozzi@users.noreply.github.com> Date: Wed, 2 Oct 2024 15:01:51 +0200 Subject: [PATCH 03/20] Update CHANGELOG.md Add Bozzi2024 and Hansen2017 info --- CHANGELOG.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 80bc72297..167a077d6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,9 @@ 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) +- Bozzi 2024 10.1038/s41598-023-40246-x (added by @DavideBozzi) +- Hansen 2017 10.1371/journal.pone.0170940 (added by @DavideBozzi) + #### Ancient Single Genome: Host Associated From 37f2d7fcd19c48eaad50a20f85144a32edd7ba19 Mon Sep 17 00:00:00 2001 From: DavideBozzi <60131768+DavideBozzi@users.noreply.github.com> Date: Thu, 3 Oct 2024 09:36:09 +0200 Subject: [PATCH 04/20] Update ancientmetagenome-hostassociated_samples.tsv Correction geo_loc_name --- ...cientmetagenome-hostassociated_samples.tsv | 44 +++++++++---------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv b/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv index bd202bc92..0b5a43c87 100644 --- a/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv +++ b/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv @@ -1497,15 +1497,15 @@ Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M4_P Homo sap Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M5_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485705 Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M7_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485709 Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M8_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485712 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V10_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485718 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V11_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485719 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V1_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485721 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V1_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485722 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V2_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485724 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V4_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485727 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V6_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485732 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V7_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485734 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V9_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485738 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V10_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485718 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V11_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485719 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V1_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485721 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V1_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485722 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V2_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485724 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V4_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485727 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V6_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485732 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V7_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485734 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V9_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485738 Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M10_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485689 Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M1_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485691 Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M1_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485693 @@ -1513,14 +1513,14 @@ Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M5_S Homo sap Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M6_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485708 Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M8_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485714 Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M9_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485715 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V2_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485723 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V3_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485726 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V4_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485728 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V5_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485729 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V6_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485731 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V7_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485733 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V8_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485735 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V8_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485736 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V2_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485723 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V3_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485726 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V4_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485728 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V5_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485729 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V6_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485731 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V7_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485733 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V8_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485735 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V8_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485736 Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M1_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485692 Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M2_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485695 Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M3_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485697 @@ -1534,8 +1534,8 @@ Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M7_S Homo sap Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M7_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485711 Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M8_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485713 Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M9_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485716 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V10_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485717 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V11_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485720 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V3_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485725 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V5_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485730 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 England V9_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485737 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V10_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485717 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V11_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485720 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V3_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485725 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V5_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485730 +Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V9_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485737 From 04365dc5f2cff3bff1967a3a61476634b0228bc9 Mon Sep 17 00:00:00 2001 From: DavideBozzi <60131768+DavideBozzi@users.noreply.github.com> Date: Thu, 3 Oct 2024 09:37:03 +0200 Subject: [PATCH 05/20] Update ancientmetagenome-hostassociated_libraries.tsv Correction library_polymerase --- ...entmetagenome-hostassociated_libraries.tsv | 38 +++++++++---------- 1 file changed, 19 insertions(+), 19 deletions(-) diff --git a/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv b/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv index fa49e55d7..8f5f88c2d 100644 --- a/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv +++ b/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv @@ -2599,25 +2599,25 @@ Austin2024 2024 10.1038/s41598-024-64818-7 ARP 21 S SRA PRJNA1056444 SRS19976919 Austin2024 2024 10.1038/s41598-024-64818-7 ARP 31 S SRA PRJNA1056444 SRS19976918 ARP31S_shotgun double KAPA HiFi Uracil+ half-udg NA NextSeq 500 PAIRED WGS 96719984 SRR27336798 ftp.sra.ebi.ac.uk/vol1/fastq/SRR273/098/SRR27336798/SRR27336798_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/SRR273/098/SRR27336798/SRR27336798_2.fastq.gz b88b1d8e4afd3b15ed74b491e1036e4b;6ae95f827831eeb1ce02e91a0e31babc 3651086684;3545748908 Austin2024 2024 10.1038/s41598-024-64818-7 ARP 13 T SRA PRJNA1056444 SRS19976914 ARP13T_shotgun double KAPA HiFi Uracil+ half-udg NA NextSeq 500 SINGLE WGS 7421314 SRR27336802 ftp.sra.ebi.ac.uk/vol1/fastq/SRR273/002/SRR27336802/SRR27336802.fastq.gz 5810e74da314eabe751ecec2030edd0c 202442256 Austin2024 2024 10.1038/s41598-024-64818-7 ARP 34 S SRA PRJNA1056444 SRS19976911 ARP34S_shotgun double KAPA HiFi Uracil+ half-udg NA NextSeq 500 SINGLE WGS 9941233 SRR27336805 ftp.sra.ebi.ac.uk/vol1/fastq/SRR273/005/SRR27336805/SRR27336805.fastq.gz 6b803041313b9c4ecc29a83ee05dd7f3 255778837 -Bozzi2024 2024 10.1038/s41598-023-40246-x MN0003 ENA PRJEB67998 ERS16595011 MN0003 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 127033674 ERR12206690 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/090/ERR12206690/ERR12206690.fastq.gz b85993652682384691f1a230e36c7e04 5242518069 -Bozzi2024 2024 10.1038/s41598-023-40246-x MN0008 ENA PRJEB67998 ERS16595020 MN0008 double Phusion High-Fidelity DNA Polymerases USER-treatment NA Illumina HiSeq 2500 SINGLE WGS 569521377 ERR12206699 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/099/ERR12206699/ERR12206699.fastq.gz 5e16418d71a85137714dfc8212c30193 21881693637 -Bozzi2024 2024 10.1038/s41598-023-40246-x MN0009 ENA PRJEB67998 ERS16595017 MN0009 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 381236503 ERR12206696 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/096/ERR12206696/ERR12206696.fastq.gz 29c9ed2afe93be03c90398a1e7e287fd 14714457403 -Bozzi2024 2024 10.1038/s41598-023-40246-x MN00010 ENA PRJEB67998 ERS16594997 MN00010 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 55475228 ERR12206676 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/076/ERR12206676/ERR12206676.fastq.gz 3d66ff055110d2430ddba575572b2b56 2138238746 -Bozzi2024 2024 10.1038/s41598-023-40246-x MN00013 ENA PRJEB67998 ERS16595018 MN00013 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 586099025 ERR12206697 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/097/ERR12206697/ERR12206697.fastq.gz df56276d1a5e4baf89d61ca73299e83f 24700734284 -Bozzi2024 2024 10.1038/s41598-023-40246-x MN00016 ENA PRJEB67998 ERS16595006 MN00016 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 51356321 ERR12206685 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/085/ERR12206685/ERR12206685.fastq.gz 1389a73b452064e168b17138bb75d30d 2279369624 -Bozzi2024 2024 10.1038/s41598-023-40246-x MN00021 ENA PRJEB67998 ERS16595013 MN00021 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 349386012 ERR12206692 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/092/ERR12206692/ERR12206692.fastq.gz d06a85c33c96f3505969a8f786e61afb 15598000000 -Bozzi2024 2024 10.1038/s41598-023-40246-x MN00022 ENA PRJEB67998 ERS16595004 MN00022 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 36160802 ERR12206683 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/083/ERR12206683/ERR12206683.fastq.gz e95c733e8f877540383d92bf62b60933 1976554190 -Bozzi2024 2024 10.1038/s41598-023-40246-x MN00023 ENA PRJEB67998 ERS16595003 MN00023 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 354185366 ERR12206682 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/082/ERR12206682/ERR12206682.fastq.gz 0f4ba70128fe5d2ee6fcd729ed348504 13679208317 -Bozzi2024 2024 10.1038/s41598-023-40246-x MN00039 ENA PRJEB67998 ERS16595002 MN00039 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 77223283 ERR12206681 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/081/ERR12206681/ERR12206681.fastq.gz 4ebdd66804d888bbe734a868a0581bac 3433882741 -Bozzi2024 2024 10.1038/s41598-023-40246-x MN00045 ENA PRJEB67998 ERS16595007 MN00045 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 86895628 ERR12206686 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/086/ERR12206686/ERR12206686.fastq.gz 1bc2faeae6ee7569b7831c3f6e0ae884 4664264133 -Bozzi2024 2024 10.1038/s41598-023-40246-x MN00056 ENA PRJEB67998 ERS16595019 MN00056 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 376352081 ERR12206698 