388 lines
13 KiB
XML
388 lines
13 KiB
XML
<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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<head>
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<title>NIH Roadmap Epigenomics - GEO - NCBI</title>
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<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
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<meta name="author" content="geo" />
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<meta name="keywords" content="NCBI, national institutes of health, nih, database, archive, central, bioinformatics, biomedicine, geo, gene, expression, omnibus, chips, microarrays, oligonucleotide, array, sage, CGH" />
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<meta name="description" content="Gene Expression Omnibus (GEO) is a database repository of high throughput gene expression data and hybridization arrays, chips, microarrays." />
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<meta name="ncbi_app" content="geo" />
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<meta name="ncbi_pdid" content="epigenomics" />
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<link rel="shortcut icon" href="/geo/img/OmixIconBare.ico" />
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<link rel="stylesheet" type="text/css" href="/geo/css/reset.css" />
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<link rel="stylesheet" type="text/css" href="/geo/css/standard_base_css.css" />
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<link rel="stylesheet" type="text/css" href="/geo/css/nav.css" />
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<link rel="stylesheet" type="text/css" href="epi.css" />
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<script type="text/javascript" src="/core/jig/1.15.10/js/jig.min.js"></script>
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<script type="text/javascript" src="epi.js"></script>
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<script type="text/javascript" src="/geo/js/jquery.transform-0.9.3.min.js"></script>
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<script type="text/javascript" src="/geo/js/dd_menu.js"></script>
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</head>
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<body class="epigenomics tab" id="studies">
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<div id="all">
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<div id="page">
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<div id="header">
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<div id="ncbi_logo">
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<a href="/">
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<img src="/geo/img/ncbi_logo.gif" alt="NCBI Logo" />
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</a>
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</div>
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<div id="geo_logo">
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<a href="/geo/"><img src="/geo/img/geo_main.gif" alt="GEO Logo" /></a>
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</div>
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</div>
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<div id="nav_bar">
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<ul id="geo_nav_bar">
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<li><a href="#">GEO Publications</a>
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<ul class="sublist">
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<li><a href="/geo/info/GEOHandoutFinal.pdf">Handout</a></li>
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<li><a href="/pmc/articles/PMC10767856/">NAR 2024 (latest)</a></li>
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<li><a href="/pmc/articles/PMC99122/">NAR 2002 (original)</a></li>
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<li><a href="/pmc/?term=10767856,4944384,3531084,3341798,3013736,2686538,2270403,1669752,1619900,1619899,539976,99122">All publications</a></li>
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</ul>
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</li>
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<li><a href="/geo/info/faq.html">FAQ</a></li>
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<li><a href="/geo/info/MIAME.html" title="Minimum Information About a Microarray Experiment">MIAME</a></li>
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<li><a href="mailto:geo@ncbi.nlm.nih.gov">Email GEO</a></li>
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</ul>
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</div>
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<div id="crumbs_login_bar"><a title="NCBI home page" href="/">NCBI</a> »
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<a id="curr_page" title="GEO home page" href="/geo/">GEO</a> »
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<a href="/geo/roadmap/epigenomics/">NIH Roadmap Epigenomics</a><span id="login_status"><a href="/geo/submitter" title="Click here to login.">Login</a></span></div>
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<div id="content">
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<div id="intro">
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<h1>NIH Roadmap Epigenomics Project Data Listings</h1>
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<div class="left-col">
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<p>
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This page summarizes <a href="http://www.roadmapepigenomics.org/">Roadmap Epigenomics</a> project
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data that are available through the GEO repository. Additional data will be added as it becomes available.
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</p>
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<p class="highlight">
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For data usage terms and conditions, please refer to <br /><a href="http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies">
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Epigenomics Data Access Policies
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</a></p>
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</div>
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<div class="right-col">
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<div id="more-info">
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<p>
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More information and resources are available:
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</p>
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<ul>
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<li>
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<a href="http://www.roadmapepigenomics.org">Roadmap Epigenomics Homepage</a>
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</li>
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<li>
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<a href="http://www.epigenomebrowser.org">Epigenome Browser</a>
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</li>
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<li>
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<a href="http://www.genboree.org/epigenomeatlas/index.rhtml">Epigenome Atlas</a>
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</li>
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</ul>
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<p>
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<a href="ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/roadmapepigenomics/">FTP download</a>
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</p>
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<p>
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<a href="#" id="using_page">How to use this page</a>
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</p>
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</div>
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</div>
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<div id="usage-dialog" title="Using this page" style="display: none;">
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<h4>The Samples tab includes:</h4>
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<ul>
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<li>
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<span class="list_text">
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A complete listing of each sample and experiment.
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</span>
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</li>
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<li>
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<span class="list_text">
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View tracks button to display selected tracks on NCBI Sequence Viewer or UCSC Genome Browser. Use check boxes to select which tracks to view.
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</span>
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</li>
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<li>
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<span class="list_text">
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Search box to filter the sample table.
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</span>
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</li>
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<li>
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<span class="list_text">
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Export button to export sample table.
