{"id":64,"date":"2015-10-09T14:11:52","date_gmt":"2015-10-09T13:41:52","guid":{"rendered":"http:\/\/jakobssonlab.iob.uu.se\/?page_id=64"},"modified":"2025-02-10T13:01:29","modified_gmt":"2025-02-10T12:01:29","slug":"data","status":"publish","type":"page","link":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/data\/","title":{"rendered":"Data"},"content":{"rendered":"\n<h1 class=\"wp-block-heading is-style-underlined-heading\">Data<\/h1>\n\n\n\n<p>Data can only be used for academic research purposes. Commercial use of the data is not allowed under our ethics and population representative council clearances.<\/p>\n\n\n\n<div class=\"wp-block-group is-layout-grid wp-container-core-group-is-layout-965512f0 wp-block-group-is-layout-grid\" style=\"padding-right:0;padding-left:0\">\n<div class=\"wp-block-group has-white-color has-dark-background-background-color has-text-color has-background has-link-color wp-elements-fe0ab8f1269613399689b81f56e1b855 is-layout-constrained wp-container-core-group-is-layout-4383d167 wp-block-group-is-layout-constrained\">\n<h2 class=\"wp-block-heading\">Hedenstierna-Jonsen et al. 2017<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li>The sequencing data (.bam) used in our study: &#8220;A female warrior confirmed by genomics&#8221;, is available at the <a href=\"https:\/\/www.ebi.ac.uk\/ena\" target=\"_blank\" rel=\"noopener\">European Nucleotide Archive <\/a>with the accession number: <strong>PRJEB22507.<\/strong><\/li>\n<\/ul>\n<\/div>\n\n\n\n<div class=\"wp-block-group has-white-background-color has-background is-layout-flow wp-block-group-is-layout-flow\">\n<h2 class=\"wp-block-heading\">Hollfelder et al. 2017<\/h2>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Data used in <a href=\"https:\/\/doi.org\/10.1371\/journal.pgen.1006976\" target=\"_blank\" rel=\"noreferrer noopener\">Hollfelder et al. 2017. Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations<\/a>.<\/li>\n<\/ul>\n\n\n\n<p><em>Plink<\/em> data files of 243 individuals of 18 Sudanese and South Sudanese populations. Data was genotyped on a Illumina HumanOmni 5M Exome SNP array and the file consist of&nbsp;unfiltered data with&nbsp;related individuals still being&nbsp;included.<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/jakobssonlab.iob.uu.se\/data_Jakobssonlab\/Hollfelder_etal_PLOSGEN.tar.gz\">Sudan.tar.gz (150MB)<\/a><\/li>\n<\/ul>\n<\/div>\n\n\n\n<div class=\"wp-block-group has-white-background-color has-background is-layout-constrained wp-container-core-group-is-layout-ef724a49 wp-block-group-is-layout-constrained\" style=\"padding-top:var(--wp--preset--spacing--20);padding-right:var(--wp--preset--spacing--30);padding-bottom:var(--wp--preset--spacing--20);padding-left:var(--wp--preset--spacing--30)\">\n<h2 class=\"wp-block-heading\">Schlebusch et al. 2016<\/h2>\n\n\n\n<p>Data used in Schlebusch et al. (2016): &#8220;The disappearing San of Southeastern Africa and their genetic affinities&#8221;. <em><strong>Human Genetics<\/strong>&nbsp;<\/em>135: 1365-1373.