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/098/ERR12206698/ERR12206698.fastq.gz 33c54926028dfbae1c92ccab07bf4e84 15905541599 -Bozzi2024 2024 10.1038/s41598-023-40246-x MN00064 ENA PRJEB67998 ERS16595009 MN00064 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 99467321 ERR12206688 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/088/ERR12206688/ERR12206688.fastq.gz 1182c36389309495f6cb9a6ab2103f12 5008316959 -Bozzi2024 2024 10.1038/s41598-023-40246-x MN00067 ENA PRJEB67998 ERS16595014 MN00067 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 372359007 ERR12206693 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/093/ERR12206693/ERR12206693.fastq.gz ffa640a3436f00c9531e76c5f63aba85 15364141727 -Bozzi2024 2024 10.1038/s41598-023-40246-x MN00068 ENA PRJEB67998 ERS16595005 MN00068 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 34774516 ERR12206684 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/084/ERR12206684/ERR12206684.fastq.gz a2d5742ace17d374eb23c901e2006b88 1766856188 -Bozzi2024 2024 10.1038/s41598-023-40246-x MN00069 ENA PRJEB67998 ERS16595000 MN00069 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 16296410 ERR12206679 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/079/ERR12206679/ERR12206679.fastq.gz 92f08e6406dadeb895245000662072c0 695960358 -Bozzi2024 2024 10.1038/s41598-023-40246-x MN00346 ENA PRJEB67998 ERS16595015 MN00346 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 472422899 ERR12206694 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/094/ERR12206694/ERR12206694.fastq.gz 2c8627452380d03246da17e6e5814a65 20230959642 -Bozzi2024 2024 10.1038/s41598-023-40246-x MN01701 ENA PRJEB67998 ERS16594998 MN01701 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 293566149 ERR12206677 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/077/ERR12206677/ERR12206677.fastq.gz 8d0623dc04e10d0779358bf8178c365d 9768291581 -Bozzi2024 2024 10.1038/s41598-023-40246-x MN1943 ENA PRJEB67998 ERS16595001 MN1943 double Phusion High-Fidelity DNA Polymerases none NA Illumina HiSeq 2500 SINGLE WGS 26332773 ERR12206680 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/080/ERR12206680/ERR12206680.fastq.gz 83ba586fa804c20aac7a3299a755cc62 1002741128 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN0003 ENA PRJEB67998 ERS16595011 MN0003 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 127033674 ERR12206690 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/090/ERR12206690/ERR12206690.fastq.gz b85993652682384691f1a230e36c7e04 5242518069 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN0008 ENA PRJEB67998 ERS16595020 MN0008 double Phusion Hot Start High-Fidelity DNA USER-treatment NA Illumina HiSeq 2500 SINGLE WGS 569521377 ERR12206699 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/099/ERR12206699/ERR12206699.fastq.gz 5e16418d71a85137714dfc8212c30193 21881693637 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN0009 ENA PRJEB67998 ERS16595017 MN0009 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 381236503 ERR12206696 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/096/ERR12206696/ERR12206696.fastq.gz 29c9ed2afe93be03c90398a1e7e287fd 14714457403 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00010 ENA PRJEB67998 ERS16594997 MN00010 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 55475228 ERR12206676 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/076/ERR12206676/ERR12206676.fastq.gz 3d66ff055110d2430ddba575572b2b56 2138238746 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00013 ENA PRJEB67998 ERS16595018 MN00013 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 586099025 ERR12206697 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/097/ERR12206697/ERR12206697.fastq.gz df56276d1a5e4baf89d61ca73299e83f 24700734284 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00016 ENA PRJEB67998 ERS16595006 MN00016 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 51356321 ERR12206685 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/085/ERR12206685/ERR12206685.fastq.gz 1389a73b452064e168b17138bb75d30d 2279369624 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00021 ENA PRJEB67998 ERS16595013 MN00021 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 349386012 ERR12206692 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/092/ERR12206692/ERR12206692.fastq.gz d06a85c33c96f3505969a8f786e61afb 15598000000 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00022 ENA PRJEB67998 ERS16595004 MN00022 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 36160802 ERR12206683 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/083/ERR12206683/ERR12206683.fastq.gz e95c733e8f877540383d92bf62b60933 1976554190 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00023 ENA PRJEB67998 ERS16595003 MN00023 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 354185366 ERR12206682 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/082/ERR12206682/ERR12206682.fastq.gz 0f4ba70128fe5d2ee6fcd729ed348504 13679208317 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00039 ENA PRJEB67998 ERS16595002 MN00039 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 77223283 ERR12206681 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/081/ERR12206681/ERR12206681.fastq.gz 4ebdd66804d888bbe734a868a0581bac 3433882741 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00045 ENA PRJEB67998 ERS16595007 MN00045 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 86895628 ERR12206686 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/086/ERR12206686/ERR12206686.fastq.gz 1bc2faeae6ee7569b7831c3f6e0ae884 4664264133 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00056 ENA PRJEB67998 ERS16595019 MN00056 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 376352081 ERR12206698 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/098/ERR12206698/ERR12206698.fastq.gz 33c54926028dfbae1c92ccab07bf4e84 15905541599 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00064 ENA PRJEB67998 ERS16595009 MN00064 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 99467321 ERR12206688 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/088/ERR12206688/ERR12206688.fastq.gz 1182c36389309495f6cb9a6ab2103f12 5008316959 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00067 ENA PRJEB67998 ERS16595014 MN00067 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 372359007 ERR12206693 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/093/ERR12206693/ERR12206693.fastq.gz ffa640a3436f00c9531e76c5f63aba85 15364141727 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00068 ENA PRJEB67998 ERS16595005 MN00068 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 34774516 ERR12206684 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/084/ERR12206684/ERR12206684.fastq.gz a2d5742ace17d374eb23c901e2006b88 1766856188 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00069 ENA PRJEB67998 ERS16595000 MN00069 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 16296410 ERR12206679 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/079/ERR12206679/ERR12206679.fastq.gz 92f08e6406dadeb895245000662072c0 695960358 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN00346 ENA PRJEB67998 ERS16595015 MN00346 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 472422899 ERR12206694 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/094/ERR12206694/ERR12206694.fastq.gz 2c8627452380d03246da17e6e5814a65 20230959642 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN01701 ENA PRJEB67998 ERS16594998 MN01701 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 293566149 ERR12206677 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/077/ERR12206677/ERR12206677.fastq.gz 8d0623dc04e10d0779358bf8178c365d 9768291581 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN1943 ENA PRJEB67998 ERS16595001 MN1943 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 26332773 ERR12206680 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/080/ERR12206680/ERR12206680.fastq.gz 83ba586fa804c20aac7a3299a755cc62 1002741128 Hansen2017 2017 10.1371/journal.pone.0170940 M10_P ENA PRJEB18722 ERS1485688 M10_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 1969191 ERR1777519 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777519/ERR1777519.fastq.gz 4806e5a4b8f976079c187cc5efa2dae8 84218155 Hansen2017 2017 10.1371/journal.pone.0170940 M10_T ENA PRJEB18722 ERS1485690 M10_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 2576499 ERR1777521 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/001/ERR1777521/ERR1777521.fastq.gz d306ddeb663b2da381609d4d19babc89 103453734 Hansen2017 2017 10.1371/journal.pone.0170940 M2_P ENA PRJEB18722 ERS1485694 M2_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777525 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/005/ERR1777525/ERR1777525.fastq.gz 0a564cf7af305b294c0d3ac1ec8a23f3 137404389 From 8281b2ad73583933d2f6d59fd155529d88abe968 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alex=20H=C3=BCbner?= Date: Thu, 3 Oct 2024 10:34:21 +0200 Subject: [PATCH 06/20] Add info for cases such as Bozzi20224 --- assets/documentation/libraries/README.md | 3 +++ assets/documentation/samples/README.md | 3 +++ 2 files changed, 6 insertions(+) diff --git a/assets/documentation/libraries/README.md b/assets/documentation/libraries/README.md index c490fd417..9145fe8ad 100644 --- a/assets/documentation/libraries/README.md +++ b/assets/documentation/libraries/README.md @@ -40,6 +40,9 @@ Library columns are as follows: 'second' key added. - e.g. Muhlemann2018 (original), Muhlemann2018b (first duplicate), Muhlemann2018c (second duplicate) etc. +- If the authors re-used data from previously published studies that have not + been added to AncientMetagenomeDir, please use the project name of the current + study for all samples. > ⚠️ [MIxS v5](https://gensc.org/mixs/) compliant field diff --git a/assets/documentation/samples/README.md b/assets/documentation/samples/README.md index aa6a21e94..253a79a8f 100644 --- a/assets/documentation/samples/README.md +++ b/assets/documentation/samples/README.md @@ -39,6 +39,9 @@ Sample columns are as follows: 'second' key added. - e.g. Muhlemann2018 (original), Muhlemann2018b (first duplicate), Muhlemann2018c (second duplicate) etc. +- If the authors re-used data from previously published studies that have not + been added to AncientMetagenomeDir, please use the project name of the current + study for all samples. > ⚠️ [MIxS v5](https://gensc.org/mixs/) compliant field From c14141f40082b63457e315d71e899899c8106126 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alex=20H=C3=BCbner?= Date: Thu, 3 Oct 2024 10:55:50 +0200 Subject: [PATCH 07/20] Change UDG treatment to the allowed values --- .../libraries/ancientmetagenome-hostassociated_libraries.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv b/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv index 8f5f88c2d..18d8e9fb7 100644 --- a/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv +++ b/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv @@ -2600,7 +2600,7 @@ Austin2024 2024 10.1038/s41598-024-64818-7 ARP 31 S SRA PRJNA1056444 SRS19976918 Austin2024 2024 10.1038/s41598-024-64818-7 ARP 13 T SRA PRJNA1056444 SRS19976914 ARP13T_shotgun double KAPA HiFi Uracil+ half-udg NA NextSeq 500 SINGLE WGS 7421314 SRR27336802 ftp.sra.ebi.ac.uk/vol1/fastq/SRR273/002/SRR27336802/SRR27336802.fastq.gz 5810e74da314eabe751ecec2030edd0c 202442256 Austin2024 2024 10.1038/s41598-024-64818-7 ARP 34 S SRA PRJNA1056444 SRS19976911 ARP34S_shotgun double KAPA HiFi Uracil+ half-udg NA NextSeq 500 SINGLE WGS 9941233 SRR27336805 ftp.sra.ebi.ac.uk/vol1/fastq/SRR273/005/SRR27336805/SRR27336805.fastq.gz 6b803041313b9c4ecc29a83ee05dd7f3 255778837 Bozzi2024 2024 10.1038/s41598-023-40246-x MN0003 ENA PRJEB67998 ERS16595011 MN0003 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 127033674 ERR12206690 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/090/ERR12206690/ERR12206690.fastq.gz b85993652682384691f1a230e36c7e04 5242518069 -Bozzi2024 2024 10.1038/s41598-023-40246-x MN0008 ENA PRJEB67998 ERS16595020 MN0008 double Phusion Hot Start High-Fidelity DNA USER-treatment NA Illumina HiSeq 2500 SINGLE WGS 569521377 ERR12206699 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/099/ERR12206699/ERR12206699.fastq.gz 5e16418d71a85137714dfc8212c30193 21881693637 +Bozzi2024 2024 10.1038/s41598-023-40246-x MN0008 ENA PRJEB67998 ERS16595020 MN0008 double Phusion Hot Start High-Fidelity DNA half-udg NA Illumina HiSeq 2500 SINGLE WGS 569521377 ERR12206699 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/099/ERR12206699/ERR12206699.fastq.gz 5e16418d71a85137714dfc8212c30193 21881693637 Bozzi2024 2024 10.1038/s41598-023-40246-x MN0009 ENA PRJEB67998 ERS16595017 MN0009 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 381236503 ERR12206696 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/096/ERR12206696/ERR12206696.fastq.gz 29c9ed2afe93be03c90398a1e7e287fd 14714457403 Bozzi2024 2024 10.1038/s41598-023-40246-x MN00010 ENA PRJEB67998 ERS16594997 MN00010 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 55475228 ERR12206676 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/076/ERR12206676/ERR12206676.fastq.gz 3d66ff055110d2430ddba575572b2b56 2138238746 Bozzi2024 2024 10.1038/s41598-023-40246-x MN00013 ENA PRJEB67998 ERS16595018 MN00013 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 586099025 ERR12206697 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/097/ERR12206697/ERR12206697.fastq.gz df56276d1a5e4baf89d61ca73299e83f 24700734284 From 9637efdb4746197187d74495977671cf216f1992 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alex=20H=C3=BCbner?