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</span>
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</li>
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<li>
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<span class="list_text">
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Download links for individual <a style="color: #336699" href="/geo/info/faq.html#seq">sra</a>, bam and wig files.
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</span>
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</li>
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<li>
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<span class="list_text">
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Links to the original GEO records which contain a complete description of the sample and experiment parameters.
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</span>
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</li>
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</ul>
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<h4>The Studies tab includes:</h4>
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<ul>
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<li>
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<span class="list_text">
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An overview of each study.
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</span>
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</li>
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<li>
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<span class="list_text">
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Batch download links for <a style="color: #336699" href="/geo/info/faq.html#seq">sra</a>, bam and wig files in a study. Alternatively, use the <a style="color: #336699" href="ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/roadmapepigenomics/">FTP download link</a> for more customized batch downloads.
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</span>
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</li>
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<li>
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<span class="list_text">
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Links to original GEO and SRA records.
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</span>
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</li>
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<li>
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<span class="list_text">
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Links to corresponding samples in the Samples tab.
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</span>
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</li>
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</ul>
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<h4>The Matrix tab includes:</h4>
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<ul>
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<li>
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<span class="list_text">
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A matrix that depicts samples (rows) and experiments (columns), and the number of assays available for each.
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</span>
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</li>
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<li>
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<span class="list_text">
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View tracks button to display selected tracks on NCBI Sequence Viewer or UCSC Genome Browser. Use check boxes to select which tracks to view. Click the box next to the sample or experiment name to select all boxes in row or column.
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</span>
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</li>
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<li>
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<span class="list_text">
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Filter by Center menu.
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</span>
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</li>
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<li>
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<span class="list_text">
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Links to corresponding samples in the Samples tab - click the sample or experiment name, or the number in each cell.
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</span>
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</li>
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</ul>
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</div>
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<div id="export-dialog" title="Export options" style="display: none;">
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<form method="post" action="#">
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<fieldset class="amount">
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<legend>Amount</legend>
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<ul>
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<li>
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<input id="this_page" type="radio" checked="checked" value="this_page" name="amount" />
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<label for="this_page">This page</label>
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</li>
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<li>
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<input id="all_results" type="radio" value="all_results" name="amount" />
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<label for="all_results">All search results</label>
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</li>
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</ul>
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</fieldset>
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<fieldset class="format">
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<legend>Format</legend>
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<ul>
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<li>
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<input id="csv" type="radio" checked="checked" value="csv" name="format" />
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<label for="csv">CSV</label>
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</li>
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<li>
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<input id="tsv" type="radio" value="tsv" name="format" />
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<label for="tsv">Tab</label>
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</li>
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</ul>
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</fieldset>
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<input title="Download text file" class="button" id="exp_dial_btn" value="Export" />
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</form>
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</div>
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</div>
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<table id="tabs_table">
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<tr>
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<td class="title">
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<a href="?view=samples">Samples</a>
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</td>
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<td class="title" id="active_tab">
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<a href="?view=studies">Studies</a>
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</td>
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<td class="title">
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<a href="?view=matrix">Matrix</a>
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</td>
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</tr>
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</table>
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<div id="studies_data" class="notoggle">
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<div class="toolbar">
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<div class="tabfile">
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<button id="export_btn_st" class="button">Export</button>
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</div>
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</div>
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<table id="epigen_studies">
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<thead>
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<tr>
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<th class="geo_acc_col">GEO Accession</th>
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<th>Title</th>
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<th class="sra_acc_col">SRA accession</th>
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<th>Batch download</th>
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<th>Samples</th>
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</tr>
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</thead>
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<tbody>
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<tr>
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<td>
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<a href="/geo/query/acc.cgi?acc=GSE16256">GSE16256</a>
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</td>
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<td>UCSD Human Reference Epigenome Mapping Project</td>
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<td>
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<a href="/sra?term=SRP000941">SRP000941</a>
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</td>
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<td>
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<a href="https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA34535">sra</a>
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<a href="https://ftp.ncbi.nlm.nih.gov/geo/series/GSE16nnn/GSE16256/suppl/">bam,bed,wig</a>
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</td>
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<td>
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<a title="View in Samples tab" href="?search=GSE16256">878</a>
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</td>
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</tr>
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<tr>
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<td>
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<a href="/geo/query/acc.cgi?acc=GSE16368">GSE16368</a>
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</td>
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<td>UCSF-UBC Human Reference Epigenome Mapping Project</td>
