diff --git a/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv b/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv index c1ec1c669..e5dc2b408 100644 --- a/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv +++ b/ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated_libraries.tsv @@ -2526,7 +2526,7 @@ Clavel2023 2023 10.1016/j.isci.2023.106787 MAJ46 ENA PRJEB59233 ERS14555596 MAJ4 Clavel2023 2023 10.1016/j.isci.2023.106787 MAJ46 ENA PRJEB59233 ERS14555596 MAJ46t11_Ages_2_9349_lr28_i56_T2.5min double AccuPrime Pfx DNA half-udg Illumina MiniSeq SINGLE Targeted-Capture 14264 ERR10822153 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/053/ERR10822153/ERR10822153.fastq.gz c56d2a92b0c401fe9c00c556c6ca8506 562321 Clavel2023 2023 10.1016/j.isci.2023.106787 MAJ46 ENA PRJEB59233 ERS14555596 MAJ46t11_Ages_2_9349_lr29_i57_T5min double AccuPrime Pfx DNA half-udg Illumina MiniSeq SINGLE Targeted-Capture 19919 ERR10822154 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/054/ERR10822154/ERR10822154.fastq.gz f6881046c5082f70699ae33fd2c17b15 769422 Clavel2023 2023 10.1016/j.isci.2023.106787 MAJ46 ENA PRJEB59233 ERS14555596 MAJ46t11_Ages_2_9349_lr31_i59_T10min double AccuPrime Pfx DNA half-udg Illumina MiniSeq SINGLE Targeted-Capture 78331 ERR10822156 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/056/ERR10822156/ERR10822156.fastq.gz 8534b3ef0f6985186f81ccee4e6bfc63 2790324 -Clavel2023 2023 10.1016/j.isci.2023.106787 ERS14555628 ENA PRJEB59234 ERS14555592 MAJ38t6_Ages_2_8153_lr03_i03_SN1 double AccuPrime Pfx DNA half-udg Illumina MiniSeq SINGLE Targeted-Capture 61848 ERR10822090 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/090/ERR10822090/ERR10822090.fastq.gz 1d821e71a831c88178975b35559c7cef 2712563 +Clavel2023 2023 10.1016/j.isci.2023.106787 MAJ38 ENA PRJEB59234 ERS14555592 MAJ38t6_Ages_2_8153_lr03_i03_SN1 double AccuPrime Pfx DNA half-udg Illumina MiniSeq SINGLE Targeted-Capture 61848 ERR10822090 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/090/ERR10822090/ERR10822090.fastq.gz 1d821e71a831c88178975b35559c7cef 2712563 Clavel2023 2023 10.1016/j.isci.2023.106787 MAJ38 ENA PRJEB59234 ERS14555592 MAJ38t6_Ages_2_8153_lr16_i26_SN2 double AccuPrime Pfx DNA half-udg Illumina MiniSeq SINGLE Targeted-Capture 95389 ERR10822091 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/091/ERR10822091/ERR10822091.fastq.gz 4d93d79f34612c23da1d931fc31871ca 4278163 Clavel2023 2023 10.1016/j.isci.2023.106787 MAJ38 ENA PRJEB59234 ERS14555592 MAJ38t6_Ages_2_8153_lr03_i03_SN1 double AccuPrime Pfx DNA half-udg Illumina MiniSeq PAIRED Targeted-Capture 18911 ERR10822438 fastq_all ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/038/ERR10822438/ERR10822438_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR108/038/ERR10822438/ERR10822438_2.fastq.gz 755eb7c0958a7286895a07358211d721;94b8a89f869e88c85e290addaa99ccef 906081;944788 Clavel2023 2023 10.1016/j.isci.2023.106787 MAJ38 ENA PRJEB59234 ERS14555592 MAJ38t6_Ages_2_8153_lr16_i26_SN2 double AccuPrime Pfx DNA half-udg Illumina MiniSeq PAIRED Targeted-Capture 69510 ERR10822439 fastq_all ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR10822439/MAJ38_E6_L18_R1_M.fastq.gz;ftp.sra.ebi.ac.uk/vol1/run/ERR108/ERR10822439/MAJ38_E6_L18_R2_M.fastq.gz 