= Date: Thu, 3 Oct 2024 11:52:36 +0200 Subject: [PATCH 08/20] Change the project_name, remove coordinates, and add polymerase --- ...entmetagenome-hostassociated_libraries.tsv | 102 ++++++++--------- ...cientmetagenome-hostassociated_samples.tsv | 104 +++++++++--------- 2 files changed, 103 insertions(+), 103 deletions(-) diff --git a/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv b/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv index 18d8e9fb7..589c825a4 100644 --- a/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv +++ b/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv @@ -2618,54 +2618,54 @@ Bozzi2024 2024 10.1038/s41598-023-40246-x MN00069 ENA PRJEB67998 ERS16595000 MN0 Bozzi2024 2024 10.1038/s41598-023-40246-x MN00346 ENA PRJEB67998 ERS16595015 MN00346 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 472422899 ERR12206694 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/094/ERR12206694/ERR12206694.fastq.gz 2c8627452380d03246da17e6e5814a65 20230959642 Bozzi2024 2024 10.1038/s41598-023-40246-x MN01701 ENA PRJEB67998 ERS16594998 MN01701 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 293566149 ERR12206677 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/077/ERR12206677/ERR12206677.fastq.gz 8d0623dc04e10d0779358bf8178c365d 9768291581 Bozzi2024 2024 10.1038/s41598-023-40246-x MN1943 ENA PRJEB67998 ERS16595001 MN1943 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 26332773 ERR12206680 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/080/ERR12206680/ERR12206680.fastq.gz 83ba586fa804c20aac7a3299a755cc62 1002741128 -Hansen2017 2017 10.1371/journal.pone.0170940 M10_P ENA PRJEB18722 ERS1485688 M10_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 1969191 ERR1777519 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777519/ERR1777519.fastq.gz 4806e5a4b8f976079c187cc5efa2dae8 84218155 -Hansen2017 2017 10.1371/journal.pone.0170940 M10_T ENA PRJEB18722 ERS1485690 M10_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 2576499 ERR1777521 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/001/ERR1777521/ERR1777521.fastq.gz d306ddeb663b2da381609d4d19babc89 103453734 -Hansen2017 2017 10.1371/journal.pone.0170940 M2_P ENA PRJEB18722 ERS1485694 M2_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777525 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/005/ERR1777525/ERR1777525.fastq.gz 0a564cf7af305b294c0d3ac1ec8a23f3 137404389 -Hansen2017 2017 10.1371/journal.pone.0170940 M2_T ENA PRJEB18722 ERS1485696 M2_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777527 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/007/ERR1777527/ERR1777527.fastq.gz 591c2709393088585eacf2ca100a5632 155308768 -Hansen2017 2017 10.1371/journal.pone.0170940 M3_S ENA PRJEB18722 ERS1485698 M3_S double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777529 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777529/ERR1777529.fastq.gz 56fe5bf53162d5609eade9db3bcd88d4 149295352 -Hansen2017 2017 10.1371/journal.pone.0170940 M4_P ENA PRJEB18722 ERS1485700 M4_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777531 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/001/ERR1777531/ERR1777531.fastq.gz b117c7a2f196bd76b75efd2609baf351 134749769 -Hansen2017 2017 10.1371/journal.pone.0170940 M5_T ENA PRJEB18722 ERS1485705 M5_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777536 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/006/ERR1777536/ERR1777536.fastq.gz 330b5384d2070963786c5174eec7ba33 147975496 -Hansen2017 2017 10.1371/journal.pone.0170940 M7_P ENA PRJEB18722 ERS1485709 M7_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777540 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/000/ERR1777540/ERR1777540.fastq.gz 4004a0d5dfddfaf019c0983ae362806c 140440673 -Hansen2017 2017 10.1371/journal.pone.0170940 M8_P ENA PRJEB18722 ERS1485712 M8_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777543 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/003/ERR1777543/ERR1777543.fastq.gz b88af542eca4128b0ca9e4f153886302 140951663 -Hansen2017 2017 10.1371/journal.pone.0170940 V10_T ENA PRJEB18722 ERS1485718 V10_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777549 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777549/ERR1777549.fastq.gz baf2a30be4627947f55be0039aea6003 192503916 -Hansen2017 2017 10.1371/journal.pone.0170940 V11_P ENA PRJEB18722 ERS1485719 V11_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777550 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/000/ERR1777550/ERR1777550.fastq.gz 6c89a1e6b74b6db84a967b1d7a3e5e09 169750850 -Hansen2017 2017 10.1371/journal.pone.0170940 V1_P ENA PRJEB18722 ERS1485721 V1_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777552 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/002/ERR1777552/ERR1777552.fastq.gz ea6c4ebfb9639f25397874e6b59810e4 170946497 -Hansen2017 2017 10.1371/journal.pone.0170940 V1_T ENA PRJEB18722 ERS1485722 V1_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777553 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/003/ERR1777553/ERR1777553.fastq.gz ab551a25f258138d8f8e70e62ad6a77f 170873100 -Hansen2017 2017 10.1371/journal.pone.0170940 V2_T ENA PRJEB18722 ERS1485724 V2_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777555 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/005/ERR1777555/ERR1777555.fastq.gz 1cb8e7191b76df89efa7a9d3df02a61a 192882043 -Hansen2017 2017 10.1371/journal.pone.0170940 V4_P ENA PRJEB18722 ERS1485727 V4_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777558 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/008/ERR1777558/ERR1777558.fastq.gz 4c0077c666d9fcfec1cde2a6a127c2d9 174703955 -Hansen2017 2017 10.1371/journal.pone.0170940 V6_T ENA PRJEB18722 ERS1485732 V6_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777563 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/003/ERR1777563/ERR1777563.fastq.gz 4b6552901c8152b3687f1afeb96d2141 149161358 -Hansen2017 2017 10.1371/journal.pone.0170940 V7_T ENA PRJEB18722 ERS1485734 V7_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777565 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/005/ERR1777565/ERR1777565.fastq.gz a9c428c080a0fccfc31ccaf4f2a7d3b0 165288978 -Hansen2017 2017 10.1371/journal.pone.0170940 V9_T ENA PRJEB18722 ERS1485738 V9_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777569 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777569/ERR1777569.fastq.gz c36d5312e9792aed265b69fe9192f9b7 220684796 -Hansen2017 2017 10.1371/journal.pone.0170940 M10_S ENA PRJEB18722 ERS1485689 M10_S double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 3403464 ERR1777520 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/000/ERR1777520/ERR1777520.fastq.gz 8e29052a204658d15a0d8871fd79f6ea 106424195 -Hansen2017 2017 10.1371/journal.pone.0170940 M1_P ENA PRJEB18722 ERS1485691 M1_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777522 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/002/ERR1777522/ERR1777522.fastq.gz 5fa41875bcd8e08bc1241c9e3d0a2490 132291555 -Hansen2017 2017 10.1371/journal.pone.0170940 M1_T ENA PRJEB18722 ERS1485693 M1_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777524 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/004/ERR1777524/ERR1777524.fastq.gz dd3c5abb1eed6923aad43381a0180ab9 144483331 -Hansen2017 2017 10.1371/journal.pone.0170940 M5_S ENA PRJEB18722 ERS1485704 M5_S double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 2887515 ERR1777535 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/005/ERR1777535/ERR1777535.fastq.gz 9cdcddd9c3b0c04630b655b3fee861b4 124268668 -Hansen2017 2017 10.1371/journal.pone.0170940 M6_T ENA PRJEB18722 ERS1485708 M6_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777539 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777539/ERR1777539.fastq.gz 6886d401499fb6ec3ff0403d9eaff5e7 131451664 -Hansen2017 2017 10.1371/journal.pone.0170940 M8_T ENA PRJEB18722 ERS1485714 M8_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777545 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/005/ERR1777545/ERR1777545.fastq.gz af5c8404925e7088f7710834e3802bcc 142873018 -Hansen2017 2017 10.1371/journal.pone.0170940 M9_P ENA PRJEB18722 ERS1485715 M9_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777546 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/006/ERR1777546/ERR1777546.fastq.gz 3b19e91c9f3ccf603bb89f4e2242ed02 149505252 -Hansen2017 2017 10.1371/journal.pone.0170940 V2_P ENA PRJEB18722 ERS1485723 V2_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777554 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/004/ERR1777554/ERR1777554.fastq.gz 828c3f8bbdc85cbc7ac90e9409823691 169553191 -Hansen2017 2017 10.1371/journal.pone.0170940 V3_T ENA PRJEB18722 ERS1485726 V3_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777557 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/007/ERR1777557/ERR1777557.fastq.gz 68166f49bcb2163f98152b2ec2bf83ef 203184689 -Hansen2017 2017 10.1371/journal.pone.0170940 V4_T ENA PRJEB18722 ERS1485728 V4_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777559 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777559/ERR1777559.fastq.gz 5f6f4302ffa1a131c7bd2253677afd08 147997278 -Hansen2017 2017 10.1371/journal.pone.0170940 V5_P ENA PRJEB18722 ERS1485729 V5_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777560 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/000/ERR1777560/ERR1777560.fastq.gz 87b68a0421abe1c01fe98acb3489f643 175230588 -Hansen2017 2017 10.1371/journal.pone.0170940 V6_P ENA PRJEB18722 ERS1485731 V6_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777562 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/002/ERR1777562/ERR1777562.fastq.gz 90149a71159da13d63a58ea53166d1c1 172934284 -Hansen2017 2017 10.1371/journal.pone.0170940 V7_P ENA PRJEB18722 ERS1485733 V7_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777564 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/004/ERR1777564/ERR1777564.fastq.gz 183a3f0758c42f251aee5bc6f0338f0b 178326323 -Hansen2017 2017 10.1371/journal.pone.0170940 V8_P ENA PRJEB18722 ERS1485735 V8_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777566 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/006/ERR1777566/ERR1777566.fastq.gz a7678244e70413365b9e9107f13284e9 172335078 -Hansen2017 2017 10.1371/journal.pone.0170940 V8_T ENA PRJEB18722 ERS1485736 V8_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777567 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/007/ERR1777567/ERR1777567.fastq.gz 033565fd19dc4c838ab3cd8b311872c2 188294390 -Hansen2017 2017 10.1371/journal.pone.0170940 M1_S ENA PRJEB18722 ERS1485692 M1_S double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777523 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/003/ERR1777523/ERR1777523.fastq.gz eb2a615170d1a2a6263580811d5da4ab 137155726 -Hansen2017 2017 10.1371/journal.pone.0170940 M2_S ENA PRJEB18722 ERS1485695 M2_S double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777526 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/006/ERR1777526/ERR1777526.fastq.gz 6504d629aa9a0f34c289d88aadf41b30 144693552 -Hansen2017 2017 10.1371/journal.pone.0170940 M3_P ENA PRJEB18722 ERS1485697 M3_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777528 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/008/ERR1777528/ERR1777528.fastq.gz 7d924557ebaf13380982f3df57bd0057 149981713 -Hansen2017 2017 10.1371/journal.pone.0170940 M3_T ENA PRJEB18722 ERS1485699 M3_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777530 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/000/ERR1777530/ERR1777530.fastq.gz e7bafa9b2480a5c4618169a07d35a8bc 157682427 -Hansen2017 2017 10.1371/journal.pone.0170940 M4_S ENA PRJEB18722 ERS1485701 M4_S double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777532 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/002/ERR1777532/ERR1777532.fastq.gz 3ca620f094a71532a0d93b47b1ade66b 150987147 -Hansen2017 2017 10.1371/journal.pone.0170940 M4_T ENA PRJEB18722 ERS1485702 M4_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777533 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/003/ERR1777533/ERR1777533.fastq.gz 447fc4a8fcdc33e97cfff84be444d518 158897813 -Hansen2017 2017 10.1371/journal.pone.0170940 M5_P ENA PRJEB18722 ERS1485703 M5_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 2066219 ERR1777534 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/004/ERR1777534/ERR1777534.fastq.gz df060ed5d72f1340a40a6de2bf72560f 79137145 -Hansen2017 2017 10.1371/journal.pone.0170940 M6_P ENA PRJEB18722 ERS1485706 M6_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777537 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/007/ERR1777537/ERR1777537.fastq.gz 2eee13f7882ea2f5d70f2c4db996ee90 148547656 -Hansen2017 2017 10.1371/journal.pone.0170940 M6_S ENA PRJEB18722 ERS1485707 M6_S double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 3971984 ERR1777538 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/008/ERR1777538/ERR1777538.fastq.gz 202d21202a5e67b1ed098e3d96750fe8 137421999 -Hansen2017 2017 10.1371/journal.pone.0170940 M7_S ENA PRJEB18722 ERS1485710 M7_S double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 3944221 ERR1777541 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/001/ERR1777541/ERR1777541.fastq.gz 0b9d34c928ac5942ce614b704d7efef0 140398815 -Hansen2017 2017 