{"id":113,"date":"2016-08-22T21:54:32","date_gmt":"2016-08-22T20:54:32","guid":{"rendered":"http:\/\/wp.cs.ucl.ac.uk\/outbredmice\/?page_id=113"},"modified":"2016-08-22T21:54:32","modified_gmt":"2016-08-22T20:54:32","slug":"heterogeneous-stock-mice","status":"publish","type":"page","link":"https:\/\/wp.cs.ucl.ac.uk\/outbredmice\/heterogeneous-stock-mice\/","title":{"rendered":"Heterogeneous Stock Mice"},"content":{"rendered":"<p>This page contains data resources relating to the population of 2000 heterogeneous stock (HS) mice phenotyped for over 100 traits, and used in the papers:<\/p>\n<p><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/16832355\">Genome-wide genetic association of complex traits in heterogeneous stock mice.\u00a0<em>Nat Genet<\/em>\u00a0<span class=\"highlight\">2006<\/span>\u00a0<strong>38(8):<\/strong>879-87<\/a><\/p>\n<p class=\"title\"><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/16888333\">Genetic and environmental effects on complex traits in mice. <em><span class=\"jrnl\" title=\"Genetics\">Genetics<\/span><\/em>.<em>\u00a0<\/em>2006<em>\u00a0<\/em>174(2):959-84.<\/a><\/p>\n<p class=\"title\"><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/16465593\">A protocol for high-throughput phenotyping, suitable for quantitative trait analysis in mice. <em><span class=\"jrnl\" title=\"Mammalian genome : official journal of the International Mammalian Genome Society\">Mamm Genome<\/span><\/em>.\u00a02006\u00a0<strong>17(2)<\/strong>:129-46.<\/a><\/p>\n<div class=\"supp\">\n<p class=\"title\">In addition we provide gene expression data from hippocampus, liver and lung measured on subsets of these mice and published in<\/p>\n<p class=\"title\"><a href=\"http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/19376938\">High resolution mapping of expression QTLs in heterogeneous stock mice in multiple tissues. <em><span class=\"jrnl\" title=\"Genome research\">Genome Res<\/span><\/em>.\u00a02009 <strong>19(6)<\/strong>:1133-40.<\/a><\/p>\n<div class=\"supp\">The data have been also used in a number of other studies.<\/div>\n<div class=\"supp\"><\/div>\n<\/div>\n<p>These data were previously available from the defunct web site mus.well.ox.ac.uk\/GSCAN.<\/p>\n<h2>Genotypes<\/h2>\n<ul>\n<li>The dataset we recommend for analysis comprises 10168 SNP genotypes mapped to build 37 of the mouse genome. The data are in this <a href=\"http:\/\/mtweb.cs.ucl.ac.uk\/HSMICE\/GENOTYPES\/\" target=\"_blank\">directory<\/a>\u00a0and are arranged by chromosome.<\/li>\n<li>Each chromosome is represented by two\u00a0files formatted for use by the R HAPPY package.<\/li>\n<li>Files are named as\u00a0chrN.Build37.data,\u00a0chrN.Build37.alleles where N is the chromosome number (1..19, X).<\/li>\n<li>.data files are in ped-format. and contain the SNP genotypes.<\/li>\n<li>.alleles files are in HAPPY alleles format and contain the genotypes of the eight founder strains of the HS at these SNPs.<\/li>\n<li>Missing data\u00a0are coded as NA.<\/li>\n<li>The file\u00a0<a href=\"http:\/\/mtweb.cs.ucl.ac.uk\/HSMICE\/GENOTYPES\/mapfile.txt\">mapfile.txt<\/a> contains the bp coordinates of these SNPs relative to build37.<\/li>\n<\/ul>\n<h2>Phenotypes<\/h2>\n<ul>\n<li>The raw phenotypes, together with relevant covariates, are in this <a href=\"http:\/\/mtweb.cs.ucl.ac.uk\/HSMICE\/PHENOTYPES\/\">directory<\/a>, as a collection of tab-delimited text files. These files, for example Glucose.txt, contain related phenotypes (in this case measurements related to the Glucose Tolernace Test) together with\u00a0covariates relevant to\u00a0these phenotypes (ie sigbificantly associated at P&lt;0.05). The phenotypes are combined in the file <a href=\"http:\/\/mtweb.cs.ucl.ac.uk\/HSMICE\/PHENOTYPES\/CombinedPhenotypes.txt\">CombinedPhenotypes.txt<\/a>.<\/li>\n<li>Residual phenotypes corrected for relevant covariates are in this <a href=\"http:\/\/mtweb.cs.ucl.ac.uk\/HSMICE\/PHENOTYPES\/RESIDUALS\/\">directory<\/a>. We recommend using these for analysis. Each trait is in a separate file with extension .resid<\/li>\n<\/ul>\n<h2>Gene Expression Data<\/h2>\n<p>This <a href=\"http:\/\/mtweb.cs.ucl.ac.uk\/HS\/EXPRESSION\/\">directory<\/a> contains transformed gene expression data for hippocampus, liver and lung. Each is held as an RData matrix. Rows are mice and columns are expression traits. Note that each expression trait has been transformed by a Box-Cox transformation.<\/p>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>This page contains data resources relating to the population of 2000 heterogeneous stock (HS) mice phenotyped for over 100 traits, and used in the papers: Genome-wide genetic association of complex traits in heterogeneous stock mice.\u00a0Nat Genet\u00a02006\u00a038(8):879-87 Genetic and environmental effects on complex traits in mice. Genetics.\u00a02006\u00a0174(2):959-84. A protocol for high-throughput phenotyping, suitable for quantitative trait &hellip; <a href=\"https:\/\/wp.cs.ucl.ac.uk\/outbredmice\/heterogeneous-stock-mice\/\" class=\"more-link\">Continue reading<span class=\"screen-reader-text\"> &#8220;Heterogeneous Stock Mice&#8221;<\/span><\/a><\/p>\n","protected":false},"author":101,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":[],"_links":{"self":[{"href":"https:\/\/wp.cs.ucl.ac.uk\/outbredmice\/wp-json\/wp\/v2\/pages\/113"}],"collection":[{"href":"https:\/\/wp.cs.ucl.ac.uk\/outbredmice\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/wp.cs.ucl.ac.uk\/outbredmice\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/wp.cs.ucl.ac.uk\/outbredmice\/wp-json\/wp\/v2\/users\/101"}],"replies":[{"embeddable":true,"href":"https:\/\/wp.cs.ucl.ac.uk\/outbredmice\/wp-json\/wp\/v2\/comments?post=113"}],"version-history":[{"count":0,"href":"https:\/\/wp.cs.ucl.ac.uk\/outbredmice\/wp-json\/wp\/v2\/pages\/113\/revisions"}],"wp:attachment":[{"href":"https:\/\/wp.cs.ucl.ac.uk\/outbredmice\/wp-json\/wp\/v2\/media?parent=113"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}