<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/jakobssonlab.iob.uu.se\/data_Jakobssonlab\/Schlebusch_etal_HUMGEN_2016\/all_CHR-KZU.unfiltered.tfam\">all_CHR-KZU.unfiltered.tfam<\/a><\/li>\n<\/ul>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/jakobssonlab.iob.uu.se\/data_Jakobssonlab\/Schlebusch_etal_HUMGEN_2016\/all_CHR-KZU.unfiltered.tped.gz\">all_CHR-KZU.unfiltered.tped.gz (27,6MB)<\/a><\/li>\n<\/ul>\n<\/div>\n\n\n\n<div class=\"wp-block-group has-white-color has-dark-background-background-color has-text-color has-background has-link-color wp-elements-65b12459aaf32359813a458e935f08cb is-layout-constrained wp-container-core-group-is-layout-4383d167 wp-block-group-is-layout-constrained\">\n<h2 class=\"wp-block-heading\">Skoglund et al. 2014<\/h2>\n\n\n\n<p>BAM files generated for <a href=\"https:\/\/doi.org\/10.1126\/science.1253448\" target=\"_blank\" rel=\"noreferrer noopener\">Skoglund et al. (2014): &#8220;Genomic Diversity and Admixture Differs for Stone-Age Scandinavian Foragers and Farmers&#8221;. <strong><em>Science&nbsp;<\/em><\/strong>344: 747-750<\/a>.<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Raw data are available from the European Nucleotide Archive under accession no. <strong>PRJEB6090<\/strong>.<\/li>\n<\/ul>\n\n\n\n<ul class=\"wp-block-list\">\n<li>The processed data can be downloaded from the <a href=\"https:\/\/export.uppmax.uu.se\/sllstore2017020\/neolithic2\" target=\"_blank\" rel=\"noreferrer noopener\">UPPMAX<\/a><\/li>\n<\/ul>\n\n\n\n<p>For more information on the processed sequence data, please contact:&nbsp;<a href=\"mailto:pontus.skoglund@gmail.com\">Pontus Skoglund<\/a> or <a href=\"mailto:torsten.guenther-AT-ebc.uu.se\">Torsten<\/a><a href=\"mailto:torsten.guenther@ebc.uu.se\"> <\/a><a href=\"mailto:torsten.guenther-AT-ebc.uu.se\">G\u00fcnther<\/a><\/p>\n<\/div>\n\n\n\n<div class=\"wp-block-group has-white-color has-dark-background-background-color has-text-color has-background has-link-color wp-elements-40ab76f65765c7940a0f3d4cc0a546b4 is-layout-constrained wp-container-core-group-is-layout-4383d167 wp-block-group-is-layout-constrained\">\n<h2 class=\"wp-block-heading\">Skoglund et al. 2012<\/h2>\n\n\n\n<p><a href=\"https:\/\/doi.org\/10.1126\/science.1216304\" target=\"_blank\" rel=\"noreferrer noopener\">Skoglund et al. (2012): &#8220;Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe&#8221;. <strong><em>Science<\/em><\/strong>, 336: 466-469<\/a>.<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/jakobssonlab.iob.uu.se\/data_Jakobssonlab\/Skoglund_etal_SCIENCE_2012\/README.txt\">README<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/jakobssonlab.iob.uu.se\/data_Jakobssonlab\/Skoglund_etal_SCIENCE_2012\/SkoglundEtAlData_animals.tar.gz\">SkoglundEtAlData_animals.tar.gz<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/jakobssonlab.iob.uu.se\/data_Jakobssonlab\/Skoglund_etal_SCIENCE_2012\/SkoglundEtAlData_Ajv52.tar.gz\">SkoglundEtAlData_Ajv52.tar.gz<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/jakobssonlab.iob.uu.se\/data_Jakobssonlab\/Skoglund_etal_SCIENCE_2012\/SkoglundEtAlData_Ajv70.tar.gz\">SkoglundEtAlData_Ajv70.tar.gz<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/jakobssonlab.iob.uu.se\/data_Jakobssonlab\/Skoglund_etal_SCIENCE_2012\/SkoglundEtAlData_Ire8.tar.gz\">SkoglundEtAlData_Ire8.tar.gz<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/jakobssonlab.iob.uu.se\/data_Jakobssonlab\/Skoglund_etal_SCIENCE_2012\/SkoglundEtAlData_Gok4.tar.gz\">SkoglundEtAlData_Gok4.tar.gz<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/jakobssonlab.iob.uu.se\/data_Jakobssonlab\/Skoglund_etal_SCIENCE_2012\/SkoglundEtAlData_Ste7.tar.gz\">SkoglundEtAlData_Ste7.tar.gz<\/a><\/li>\n<\/ul>\n<\/div>\n\n\n\n<div class=\"wp-block-group has-white-background-color has-background is-layout-constrained wp-container-core-group-is-layout-4383d167 wp-block-group-is-layout-constrained\">\n<h2 class=\"wp-block-heading\">Schlebusch et al. 2012<\/h2>\n\n\n\n<p><a href=\"https:\/\/doi.org\/10.1126\/science.1227721\" target=\"_blank\" rel=\"noreferrer noopener\">Schlebusch*, Skoglund*&nbsp;et al. (2012): &#8220;Genomic variation in seven Khoe-San groups reveals adaptation and complex African history&#8221;.