5b21c69e610f47178058addd5c49674b;a559f05ff8beb017a8efaf7a1a3d7203 2939990;2939990 diff --git a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv index 4a8038837..6e900c43f 100644 --- a/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv +++ b/ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_samples.tsv @@ -587,7 +587,7 @@ Swali2023 2023 10.1038/s41467-023-38393-w Charterhouse Warren, Mendip Hills, Som Swali2023 2023 10.1038/s41467-023-38393-w Levens Deer Park ring cairn, Leven, Cumbria 54.268 -2.761 United Kingdom C10928 Homo sapiens 3900 10.1038/s41467-023-38393-w bacteria Yersinia pestis tooth chromosome ENA raw PRJEB61230 ERS14909714,ERS14891343 Clavel2023 2023 10.1016/j.isci.2023.106787 La Major Cathedral, Marseille, Bouches-du-Rhône 43.3 5.365 France MAJ75 Homo sapiens 300 10.1016/j.isci.2023.106787 bacteria Yersinia pestis tooth chromosome ENA raw PRJEB59233 ERS14555610,ERS14555611,ERS14555612,ERS14555613,ERS14555614,ERS14555615,ERS14555616,ERS14555617 Clavel2023 2023 10.1016/j.isci.2023.106787 La Major Cathedral, Marseille, Bouches-du-Rhône 43.3 5.365 France MAJ46 Homo sapiens 300 10.1016/j.isci.2023.106787 bacteria Yersinia pestis tooth chromosome ENA raw PRJEB59233 ERS14555595,ERS14555596,ERS14555597,ERS14555598,ERS14555599,ERS14555600,ERS14555601,ERS14555602,ERS14555603,ERS14555604 -Clavel2023 2023 10.1016/j.isci.2023.106787 La Major Cathedral, Marseille, Bouches-du-Rhône 43.3 5.365 France MAJ38 Homo sapiens 300 10.1016/j.isci.2023.106787 bacteria Yersinia pestis tooth chromosome ENA raw PRJEB59233 ERS14555592,ERS14555591,ERS14555590,ERS14555589,ERS14555588,ERS14555587 +Clavel2023 2023 10.1016/j.isci.2023.106787 La Major Cathedral, Marseille, Bouches-du-Rhône 43.3 5.365 France MAJ38 Homo sapiens 300 10.1016/j.isci.2023.106787 bacteria Yersinia pestis tooth chromosome ENA raw PRJEB59233,PRJEB59234 ERS14555592,ERS14555591,ERS14555590,ERS14555589,ERS14555588,ERS14555587 Clavel2023 2023 10.1016/j.isci.2023.106787 Hôtel-Dieu Saint-Jean-Baptiste, Amiens 49.898 2.299 France AMIENS268 Homo sapiens 400 10.1016/j.isci.2023.106787 bacteria Yersinia pestis tooth chromosome ENA raw PRJEB59233 ERS14555669,ERS14555670,ERS14555671 Clavel2023 2023 10.1016/j.isci.2023.106787 Les Rayettes, Martigues 43.415 5.039 France RAY1015 Homo sapiens 300 10.1016/j.isci.2023.106787 bacteria Yersinia pestis tooth chromosome ENA raw PRJEB59233 ERS14555624,ERS14555625,ERS14555626 Clavel2023 2023 10.1016/j.isci.2023.106787 Les Rayettes, Martigues 43.415 5.039 France RAY1028 Homo sapiens 300 10.1016/j.isci.2023.106787 bacteria Yersinia pestis tooth chromosome ENA raw PRJEB59233 ERS14555627,ERS14555628 diff --git a/assets/analysis/prerelease-validation-crosstable.R b/assets/analysis/prerelease-validation-crosstable.R index 4a4f37a1b..c1f917ead 100644 --- a/assets/analysis/prerelease-validation-crosstable.R +++ b/assets/analysis/prerelease-validation-crosstable.R @@ -33,4 +33,5 @@ cat("\n") cat("POSSIBLE PROBLEMS FOR:", paste0(unique(publication_doi_na$project_name), sep = ","), "\n") cat("EXCEPTIONS ALLOWED:\n") cat("-(ancientmetagenome-hostassociated): Klapper2023 [reseq. of FellowsYates2023 - no new samples]\n") +cat("-(ancientsinglegenome-hostassociated): Clavel2023 [Reseq of previous human study not in AMDir, different PRJ code]") cat("\n")