10.1371/journal.pone.0170940 M7_T ENA PRJEB18722 ERS1485711 M7_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777542 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/002/ERR1777542/ERR1777542.fastq.gz ac5585d7534f0e8d9a4a2bb7323f161b 152708452 -Hansen2017 2017 10.1371/journal.pone.0170940 M8_S ENA PRJEB18722 ERS1485713 M8_S double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 2141948 ERR1777544 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/004/ERR1777544/ERR1777544.fastq.gz 7ce712e6524cc296928d96d1b9f8dbd0 70911496 -Hansen2017 2017 10.1371/journal.pone.0170940 M9_T ENA PRJEB18722 ERS1485716 M9_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777547 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/007/ERR1777547/ERR1777547.fastq.gz 5b89fe79668860fde638c44ab762d7b4 135379904 -Hansen2017 2017 10.1371/journal.pone.0170940 V10_P ENA PRJEB18722 ERS1485717 V10_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777548 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/008/ERR1777548/ERR1777548.fastq.gz 28822b97bc84ff1bfc663082df8c810b 170609451 -Hansen2017 2017 10.1371/journal.pone.0170940 V11_T ENA PRJEB18722 ERS1485720 V11_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777551 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/001/ERR1777551/ERR1777551.fastq.gz cd2f00158fea3bc7476428d9fc159e0d 188022380 -Hansen2017 2017 10.1371/journal.pone.0170940 V3_P ENA PRJEB18722 ERS1485725 V3_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777556 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/006/ERR1777556/ERR1777556.fastq.gz 262b72279b0e4778786907e8b23a80c9 174539467 -Hansen2017 2017 10.1371/journal.pone.0170940 V5_T ENA PRJEB18722 ERS1485730 V5_T double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777561 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/001/ERR1777561/ERR1777561.fastq.gz 42c22f3b88feeaf5d84c8e493783c245 156582293 -Hansen2017 2017 10.1371/journal.pone.0170940 V9_P ENA PRJEB18722 ERS1485737 V9_P double Unknown none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777568 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/008/ERR1777568/ERR1777568.fastq.gz 10396cb2aad632e275194c2f9cccd636 174445223 +Bozzi2024 2024 10.1038/s41598-023-40246-x M10_P ENA PRJEB18722 ERS1485688 M10_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 1969191 ERR1777519 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777519/ERR1777519.fastq.gz 4806e5a4b8f976079c187cc5efa2dae8 84218155 +Bozzi2024 2024 10.1038/s41598-023-40246-x M10_T ENA PRJEB18722 ERS1485690 M10_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 2576499 ERR1777521 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/001/ERR1777521/ERR1777521.fastq.gz d306ddeb663b2da381609d4d19babc89 103453734 +Bozzi2024 2024 10.1038/s41598-023-40246-x M2_P ENA PRJEB18722 ERS1485694 M2_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777525 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/005/ERR1777525/ERR1777525.fastq.gz 0a564cf7af305b294c0d3ac1ec8a23f3 137404389 +Bozzi2024 2024 10.1038/s41598-023-40246-x M2_T ENA PRJEB18722 ERS1485696 M2_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777527 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/007/ERR1777527/ERR1777527.fastq.gz 591c2709393088585eacf2ca100a5632 155308768 +Bozzi2024 2024 10.1038/s41598-023-40246-x M3_S ENA PRJEB18722 ERS1485698 M3_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777529 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777529/ERR1777529.fastq.gz 56fe5bf53162d5609eade9db3bcd88d4 149295352 +Bozzi2024 2024 10.1038/s41598-023-40246-x M4_P ENA PRJEB18722 ERS1485700 M4_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777531 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/001/ERR1777531/ERR1777531.fastq.gz b117c7a2f196bd76b75efd2609baf351 134749769 +Bozzi2024 2024 10.1038/s41598-023-40246-x M5_T ENA PRJEB18722 ERS1485705 M5_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777536 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/006/ERR1777536/ERR1777536.fastq.gz 330b5384d2070963786c5174eec7ba33 147975496 +Bozzi2024 2024 10.1038/s41598-023-40246-x M7_P ENA PRJEB18722 ERS1485709 M7_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777540 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/000/ERR1777540/ERR1777540.fastq.gz 4004a0d5dfddfaf019c0983ae362806c 140440673 +Bozzi2024 2024 10.1038/s41598-023-40246-x M8_P ENA PRJEB18722 ERS1485712 M8_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777543 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/003/ERR1777543/ERR1777543.fastq.gz b88af542eca4128b0ca9e4f153886302 140951663 +Bozzi2024 2024 10.1038/s41598-023-40246-x V10_T ENA PRJEB18722 ERS1485718 V10_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777549 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777549/ERR1777549.fastq.gz baf2a30be4627947f55be0039aea6003 192503916 +Bozzi2024 2024 10.1038/s41598-023-40246-x V11_P ENA PRJEB18722 ERS1485719 V11_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777550 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/000/ERR1777550/ERR1777550.fastq.gz 6c89a1e6b74b6db84a967b1d7a3e5e09 169750850 +Bozzi2024 2024 10.1038/s41598-023-40246-x V1_P ENA PRJEB18722 ERS1485721 V1_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777552 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/002/ERR1777552/ERR1777552.fastq.gz ea6c4ebfb9639f25397874e6b59810e4 170946497 +Bozzi2024 2024 10.1038/s41598-023-40246-x V1_T ENA PRJEB18722 ERS1485722 V1_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777553 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/003/ERR1777553/ERR1777553.fastq.gz ab551a25f258138d8f8e70e62ad6a77f 170873100 +Bozzi2024 2024 10.1038/s41598-023-40246-x V2_T ENA PRJEB18722 ERS1485724 V2_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777555 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/005/ERR1777555/ERR1777555.fastq.gz 1cb8e7191b76df89efa7a9d3df02a61a 192882043 +Bozzi2024 2024 10.1038/s41598-023-40246-x V4_P ENA PRJEB18722 ERS1485727 V4_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777558 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/008/ERR1777558/ERR1777558.fastq.gz 4c0077c666d9fcfec1cde2a6a127c2d9 174703955 +Bozzi2024 2024 10.1038/s41598-023-40246-x V6_T ENA PRJEB18722 ERS1485732 V6_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777563 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/003/ERR1777563/ERR1777563.fastq.gz 4b6552901c8152b3687f1afeb96d2141 149161358 +Bozzi2024 2024 10.1038/s41598-023-40246-x V7_T ENA PRJEB18722 ERS1485734 V7_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777565 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/005/ERR1777565/ERR1777565.fastq.gz a9c428c080a0fccfc31ccaf4f2a7d3b0 165288978 +Bozzi2024 2024 10.1038/s41598-023-40246-x V9_T ENA PRJEB18722 ERS1485738 V9_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777569 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777569/ERR1777569.fastq.gz c36d5312e9792aed265b69fe9192f9b7 220684796 +Bozzi2024 2024 10.1038/s41598-023-40246-x M10_S ENA PRJEB18722 ERS1485689 M10_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 3403464 ERR1777520 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/000/ERR1777520/ERR1777520.fastq.gz 8e29052a204658d15a0d8871fd79f6ea 106424195 +Bozzi2024 2024 10.1038/s41598-023-40246-x M1_P ENA PRJEB18722 ERS1485691 M1_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777522 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/002/ERR1777522/ERR1777522.fastq.gz 5fa41875bcd8e08bc1241c9e3d0a2490 132291555 +Bozzi2024 2024 10.1038/s41598-023-40246-x M1_T ENA PRJEB18722 ERS1485693 M1_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777524 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/004/ERR1777524/ERR1777524.fastq.gz dd3c5abb1eed6923aad43381a0180ab9 144483331 +Bozzi2024 2024 10.1038/s41598-023-40246-x M5_S ENA PRJEB18722 ERS1485704 M5_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 2887515 ERR1777535 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/005/ERR1777535/ERR1777535.fastq.gz 9cdcddd9c3b0c04630b655b3fee861b4 124268668 +Bozzi2024 2024 10.1038/s41598-023-40246-x M6_T ENA PRJEB18722 ERS1485708 M6_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777539 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777539/ERR1777539.fastq.gz 6886d401499fb6ec3ff0403d9eaff5e7 131451664 +Bozzi2024 2024 10.1038/s41598-023-40246-x M8_T ENA PRJEB18722 ERS1485714 M8_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777545 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/005/ERR1777545/ERR1777545.fastq.gz af5c8404925e7088f7710834e3802bcc 142873018 +Bozzi2024 2024 10.1038/s41598-023-40246-x M9_P ENA PRJEB18722 ERS1485715 M9_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777546 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/006/ERR1777546/ERR1777546.fastq.gz 3b19e91c9f3ccf603bb89f4e2242ed02 149505252 +Bozzi2024 2024 10.1038/s41598-023-40246-x V2_P ENA PRJEB18722 ERS1485723 V2_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777554 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/004/ERR1777554/ERR1777554.fastq.gz 828c3f8bbdc85cbc7ac90e9409823691 169553191 +Bozzi2024 2024 10.1038/s41598-023-40246-x V3_T ENA PRJEB18722 ERS1485726 V3_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777557 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/007/ERR1777557/ERR1777557.fastq.gz 68166f49bcb2163f98152b2ec2bf83ef 203184689 +Bozzi2024 2024 10.1038/s41598-023-40246-x V4_T ENA PRJEB18722 ERS1485728 V4_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777559 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777559/ERR1777559.fastq.gz 5f6f4302ffa1a131c7bd2253677afd08 147997278 +Bozzi2024 2024 10.1038/s41598-023-40246-x V5_P ENA PRJEB18722 ERS1485729 V5_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777560 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/000/ERR1777560/ERR1777560.fastq.gz 87b68a0421abe1c01fe98acb3489f643 175230588 +Bozzi2024 2024 10.1038/s41598-023-40246-x V6_P ENA PRJEB18722 ERS1485731 V6_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777562 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/002/ERR1777562/ERR1777562.fastq.gz 90149a71159da13d63a58ea53166d1c1 172934284 +Bozzi2024 2024 10.1038/s41598-023-40246-x V7_P ENA PRJEB18722 ERS1485733 V7_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777564 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/004/ERR1777564/ERR1777564.fastq.gz 183a3f0758c42f251aee5bc6f0338f0b 178326323 +Bozzi2024 2024 10.1038/s41598-023-40246-x V8_P ENA PRJEB18722 ERS1485735 V8_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777566 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/006/ERR1777566/ERR1777566.fastq.gz a7678244e70413365b9e9107f13284e9 172335078 +Bozzi2024 2024 10.1038/s41598-023-40246-x V8_T ENA PRJEB18722 ERS1485736 V8_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777567 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/007/ERR1777567/ERR1777567.fastq.gz 033565fd19dc4c838ab3cd8b311872c2 188294390 +Bozzi2024 2024 10.1038/s41598-023-40246-x M1_S ENA PRJEB18722 ERS1485692 M1_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777523 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/003/ERR1777523/ERR1777523.fastq.gz eb2a615170d1a2a6263580811d5da4ab 137155726 +Bozzi2024 2024 10.1038/s41598-023-40246-x M2_S ENA PRJEB18722 ERS1485695 M2_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777526 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/006/ERR1777526/ERR1777526.fastq.gz 6504d629aa9a0f34c289d88aadf41b30 144693552 +Bozzi2024 2024 10.1038/s41598-023-40246-x M3_P ENA PRJEB18722 ERS1485697 M3_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777528 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/008/ERR1777528/ERR1777528.fastq.gz 7d924557ebaf13380982f3df57bd0057 149981713 +Bozzi2024 2024 10.1038/s41598-023-40246-x M3_T ENA PRJEB18722 ERS1485699 M3_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777530 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/000/ERR1777530/ERR1777530.fastq.gz e7bafa9b2480a5c4618169a07d35a8bc 157682427 +Bozzi2024 2024 10.1038/s41598-023-40246-x M4_S ENA PRJEB18722 ERS1485701 M4_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777532 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/002/ERR1777532/ERR1777532.fastq.gz 3ca620f094a71532a0d93b47b1ade66b 150987147 +Bozzi2024 2024 10.1038/s41598-023-40246-x M4_T ENA PRJEB18722 ERS1485702 M4_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777533 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/003/ERR1777533/ERR1777533.fastq.gz 447fc4a8fcdc33e97cfff84be444d518 158897813 +Bozzi2024 2024 10.1038/s41598-023-40246-x M5_P ENA PRJEB18722 ERS1485703 M5_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 2066219 ERR1777534 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/004/ERR1777534/ERR1777534.fastq.gz df060ed5d72f1340a40a6de2bf72560f 79137145 +Bozzi2024 2024 10.1038/s41598-023-40246-x M6_P ENA PRJEB18722 ERS1485706 M6_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777537 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/007/ERR1777537/ERR1777537.fastq.gz 2eee13f7882ea2f5d70f2c4db996ee90 148547656 +Bozzi2024 2024 10.1038/s41598-023-40246-x M6_S ENA PRJEB18722 ERS1485707 M6_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 3971984 ERR1777538 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/008/ERR1777538/ERR1777538.fastq.gz 202d21202a5e67b1ed098e3d96750fe8 137421999 +Bozzi2024 2024 10.1038/s41598-023-40246-x