&nbsp;<strong><em>Science<\/em><\/strong>&nbsp;338: 374-379<\/a>.<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/jakobssonlab.iob.uu.se\/data_Jakobssonlab\/Schlebusch_etal_SCIENCE_2012\/README.txt\">README<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/jakobssonlab.iob.uu.se\/data_Jakobssonlab\/Schlebusch_etal_SCIENCE_2012\/Schlebusch_etal_Science2012_autosomal_phased.tfam\">Schlebusch_etal_Science2012_autosomal_phased.tfam<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/jakobssonlab.iob.uu.se\/data_Jakobssonlab\/Schlebusch_etal_SCIENCE_2012\/Schlebusch_etal_Science2012_autosomal_phased.tped.tar.gz\">Schlebusch_etal_Science2012_autosomal_phased.tped.tar.gz<\/a> (146MB)<\/li>\n\n\n\n<li><a href=\"https:\/\/jakobssonlab.iob.uu.se\/data_Jakobssonlab\/Schlebusch_etal_SCIENCE_2012\/Schlebusch_etal_Science2012_autosomal_unphased.tfam\">Schlebusch_etal_Science2012_autosomal_unphased.tfam<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/jakobssonlab.iob.uu.se\/data_Jakobssonlab\/Schlebusch_etal_SCIENCE_2012\/Schlebusch_etal_Science2012_autosomal_unphased.tped.tar.gz\">Schlebusch_etal_Science2012_autosomal_unphased.tped.tar.gz<\/a> (150MB)<\/li>\n\n\n\n<li><a href=\"https:\/\/jakobssonlab.iob.uu.se\/data_Jakobssonlab\/Schlebusch_etal_SCIENCE_2012\/Schlebusch_etal_Science2012_mito.tfam\">Schlebusch_etal_Science2012_mito.tfam<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/jakobssonlab.iob.uu.se\/data_Jakobssonlab\/Schlebusch_etal_SCIENCE_2012\/Schlebusch_etal_Science2012_mito.tped.tar.gz\">Schlebusch_etal_Science2012_mito.tped.tar.gz<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/jakobssonlab.iob.uu.se\/data_Jakobssonlab\/Schlebusch_etal_SCIENCE_2012\/Schlebusch_etal_Science2012_ychr.tfam\">Schlebusch_etal_Science2012_ychr.tfam<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/jakobssonlab.iob.uu.se\/data_Jakobssonlab\/Schlebusch_etal_SCIENCE_2012\/Schlebusch_etal_Science2012_ychr.tped.tar.gz\">Schlebusch_etal_Science2012_ychr.tped.tar.gz<\/a><\/li>\n\n\n\n<li><a href=\"https:\/\/jakobssonlab.iob.uu.se\/data_Jakobssonlab\/Schlebusch_etal_SCIENCE_2012\/Schlebusch_etal_Science2012_listadmixed_rem.txt\">Schlebusch_etal_Science2012_listadmixed_rem.txt<\/a><\/li>\n<\/ul>\n<\/div>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Data Data can only be used for academic research purposes. Commercial use of the data is not allowed under our [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":2,"comment_status":"closed","ping_status":"closed","template":"page-no-title","meta":{"footnotes":""},"class_list":["post-64","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/pages\/64","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/comments?post=64"}],"version-history":[{"count":2,"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/pages\/64\/revisions"}],"predecessor-version":[{"id":2679,"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/pages\/64\/revisions\/2679"}],"wp:attachment":[{"href":"https:\/\/jakobssonlab.iob.uu.se\/index.php\/wp-json\/wp\/v2\/media?parent=64"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}