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title="Dismiss find">✘</a></nav><nav id="jr-fip-info-p"><a id="jr-fip-prev" class="wsprkl btn" title="Jump to previuos match">◀</a><button id="jr-fip-matches">no matches yet</button><a id="jr-fip-next" class="wsprkl btn" title="Jump to next match">▶</a></nav></nav></div><div id="jr-epub-interstitial" class="hidden"></div><div id="jr-content"><article data-type="main"><p class="vip-notice retraction"><strong>This publication is provided for historical reference only and the information may be out of date.</strong></p><div class="main-content lit-style" itemscope="itemscope" itemtype="http://schema.org/CreativeWork"><div class="meta-content fm-sec"><div class="fm-sec"><h1 id="_NBK569243_"><span class="title" itemprop="name">Searching for Specific Molecule Types</span></h1><p class="fm-aai"><a href="#_NBK569243_pubdet_">Publication Details</a></p><p><em>Estimated reading time: 1 minute</em></p></div></div><div class="body-content whole_rhythm" itemprop="text"><div><h4 id="srch_SpecifMolecule.how_do_i_find_all_of">How do I find all of the human transcriptome (RNA) data in SRA?</h4><blockquote><dl class="temp-labeled-list"><dl class="bkr_refwrap"><dt>1.</dt><dd><p class="no_top_margin">Go to the <a href="/sra" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Entrez SRA</a> page.</p></dd></dl><dl class="bkr_refwrap"><dt>2.</dt><dd><p class="no_top_margin">Enter <span class="bk_pgobj">human AND RNA </span>in the search box at the top of the page.</p></dd></dl><dl class="bkr_refwrap"><dt>3.</dt><dd><p class="no_top_margin">Click the “Search” button.</p></dd></dl><dl class="bkr_refwrap"><dt>4.</dt><dd><p class="no_top_margin">Your search results will be presented as a list of human transcriptome experiments (<a href="/books/n/helpsrakb/srch_Understand_SRA/?report=reader#srch_Understand_SRA.what_do_the_differen">SRX/ERX/DRX</a> accessions) available in the SRA.</p></dd></dl><dl class="bkr_refwrap"><dt>5.</dt><dd><p class="no_top_margin">Click on the SRX record of interest. The record will include</p><dl class="temp-labeled-list"><dl class="bkr_refwrap"><dt>a.</dt><dd><p class="no_top_margin">Links to each run in the experiment</p></dd></dl><dl class="bkr_refwrap"><dt>b.</dt><dd><p class="no_top_margin">Experiment design information (if available)</p></dd></dl><dl class="bkr_refwrap"><dt>c.</dt><dd><p class="no_top_margin">Submission accession and submitter name</p></dd></dl><dl class="bkr_refwrap"><dt>d.</dt><dd><p class="no_top_margin">Study summary and abstract (if available)</p></dd></dl><dl class="bkr_refwrap"><dt>e.</dt><dd><p class="no_top_margin">Experiment sample (SRS) information</p></dd></dl><dl class="bkr_refwrap"><dt>f.</dt><dd><p class="no_top_margin">Links to a list of experiments (SRX)</p></dd></dl><dl class="bkr_refwrap"><dt>g.</dt><dd><p class="no_top_margin">Library information (if available)</p></dd></dl><dl class="bkr_refwrap"><dt>h.</dt><dd><p class="no_top_margin">Platform information</p></dd></dl><dl class="bkr_refwrap"><dt>i.</dt><dd><p class="no_top_margin">Processing information (base calls and quality scores)</p></dd></dl><dl class="bkr_refwrap"><dt>j.</dt><dd><p class="no_top_margin">Spot descriptor information</p></dd></dl><dl class="bkr_refwrap"><dt>k.</dt><dd><p class="no_top_margin">Links to related information</p></dd></dl></dl></dd></dl><dl class="bkr_refwrap"><dt>6.</dt><dd><p class="no_top_margin">At this point, you can do one of the following:</p><dl class="temp-labeled-list"><dl class="bkr_refwrap"><dt>a.</dt><dd><p class="no_top_margin"><b>Click on the “All experiments” link</b> to see a complete list of the experiments included in the study.</p></dd></dl><dl class="bkr_refwrap"><dt>b.</dt><dd><p class="no_top_margin"><b>Download the data for a particular experiment</b> by clicking on the SRA or the SRA-lite download links. These links will take you to the SRA FTP site where the files are available for download. If there are no download links visible for the experiment record, please contact <a href="mailto:dev@null" data-email="vog.hin.mln.ibcn@ars" class="oemail">vog.hin.mln.ibcn@ars</a>.</p></dd></dl><dl class="bkr_refwrap"><dt>c.</dt><dd><p class="no_top_margin"><b>Click on one of the</b>
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<a href="/books/n/helpsrakb/srch_Understand_SRA/?report=reader#srch_Understand_SRA.each_srx_entry_in_th"><b>run links</b></a>
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<b>(</b><a href="/books/n/helpsrakb/srch_Understand_SRA/?report=reader#srch_Understand_SRA.what_do_the_differen">SRR/ERR/DRR</a>
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<b>accessions)</b> to go to the SRA Run Browser, where you can look at individual reads, search the spots for a specific sequence, or download a set of spots from the run.</p></dd></dl></dl></dd></dl></dl><p><b>Note:</b> Search results may not include all studies that used the specified platform or instrument since SRA is a raw data archive (not curated) and can index only those terms that a submitter provides in the metadata of their submission.</p><p><b>Note</b>: If you choose to download files, install the “<a href="http://www.asperasoft.com/download_connect/" ref="pagearea=body&targetsite=external&targetcat=link&targettype=uri">Aspera Connect</a>” plug-in to transfer files at a significantly faster rate than ftp.</p></blockquote></div><div id="bk_toc_contnr"></div></div></div><div class="fm-sec"><h2 id="_NBK569243_pubdet_">Publication Details</h2><h3>Publication History</h3><p class="small">Created: <span itemprop="datePublished">August 22, 2011</span>; Last Update: <span itemprop="dateModified">March 18, 2014</span>.</p><h3>Copyright</h3><div><div class="half_rhythm"><a href="/books/about/copyright/">Copyright Notice</a></div></div><h3>Publisher</h3><p><a href="http://www.ncbi.nlm.nih.gov/" ref="pagearea=page-banner&targetsite=external&targetcat=link&targettype=publisher">National Center for Biotechnology Information (US)</a>, Bethesda (MD)</p><h3>NLM Citation</h3><p>SRA Knowledge Base [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2011-. Searching for Specific Molecule Types. 2011 Aug 22 [Updated 2014 Mar 18].<span class="bk_cite_avail"></span></p></div><div class="small-screen-prev"><a href="/books/n/helpsrakb/srch_SpecifStudType/?report=reader"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 100 100" preserveAspectRatio="none"><path d="M75,30 c-80,60 -80,0 0,60 c-30,-60 -30,0 0,-60"></path><text x="20" y="28" textLength="60" style="font-size:25px">Prev</text></svg></a></div><div class="small-screen-next"><a href="/books/n/helpsrakb/srch_by_platform/?report=reader"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 100 100" preserveAspectRatio="none"><path d="M25,30c80,60 80,0 0,60 c30,-60 30,0 0,-60"></path><text x="20" y="28" textLength="60" style="font-size:25px">Next</text></svg></a></div></article></div><div id="jr-scripts"><script src="/corehtml/pmc/jatsreader/ptpmc_3.22/js/libs.min.js"> </script><script src="/corehtml/pmc/jatsreader/ptpmc_3.22/js/jr.min.js"> </script></div></div>
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