M7_S ENA PRJEB18722 ERS1485710 M7_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 3944221 ERR1777541 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/001/ERR1777541/ERR1777541.fastq.gz 0b9d34c928ac5942ce614b704d7efef0 140398815 +Bozzi2024 2024 10.1038/s41598-023-40246-x M7_T ENA PRJEB18722 ERS1485711 M7_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777542 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/002/ERR1777542/ERR1777542.fastq.gz ac5585d7534f0e8d9a4a2bb7323f161b 152708452 +Bozzi2024 2024 10.1038/s41598-023-40246-x M8_S ENA PRJEB18722 ERS1485713 M8_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 2141948 ERR1777544 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/004/ERR1777544/ERR1777544.fastq.gz 7ce712e6524cc296928d96d1b9f8dbd0 70911496 +Bozzi2024 2024 10.1038/s41598-023-40246-x M9_T ENA PRJEB18722 ERS1485716 M9_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777547 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/007/ERR1777547/ERR1777547.fastq.gz 5b89fe79668860fde638c44ab762d7b4 135379904 +Bozzi2024 2024 10.1038/s41598-023-40246-x V10_P ENA PRJEB18722 ERS1485717 V10_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777548 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/008/ERR1777548/ERR1777548.fastq.gz 28822b97bc84ff1bfc663082df8c810b 170609451 +Bozzi2024 2024 10.1038/s41598-023-40246-x V11_T ENA PRJEB18722 ERS1485720 V11_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777551 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/001/ERR1777551/ERR1777551.fastq.gz cd2f00158fea3bc7476428d9fc159e0d 188022380 +Bozzi2024 2024 10.1038/s41598-023-40246-x V3_P ENA PRJEB18722 ERS1485725 V3_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777556 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/006/ERR1777556/ERR1777556.fastq.gz 262b72279b0e4778786907e8b23a80c9 174539467 +Bozzi2024 2024 10.1038/s41598-023-40246-x V5_T ENA PRJEB18722 ERS1485730 V5_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777561 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/001/ERR1777561/ERR1777561.fastq.gz 42c22f3b88feeaf5d84c8e493783c245 156582293 +Bozzi2024 2024 10.1038/s41598-023-40246-x V9_P ENA PRJEB18722 ERS1485737 V9_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777568 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/008/ERR1777568/ERR1777568.fastq.gz 10396cb2aad632e275194c2f9cccd636 174445223 diff --git a/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv b/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv index 0b5a43c87..ba6d0c75e 100644 --- a/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv +++ b/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv @@ -1486,56 +1486,56 @@ Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown -13 -50 Brazil MN00067 Homo sa Bozzi2024 2024 10.1038/s41598-023-40246-x Mutum -19.82 -41.44 Brazil MN00068 Homo sapiens 100 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16595005 Bozzi2024 2024 10.1038/s41598-023-40246-x Rio Mucuri -17.51 -41.34 Brazil MN00069 Homo sapiens 100 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16595000 Bozzi2024 2024 10.1038/s41598-023-40246-x Rio Prado -16.61 -40.57 Brazil MN00346 Homo sapiens 100 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16595015 -Bozzi2024 2024 10.1038/s41598-023-40246-x Laguna -28.48 -48.78 Brazil MN01701 Homo sapiens 1800 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16594998 +Bozzi2024 2024 10.1038/s41598-023-40246-x Laguna -28.48 -48.78 Brazil MN01701 Homo sapiens 1900 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16594998 Bozzi2024 2024 10.1038/s41598-023-40246-x Serra de Babilonia -18 -44 Brazil MN1943 Homo sapiens 900 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16595001 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M10_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485688 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M10_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485690 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M2_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485694 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M2_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485696 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M3_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485698 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M4_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485700 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M5_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485705 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M7_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485709 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M8_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485712 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V10_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485718 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V11_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485719 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V1_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485721 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V1_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485722 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V2_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485724 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V4_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485727 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V6_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485732 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V7_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485734 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V9_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485738 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M10_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485689 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M1_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485691 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M1_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485693 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M5_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485704 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M6_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485708 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M8_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485714 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M9_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485715 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V2_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485723 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V3_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485726 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V4_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485728 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V5_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485729 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V6_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485731 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V7_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485733 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V8_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485735 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V8_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485736 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M1_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485692 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M2_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485695 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M3_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485697 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M3_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485699 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M4_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485701 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M4_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485702 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M5_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485703 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M6_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485706 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M6_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485707 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M7_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485710 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M7_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485711 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M8_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485713 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 55 10 Denmark M9_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485716 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V10_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485717 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V11_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485720 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V3_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485725 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V5_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485730 -Hansen2017 2017 10.1371/journal.pone.0170940 Unknown 53 2 United Kingdom V9_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485737 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M10_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485688 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M10_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485690 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M2_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485694 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M2_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485696 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M3_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485698 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M4_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485700 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M5_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485705 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M7_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485709 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M8_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485712 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V10_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485718 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V11_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485719 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V1_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485721 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V1_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485722 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V2_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485724 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V4_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485727 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V6_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485732 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V7_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485734 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V9_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485738 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M10_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485689 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M1_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485691 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M1_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485693 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M5_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485704 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M6_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485708 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M8_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485714 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M9_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485715 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V2_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485723 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V3_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485726 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V4_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485728 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V5_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485729 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V6_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485731 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V7_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485733 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V8_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485735 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V8_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485736 