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<td>
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<a href="/sra?term=SRP046944">SRP046944</a>
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</td>
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<td>
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<a href="https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA34535">sra</a>
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<a href="https://ftp.ncbi.nlm.nih.gov/geo/series/GSE16nnn/GSE16368/suppl/">bam,bed,tab,wig</a>
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</td>
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<td>
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<a title="View in Samples tab" href="?search=GSE16368">529</a>
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</td>
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</tr>
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<tr>
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<td>
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<a href="/geo/query/acc.cgi?acc=GSE17312">GSE17312</a>
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</td>
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<td>BI Human Reference Epigenome Mapping Project</td>
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<td>
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<a href="/sra?term=SRP000996">SRP000996</a>
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</td>
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<td>
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<a href="https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA34535">sra</a>
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<a href="https://ftp.ncbi.nlm.nih.gov/geo/series/GSE17nnn/GSE17312/suppl/">bam,bed,cel,wig</a>
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</td>
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<td>
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<a title="View in Samples tab" href="?search=GSE17312">633</a>
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</td>
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</tr>
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<tr>
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<td>
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<a href="/geo/query/acc.cgi?acc=GSE18927">GSE18927</a>
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</td>
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<td>University of Washington Human Reference Epigenome Mapping Project</td>
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<td>
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<a href="/sra?term=SRP001371">SRP001371</a>
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</td>
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<td>
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<a href="https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA34535">sra</a>
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<a href="https://ftp.ncbi.nlm.nih.gov/geo/series/GSE18nnn/GSE18927/suppl/">bam,bed,cel,txt,wig</a>
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</td>
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<td>
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<a title="View in Samples tab" href="?search=GSE18927">758</a>
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</td>
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</tr>
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<tr>
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<td>
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<a href="/geo/query/acc.cgi?acc=GSE19465">GSE19465</a>
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</td>
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<td>BI Human Reference Epigenome Mapping Project: ChIP-Seq in human subject</td>
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<td>
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<a href="/sra?term=SRP001534">SRP001534</a>
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</td>
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<td>
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<a href="https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA34535">sra</a>
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<a href="https://ftp.ncbi.nlm.nih.gov/geo/series/GSE19nnn/GSE19465/suppl/">bed,wig</a>
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</td>
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<td>
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<a title="View in Samples tab" href="?search=GSE19465">358</a>
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</td>
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</tr>
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<tr>
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<td>
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<a href="/geo/query/acc.cgi?acc=GSE25246">GSE25246</a>
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</td>
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<td>BI Human Reference Epigenome Mapping Project: Characterization of DNA methylation by RRBS</td>
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<td>
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<a href="/sra?term=SRP004506">SRP004506</a>
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</td>
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<td>
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<a href="https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA34535">sra</a>
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<a href="https://ftp.ncbi.nlm.nih.gov/geo/series/GSE25nnn/GSE25246/suppl/">wig</a>
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</td>
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<td>
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<a title="View in Samples tab" href="?search=GSE25246">10</a>
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</td>
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</tr>
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<tr>
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<td>
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<a href="/geo/query/acc.cgi?acc=GSE25247">GSE25247</a>
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</td>
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<td>BI Human Reference Epigenome Mapping Project: Characterization of DNA methylation by RRBS in human subject</td>
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<td>
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<a href="/sra?term=SRP004244">SRP004244</a>
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</td>
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<td>
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<a href="https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA34535">sra</a>
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<a href="https://ftp.ncbi.nlm.nih.gov/geo/series/GSE25nnn/GSE25247/suppl/">wig</a>
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</td>
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<td>
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<a title="View in Samples tab" href="?search=GSE25247">55</a>
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</td>
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</tr>
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<tr>
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<td>
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<a href="/geo/query/acc.cgi?acc=GSE25248">GSE25248</a>
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</td>
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<td>BI Human Reference Epigenome Mapping Project: Characterization of DNA methylation by RRBS in HUES lines</td>
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<td>
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<a href="/sra?term=SRP004245">SRP004245</a>
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</td>
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<td>
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<a href="https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA34535">sra</a>
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<a href="https://ftp.ncbi.nlm.nih.gov/geo/series/GSE25nnn/GSE25248/suppl/">wig</a>
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</td>
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<td>
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<a title="View in Samples tab" href="?search=GSE25248">11</a>
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</td>
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</tr>
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<tr>
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<td>
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<a href="/geo/query/acc.cgi?acc=GSE25249">GSE25249</a>
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</td>
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<td>BI Human Reference Epigenome Mapping Project: Characterization of chromatin modification by ChIP-Seq in human subject</td>
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<td></td>
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<td>
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<a href="https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA34535">sra</a>
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<a href="https://ftp.ncbi.nlm.nih.gov/geo/series/GSE25nnn/GSE25249/suppl/">bed,wig</a>
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</td>
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<td>
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<a title="View in Samples tab" href="?search=GSE25249">24</a>
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</td>
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</tr>
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</tbody>
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</table>
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</div>
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</div>
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</div>
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<div id="footer">
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<span class="helpbar">|<a href="https://www.nlm.nih.gov"> NLM </a>|<a href="https://www.nih.gov"> NIH </a>|<a href="mailto:geo@ncbi.nlm.nih.gov"> Email GEO </a>|<a href="/geo/info/disclaimer.html"> Disclaimer </a>|<a href="https://www.nlm.nih.gov/accessibility.html"> Accessibility </a>|<a href="https://www.hhs.gov/vulnerability-disclosure-policy/index.html"> HHS Vulnerability Disclosure </a>|
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</span>
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</div>
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</div>
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<script type="text/javascript" src="/portal/portal3rc.fcgi/rlib/js/InstrumentOmnitureBaseJS/InstrumentNCBIBaseJS/InstrumentPageStarterJS.js"></script>
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