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M1_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485692 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M2_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485695 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M3_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485697 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M3_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485699 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M4_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485701 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M4_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485702 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M5_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485703 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M6_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485706 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M6_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485707 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M7_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485710 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M7_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485711 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M8_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485713 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M9_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485716 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V10_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485717 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V11_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485720 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V3_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485725 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V5_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485730 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V9_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485737 From d14e45734c0764d9716bbb933cdba9592e67a4dd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alex=20H=C3=BCbner?= Date: Thu, 3 Oct 2024 11:56:06 +0200 Subject: [PATCH 09/20] Remove Hansen2017 from CHANGELOG.md --- CHANGELOG.md | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 167a077d6..39b9e45f6 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,10 +11,8 @@ 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) -- Bozzi 2024 10.1038/s41598-023-40246-x (added by @DavideBozzi) -- Hansen 2017 10.1371/journal.pone.0170940 (added by @DavideBozzi) - +- 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) #### Ancient Single Genome: Host Associated From 697349998567e465778fa9fa870fdbc660e23693 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alex=20H=C3=BCbner?= Date: Thu, 3 Oct 2024 11:57:33 +0200 Subject: [PATCH 10/20] Update assets/documentation/libraries/README.md Co-authored-by: James A. Fellows Yates --- assets/documentation/libraries/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/assets/documentation/libraries/README.md b/assets/documentation/libraries/README.md index 9145fe8ad..b4f1c8a5c 100644 --- a/assets/documentation/libraries/README.md +++ b/assets/documentation/libraries/README.md @@ -42,7 +42,7 @@ Library columns are as follows: Muhlemann2018c (second duplicate) etc. - If the authors re-used data from previously published studies that have not been added to AncientMetagenomeDir, please use the project name of the current - study for all samples. + study where metagenomics or microbial genomic analysis has been performed for all samples. > ⚠️ [MIxS v5](https://gensc.org/mixs/) compliant field From 0469d3118a3b1a986a46ae9523ec4b09a0872528 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alex=20H=C3=BCbner?= Date: Thu, 3 Oct 2024 13:03:26 +0200 Subject: [PATCH 11/20] Copy changes to samples README --- assets/documentation/libraries/README.md | 3 ++- assets/documentation/samples/README.md | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/assets/documentation/libraries/README.md b/assets/documentation/libraries/README.md index b4f1c8a5c..a00d94511 100644 --- a/assets/documentation/libraries/README.md +++ b/assets/documentation/libraries/README.md @@ -42,7 +42,8 @@ Library columns are as follows: Muhlemann2018c (second duplicate) etc. - If the authors re-used data from previously published studies that have not been added to AncientMetagenomeDir, please use the project name of the current - study where metagenomics or microbial genomic analysis has been performed for all samples. + study where metagenomics or microbial genomic analysis has been performed for + all samples. > ⚠️ [MIxS v5](https://gensc.org/mixs/) compliant field diff --git a/assets/documentation/samples/README.md b/assets/documentation/samples/README.md index 253a79a8f..aac222826 100644 --- a/assets/documentation/samples/README.md +++ b/assets/documentation/samples/README.md @@ -41,7 +41,8 @@ Sample columns are as follows: Muhlemann2018c (second duplicate) etc. - If the authors re-used data from previously published studies that have not been added to AncientMetagenomeDir, please use the project name of the current - study for all samples. + study where metagenomics or microbial genomic analysis has been performed for + all samples. > ⚠️ [MIxS v5](https://gensc.org/mixs/) compliant field From 3ddfb18da20e0169df09d29700107494252c319c Mon Sep 17 00:00:00 2001 From: alexhbnr Date: Thu, 3 Oct 2024 11:06:23 +0000 Subject: [PATCH 12/20] [skip ci] Update AncientMetagenomeDir geojson --- .../figures/ancientmetagenomedir.geojson | 5648 ++++++++--------- 1 file changed, 2824 insertions(+), 2824 deletions(-) diff --git a/assets/images/figures/ancientmetagenomedir.geojson b/assets/images/figures/ancientmetagenomedir.geojson index 2f3e65acf..6714723b7 100644 --- a/assets/images/figures/ancientmetagenomedir.geojson +++ b/assets/images/figures/ancientmetagenomedir.geojson @@ -2,1517 +2,1517 @@ "type": "FeatureCollection", "name": "ancientmetagenomedir", "features": [ -{ "type": "Feature", "properties": { "project_name": "Ahmed2018", "publication_year": 2018, "publication_doi": "10.1016/j.quascirev.2017.11.037", "site_name": "Hässeldala Port", "latitude": 56.16, "longitude": 15.01, "geo_loc_name": "Sweden", "study_primary_focus": "microbial", "sequence_name": "Sediment core #7.4", "depth": 435.0, "sample_name": "HA1.1", "sample_age": 13900, "sample_age_doi": "10.3389/fevo.2019.00189", "feature": "lake", "material": "lake sediment", "sampling_date": 2015.0, "archive": "ENA", "archive_project": "PRJNA378719", "archive_accession": "SRS2040659", "dir_type": "Ancient Metagenome - 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Host-associated", "sample_host": "Homo sapiens", "community_type": null, "singlegenome_domain": "bacteria", "singlegenome_species": "Porphyromonas gingivalis", "genome_type": "chromosome", "data_type": "raw", "plot_latitude": 51.103017458467519, "plot_longitude": 71.719979963676209, "marker-color": "#D3498E" }, "geometry": { "type": "Point", "coordinates": [ 71.719979963676209, 51.103017458467519 ] } }, +{ "type": "Feature", "properties": { "project_name": "White2021", "publication_year": 2021, "publication_doi": "10.3390/biology10121324", "site_name": "Kuygenzhar", "latitude": 51.103, "longitude": 71.72, "geo_loc_name": "Kazakhstan", "study_primary_focus": null, "sequence_name": null, "depth": null, "sample_name": "B2_B7", "sample_age": 200, "sample_age_doi": "10.3390/biology10121324", "feature": null, "material": "tooth", "sampling_date": null, "archive": "ENA", "archive_project": "PRJEB49091", "archive_accession": "ERS9769383", "dir_type": "Ancient Single-genome - Host-associated", "sample_host": "Homo sapiens", "community_type": null, "singlegenome_domain": "bacteria", "singlegenome_species": "Porphyromonas gingivalis", "genome_type": "chromosome", "data_type": "raw", "plot_latitude": 51.102941585009816, "plot_longitude": 71.720032265452332, "marker-color": "#D3498E" }, "geometry": { "type": "Point", "coordinates": [ 71.720032265452332, 51.102941585009816 ] } } ] } From a2bb3731149ffe3c6e1c11a6165d61883c3b87f9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Alex=20H=C3=BCbner?= Date: Thu, 3 Oct 2024 14:45:12 +0200 Subject: [PATCH 13/20] Replace sample codes from Hansen2017 with ones from Bozzi2024 On ENA, Hansen et al. have prefixed the samples with "M", while Bozzi et al. have prefixed the same samples with "H". For consistency with the original publication, we will stick to the sample naming scheme used by Bozzi et al. --- ...entmetagenome-hostassociated_libraries.tsv | 58 +++++++++---------- ...cientmetagenome-hostassociated_samples.tsv | 58 +++++++++---------- 2 files changed, 58 insertions(+), 58 deletions(-) diff --git a/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv b/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv index 589c825a4..a113bb9c6 100644 --- a/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv +++ b/ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libraries.tsv @@ -2618,15 +2618,15 @@ Bozzi2024 2024 10.1038/s41598-023-40246-x MN00069 ENA PRJEB67998 ERS16595000 MN0 Bozzi2024 2024 10.1038/s41598-023-40246-x MN00346 ENA PRJEB67998 ERS16595015 MN00346 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 472422899 ERR12206694 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/094/ERR12206694/ERR12206694.fastq.gz 2c8627452380d03246da17e6e5814a65 20230959642 Bozzi2024 2024 10.1038/s41598-023-40246-x MN01701 ENA PRJEB67998 ERS16594998 MN01701 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 293566149 ERR12206677 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/077/ERR12206677/ERR12206677.fastq.gz 8d0623dc04e10d0779358bf8178c365d 9768291581 Bozzi2024 2024 10.1038/s41598-023-40246-x MN1943 ENA PRJEB67998 ERS16595001 MN1943 double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 26332773 ERR12206680 ftp.sra.ebi.ac.uk/vol1/fastq/ERR122/080/ERR12206680/ERR12206680.fastq.gz 83ba586fa804c20aac7a3299a755cc62 1002741128 -Bozzi2024 2024 10.1038/s41598-023-40246-x M10_P ENA PRJEB18722 ERS1485688 M10_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 1969191 ERR1777519 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777519/ERR1777519.fastq.gz 4806e5a4b8f976079c187cc5efa2dae8 84218155 -Bozzi2024 2024 10.1038/s41598-023-40246-x M10_T ENA PRJEB18722 ERS1485690 M10_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 2576499 ERR1777521 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/001/ERR1777521/ERR1777521.fastq.gz d306ddeb663b2da381609d4d19babc89 103453734 -Bozzi2024 2024 10.1038/s41598-023-40246-x M2_P ENA PRJEB18722 ERS1485694 M2_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777525 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/005/ERR1777525/ERR1777525.fastq.gz 0a564cf7af305b294c0d3ac1ec8a23f3 137404389 -Bozzi2024 2024 10.1038/s41598-023-40246-x M2_T ENA PRJEB18722 ERS1485696 M2_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777527 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/007/ERR1777527/ERR1777527.fastq.gz 591c2709393088585eacf2ca100a5632 155308768 -Bozzi2024 2024 10.1038/s41598-023-40246-x M3_S ENA PRJEB18722 ERS1485698 M3_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777529 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777529/ERR1777529.fastq.gz 56fe5bf53162d5609eade9db3bcd88d4 149295352 -Bozzi2024 2024 10.1038/s41598-023-40246-x M4_P ENA PRJEB18722 ERS1485700 M4_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777531 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/001/ERR1777531/ERR1777531.fastq.gz b117c7a2f196bd76b75efd2609baf351 134749769 -Bozzi2024 2024 10.1038/s41598-023-40246-x M5_T ENA PRJEB18722 ERS1485705 M5_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777536 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/006/ERR1777536/ERR1777536.fastq.gz 330b5384d2070963786c5174eec7ba33 147975496 -Bozzi2024 2024 10.1038/s41598-023-40246-x M7_P ENA PRJEB18722 ERS1485709 M7_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777540 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/000/ERR1777540/ERR1777540.fastq.gz 4004a0d5dfddfaf019c0983ae362806c 140440673 -Bozzi2024 2024 10.1038/s41598-023-40246-x M8_P ENA PRJEB18722 ERS1485712 M8_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777543 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/003/ERR1777543/ERR1777543.fastq.gz b88af542eca4128b0ca9e4f153886302 140951663 +Bozzi2024 2024 10.1038/s41598-023-40246-x H10_P ENA PRJEB18722 ERS1485688 H10_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 1969191 ERR1777519 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777519/ERR1777519.fastq.gz 4806e5a4b8f976079c187cc5efa2dae8 84218155 +Bozzi2024 2024 10.1038/s41598-023-40246-x H10_T ENA PRJEB18722 ERS1485690 H10_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 2576499 ERR1777521 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/001/ERR1777521/ERR1777521.fastq.gz d306ddeb663b2da381609d4d19babc89 103453734 +Bozzi2024 2024 10.1038/s41598-023-40246-x H2_P ENA PRJEB18722 ERS1485694 H2_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777525 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/005/ERR1777525/ERR1777525.fastq.gz 0a564cf7af305b294c0d3ac1ec8a23f3 137404389 +Bozzi2024 2024 10.1038/s41598-023-40246-x H2_T ENA PRJEB18722 ERS1485696 H2_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777527 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/007/ERR1777527/ERR1777527.fastq.gz 591c2709393088585eacf2ca100a5632 155308768 +Bozzi2024 2024 10.1038/s41598-023-40246-x H3_S ENA PRJEB18722 ERS1485698 H3_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777529 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777529/ERR1777529.fastq.gz 56fe5bf53162d5609eade9db3bcd88d4 149295352 +Bozzi2024 2024 10.1038/s41598-023-40246-x H4_P ENA PRJEB18722 ERS1485700 H4_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777531 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/001/ERR1777531/ERR1777531.fastq.gz b117c7a2f196bd76b75efd2609baf351 134749769 +Bozzi2024 2024 10.1038/s41598-023-40246-x H5_T ENA PRJEB18722 ERS1485705 H5_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777536 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/006/ERR1777536/ERR1777536.fastq.gz 330b5384d2070963786c5174eec7ba33 147975496 +Bozzi2024 2024 10.1038/s41598-023-40246-x H7_P ENA PRJEB18722 ERS1485709 H7_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777540 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/000/ERR1777540/ERR1777540.fastq.gz 4004a0d5dfddfaf019c0983ae362806c 140440673 +Bozzi2024 2024 10.1038/s41598-023-40246-x H8_P ENA PRJEB18722 ERS1485712 H8_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777543 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/003/ERR1777543/ERR1777543.fastq.gz b88af542eca4128b0ca9e4f153886302 140951663 Bozzi2024 2024 10.1038/s41598-023-40246-x V10_T ENA PRJEB18722 ERS1485718 V10_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777549 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777549/ERR1777549.fastq.gz baf2a30be4627947f55be0039aea6003 192503916 Bozzi2024 2024 10.1038/s41598-023-40246-x V11_P ENA PRJEB18722 ERS1485719 V11_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777550 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/000/ERR1777550/ERR1777550.fastq.gz 6c89a1e6b74b6db84a967b1d7a3e5e09 169750850 Bozzi2024 2024 10.1038/s41598-023-40246-x V1_P ENA PRJEB18722 ERS1485721 V1_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777552 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/002/ERR1777552/ERR1777552.fastq.gz ea6c4ebfb9639f25397874e6b59810e4 170946497 @@ -2636,13 +2636,13 @@ Bozzi2024 2024 10.1038/s41598-023-40246-x V4_P ENA PRJEB18722 ERS1485727 V4_P do Bozzi2024 2024 10.1038/s41598-023-40246-x V6_T ENA PRJEB18722 ERS1485732 V6_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777563 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/003/ERR1777563/ERR1777563.fastq.gz 4b6552901c8152b3687f1afeb96d2141 149161358 Bozzi2024 2024 10.1038/s41598-023-40246-x V7_T ENA PRJEB18722 ERS1485734 V7_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777565 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/005/ERR1777565/ERR1777565.fastq.gz a9c428c080a0fccfc31ccaf4f2a7d3b0 165288978 Bozzi2024 2024 10.1038/s41598-023-40246-x V9_T ENA PRJEB18722 ERS1485738 V9_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777569 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777569/ERR1777569.fastq.gz c36d5312e9792aed265b69fe9192f9b7 220684796 -Bozzi2024 2024 10.1038/s41598-023-40246-x M10_S ENA PRJEB18722 ERS1485689 M10_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 3403464 ERR1777520 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/000/ERR1777520/ERR1777520.fastq.gz 8e29052a204658d15a0d8871fd79f6ea 106424195 -Bozzi2024 2024 10.1038/s41598-023-40246-x M1_P ENA PRJEB18722 ERS1485691 M1_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777522 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/002/ERR1777522/ERR1777522.fastq.gz 5fa41875bcd8e08bc1241c9e3d0a2490 132291555 -Bozzi2024 2024 10.1038/s41598-023-40246-x M1_T ENA PRJEB18722 ERS1485693 M1_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777524 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/004/ERR1777524/ERR1777524.fastq.gz dd3c5abb1eed6923aad43381a0180ab9 144483331 -Bozzi2024 2024 10.1038/s41598-023-40246-x M5_S ENA PRJEB18722 ERS1485704 M5_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 2887515 ERR1777535 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/005/ERR1777535/ERR1777535.fastq.gz 9cdcddd9c3b0c04630b655b3fee861b4 124268668 -Bozzi2024 2024 10.1038/s41598-023-40246-x M6_T ENA PRJEB18722 ERS1485708 M6_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777539 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777539/ERR1777539.fastq.gz 6886d401499fb6ec3ff0403d9eaff5e7 131451664 -Bozzi2024 2024 10.1038/s41598-023-40246-x M8_T ENA PRJEB18722 ERS1485714 M8_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777545 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/005/ERR1777545/ERR1777545.fastq.gz af5c8404925e7088f7710834e3802bcc 142873018 -Bozzi2024 2024 10.1038/s41598-023-40246-x M9_P ENA PRJEB18722 ERS1485715 M9_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777546 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/006/ERR1777546/ERR1777546.fastq.gz 3b19e91c9f3ccf603bb89f4e2242ed02 149505252 +Bozzi2024 2024 10.1038/s41598-023-40246-x H10_S ENA PRJEB18722 ERS1485689 H10_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 3403464 ERR1777520 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/000/ERR1777520/ERR1777520.fastq.gz 8e29052a204658d15a0d8871fd79f6ea 106424195 +Bozzi2024 2024 10.1038/s41598-023-40246-x H1_P ENA PRJEB18722 ERS1485691 H1_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777522 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/002/ERR1777522/ERR1777522.fastq.gz 5fa41875bcd8e08bc1241c9e3d0a2490 132291555 +Bozzi2024 2024 10.1038/s41598-023-40246-x H1_T ENA PRJEB18722 ERS1485693 H1_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777524 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/004/ERR1777524/ERR1777524.fastq.gz dd3c5abb1eed6923aad43381a0180ab9 144483331 +Bozzi2024 2024 10.1038/s41598-023-40246-x H5_S ENA PRJEB18722 ERS1485704 H5_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 2887515 ERR1777535 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/005/ERR1777535/ERR1777535.fastq.gz 9cdcddd9c3b0c04630b655b3fee861b4 124268668 +Bozzi2024 2024 10.1038/s41598-023-40246-x H6_T ENA PRJEB18722 ERS1485708 H6_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777539 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777539/ERR1777539.fastq.gz 6886d401499fb6ec3ff0403d9eaff5e7 131451664 +Bozzi2024 2024 10.1038/s41598-023-40246-x H8_T ENA PRJEB18722 ERS1485714 H8_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777545 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/005/ERR1777545/ERR1777545.fastq.gz af5c8404925e7088f7710834e3802bcc 142873018 +Bozzi2024 2024 10.1038/s41598-023-40246-x H9_P ENA PRJEB18722 ERS1485715 H9_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777546 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/006/ERR1777546/ERR1777546.fastq.gz 3b19e91c9f3ccf603bb89f4e2242ed02 149505252 Bozzi2024 2024 10.1038/s41598-023-40246-x V2_P ENA PRJEB18722 ERS1485723 V2_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777554 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/004/ERR1777554/ERR1777554.fastq.gz 828c3f8bbdc85cbc7ac90e9409823691 169553191 Bozzi2024 2024 10.1038/s41598-023-40246-x V3_T ENA PRJEB18722 ERS1485726 V3_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777557 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/007/ERR1777557/ERR1777557.fastq.gz 68166f49bcb2163f98152b2ec2bf83ef 203184689 Bozzi2024 2024 10.1038/s41598-023-40246-x V4_T ENA PRJEB18722 ERS1485728 V4_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777559 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/009/ERR1777559/ERR1777559.fastq.gz 5f6f4302ffa1a131c7bd2253677afd08 147997278 @@ -2651,19 +2651,19 @@ Bozzi2024 2024 10.1038/s41598-023-40246-x V6_P ENA PRJEB18722 ERS1485731 V6_P do Bozzi2024 2024 10.1038/s41598-023-40246-x V7_P ENA PRJEB18722 ERS1485733 V7_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777564 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/004/ERR1777564/ERR1777564.fastq.gz 183a3f0758c42f251aee5bc6f0338f0b 178326323 Bozzi2024 2024 10.1038/s41598-023-40246-x V8_P ENA PRJEB18722 ERS1485735 V8_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777566 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/006/ERR1777566/ERR1777566.fastq.gz a7678244e70413365b9e9107f13284e9 172335078 Bozzi2024 2024 10.1038/s41598-023-40246-x V8_T ENA PRJEB18722 ERS1485736 V8_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777567 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/007/ERR1777567/ERR1777567.fastq.gz 033565fd19dc4c838ab3cd8b311872c2 188294390 -Bozzi2024 2024 10.1038/s41598-023-40246-x M1_S ENA PRJEB18722 ERS1485692 M1_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777523 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/003/ERR1777523/ERR1777523.fastq.gz eb2a615170d1a2a6263580811d5da4ab 137155726 -Bozzi2024 2024 10.1038/s41598-023-40246-x M2_S ENA PRJEB18722 ERS1485695 M2_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777526 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/006/ERR1777526/ERR1777526.fastq.gz 6504d629aa9a0f34c289d88aadf41b30 144693552 -Bozzi2024 2024 10.1038/s41598-023-40246-x M3_P ENA PRJEB18722 ERS1485697 M3_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777528 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/008/ERR1777528/ERR1777528.fastq.gz 7d924557ebaf13380982f3df57bd0057 149981713 -Bozzi2024 2024 10.1038/s41598-023-40246-x M3_T ENA PRJEB18722 ERS1485699 M3_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777530 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/000/ERR1777530/ERR1777530.fastq.gz e7bafa9b2480a5c4618169a07d35a8bc 157682427 -Bozzi2024 2024 10.1038/s41598-023-40246-x M4_S ENA PRJEB18722 ERS1485701 M4_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777532 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/002/ERR1777532/ERR1777532.fastq.gz 3ca620f094a71532a0d93b47b1ade66b 150987147 -Bozzi2024 2024 10.1038/s41598-023-40246-x M4_T ENA PRJEB18722 ERS1485702 M4_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777533 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/003/ERR1777533/ERR1777533.fastq.gz 447fc4a8fcdc33e97cfff84be444d518 158897813 -Bozzi2024 2024 10.1038/s41598-023-40246-x M5_P ENA PRJEB18722 ERS1485703 M5_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 2066219 ERR1777534 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/004/ERR1777534/ERR1777534.fastq.gz df060ed5d72f1340a40a6de2bf72560f 79137145 -Bozzi2024 2024 10.1038/s41598-023-40246-x M6_P ENA PRJEB18722 ERS1485706 M6_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777537 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/007/ERR1777537/ERR1777537.fastq.gz 2eee13f7882ea2f5d70f2c4db996ee90 148547656 -Bozzi2024 2024 10.1038/s41598-023-40246-x M6_S ENA PRJEB18722 ERS1485707 M6_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 3971984 ERR1777538 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/008/ERR1777538/ERR1777538.fastq.gz 202d21202a5e67b1ed098e3d96750fe8 137421999 -Bozzi2024 2024 10.1038/s41598-023-40246-x M7_S ENA PRJEB18722 ERS1485710 M7_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 3944221 ERR1777541 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/001/ERR1777541/ERR1777541.fastq.gz 0b9d34c928ac5942ce614b704d7efef0 140398815 -Bozzi2024 2024 10.1038/s41598-023-40246-x M7_T ENA PRJEB18722 ERS1485711 M7_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777542 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/002/ERR1777542/ERR1777542.fastq.gz ac5585d7534f0e8d9a4a2bb7323f161b 152708452 -Bozzi2024 2024 10.1038/s41598-023-40246-x M8_S ENA PRJEB18722 ERS1485713 M8_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 2141948 ERR1777544 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/004/ERR1777544/ERR1777544.fastq.gz 7ce712e6524cc296928d96d1b9f8dbd0 70911496 -Bozzi2024 2024 10.1038/s41598-023-40246-x M9_T ENA PRJEB18722 ERS1485716 M9_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777547 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/007/ERR1777547/ERR1777547.fastq.gz 5b89fe79668860fde638c44ab762d7b4 135379904 +Bozzi2024 2024 10.1038/s41598-023-40246-x H1_S ENA PRJEB18722 ERS1485692 H1_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777523 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/003/ERR1777523/ERR1777523.fastq.gz eb2a615170d1a2a6263580811d5da4ab 137155726 +Bozzi2024 2024 10.1038/s41598-023-40246-x H2_S ENA PRJEB18722 ERS1485695 H2_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777526 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/006/ERR1777526/ERR1777526.fastq.gz 6504d629aa9a0f34c289d88aadf41b30 144693552 +Bozzi2024 2024 10.1038/s41598-023-40246-x H3_P ENA PRJEB18722 ERS1485697 H3_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777528 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/008/ERR1777528/ERR1777528.fastq.gz 7d924557ebaf13380982f3df57bd0057 149981713 +Bozzi2024 2024 10.1038/s41598-023-40246-x H3_T ENA PRJEB18722 ERS1485699 H3_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777530 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/000/ERR1777530/ERR1777530.fastq.gz e7bafa9b2480a5c4618169a07d35a8bc 157682427 +Bozzi2024 2024 10.1038/s41598-023-40246-x H4_S ENA PRJEB18722 ERS1485701 H4_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777532 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/002/ERR1777532/ERR1777532.fastq.gz 3ca620f094a71532a0d93b47b1ade66b 150987147 +Bozzi2024 2024 10.1038/s41598-023-40246-x H4_T ENA PRJEB18722 ERS1485702 H4_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777533 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/003/ERR1777533/ERR1777533.fastq.gz 447fc4a8fcdc33e97cfff84be444d518 158897813 +Bozzi2024 2024 10.1038/s41598-023-40246-x H5_P ENA PRJEB18722 ERS1485703 H5_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 2066219 ERR1777534 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/004/ERR1777534/ERR1777534.fastq.gz df060ed5d72f1340a40a6de2bf72560f 79137145 +Bozzi2024 2024 10.1038/s41598-023-40246-x H6_P ENA PRJEB18722 ERS1485706 H6_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777537 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/007/ERR1777537/ERR1777537.fastq.gz 2eee13f7882ea2f5d70f2c4db996ee90 148547656 +Bozzi2024 2024 10.1038/s41598-023-40246-x H6_S ENA PRJEB18722 ERS1485707 H6_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 3971984 ERR1777538 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/008/ERR1777538/ERR1777538.fastq.gz 202d21202a5e67b1ed098e3d96750fe8 137421999 +Bozzi2024 2024 10.1038/s41598-023-40246-x H7_S ENA PRJEB18722 ERS1485710 H7_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 3944221 ERR1777541 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/001/ERR1777541/ERR1777541.fastq.gz 0b9d34c928ac5942ce614b704d7efef0 140398815 +Bozzi2024 2024 10.1038/s41598-023-40246-x H7_T ENA PRJEB18722 ERS1485711 H7_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777542 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/002/ERR1777542/ERR1777542.fastq.gz ac5585d7534f0e8d9a4a2bb7323f161b 152708452 +Bozzi2024 2024 10.1038/s41598-023-40246-x H8_S ENA PRJEB18722 ERS1485713 H8_S double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 2141948 ERR1777544 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/004/ERR1777544/ERR1777544.fastq.gz 7ce712e6524cc296928d96d1b9f8dbd0 70911496 +Bozzi2024 2024 10.1038/s41598-023-40246-x H9_T ENA PRJEB18722 ERS1485716 H9_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777547 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/007/ERR1777547/ERR1777547.fastq.gz 5b89fe79668860fde638c44ab762d7b4 135379904 Bozzi2024 2024 10.1038/s41598-023-40246-x V10_P ENA PRJEB18722 ERS1485717 V10_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777548 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/008/ERR1777548/ERR1777548.fastq.gz 28822b97bc84ff1bfc663082df8c810b 170609451 Bozzi2024 2024 10.1038/s41598-023-40246-x V11_T ENA PRJEB18722 ERS1485720 V11_T double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777551 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/001/ERR1777551/ERR1777551.fastq.gz cd2f00158fea3bc7476428d9fc159e0d 188022380 Bozzi2024 2024 10.1038/s41598-023-40246-x V3_P ENA PRJEB18722 ERS1485725 V3_P double Phusion Hot Start High-Fidelity DNA none NA Illumina HiSeq 2500 SINGLE WGS 4000000 ERR1777556 ftp.sra.ebi.ac.uk/vol1/fastq/ERR177/006/ERR1777556/ERR1777556.fastq.gz 262b72279b0e4778786907e8b23a80c9 174539467 diff --git a/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv b/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv index ba6d0c75e..c51698a14 100644 --- a/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv +++ b/ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_samples.tsv @@ -1488,15 +1488,15 @@ Bozzi2024 2024 10.1038/s41598-023-40246-x Rio Mucuri -17.51 -41.34 Brazil MN0006 Bozzi2024 2024 10.1038/s41598-023-40246-x Rio Prado -16.61 -40.57 Brazil MN00346 Homo sapiens 100 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16595015 Bozzi2024 2024 10.1038/s41598-023-40246-x Laguna -28.48 -48.78 Brazil MN01701 Homo sapiens 1900 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16594998 Bozzi2024 2024 10.1038/s41598-023-40246-x Serra de Babilonia -18 -44 Brazil MN1943 Homo sapiens 900 10.1101/2022.01.27.477466 skeletal tissue tooth ENA PRJEB67998 ERS16595001 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M10_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485688 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M10_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485690 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M2_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485694 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M2_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485696 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M3_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485698 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M4_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485700 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M5_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485705 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M7_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485709 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M8_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485712 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H10_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485688 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H10_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485690 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H2_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485694 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H2_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485696 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H3_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485698 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H4_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485700 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H5_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485705 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H7_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485709 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H8_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485712 Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V10_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485718 Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V11_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485719 Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V1_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485721 @@ -1506,13 +1506,13 @@ Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V4_P Homo Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V6_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485732 Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V7_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485734 Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V9_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485738 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M10_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485689 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M1_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485691 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M1_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485693 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M5_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485704 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M6_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485708 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M8_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485714 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M9_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485715 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H10_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485689 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H1_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485691 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H1_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485693 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H5_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485704 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H6_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485708 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H8_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485714 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H9_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485715 Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V2_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485723 Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V3_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485726 Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V4_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485728 @@ -1521,19 +1521,19 @@ Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V6_P Homo Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V7_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485733 Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V8_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485735 Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V8_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485736 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M1_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485692 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M2_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485695 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M3_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485697 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M3_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485699 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M4_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485701 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M4_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485702 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M5_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485703 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M6_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485706 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M6_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485707 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M7_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485710 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M7_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485711 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M8_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485713 -Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark M9_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485716 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H1_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485692 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H2_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485695 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H3_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485697 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H3_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485699 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H4_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485701 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H4_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485702 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H5_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485703 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H6_P Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485706 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H6_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485707 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H7_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485710 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H7_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485711 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H8_S Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485713 +Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA Denmark H9_T Homo sapiens 200 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485716 Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V10_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485717 Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V11_T Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue tooth ENA PRJEB18722 ERS1485720 Bozzi2024 2024 10.1038/s41598-023-40246-x Unknown NA NA United Kingdom V3_P Homo sapiens 1000 10.1371/journal.pone.0170940 skeletal tissue bone ENA PRJEB18722 ERS1485725 From 2484be63a58db31f842db3e05e4ef54beedf141d Mon Sep 17 00:00:00 2001 From: alexhbnr Date: Thu, 3 Oct 2024 12:50:05 +0000 Subject: [PATCH 14/20] [skip ci] Update AncientMetagenomeDir live-status images --- ...tagenomeDir-Library_Timeline_Libraries.png | Bin 102016 -> 106454 bytes ...tagenomeDir-Library_Timeline_Libraries.svg | 124 ++++---- ...ary_Timeline_Libraries_InstrumentModel.png | Bin 295926 -> 303153 bytes ...ary_Timeline_Libraries_InstrumentModel.svg | 122 ++++---- ...brary_Timeline_Libraries_LibraryLayout.png | Bin 115434 -> 115455 bytes ...brary_Timeline_Libraries_LibraryLayout.svg | 186 +++++------ ...ry_Timeline_Libraries_LibraryTreatment.png | Bin 114504 -> 119021 bytes ...ry_Timeline_Libraries_LibraryTreatment.svg | 296 +++++++++--------- ...-Library_Timeline_Libraries_StrandType.png | Bin 113929 -> 118279 bytes 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