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<div class="pre-content"><div><div class="bk_prnt"><p class="small">NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.</p><p>SRA Knowledge Base [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2011-. </p></div><div class="messagearea bk_noprnt" style="margin-bottom:1.3846em "><ul class="messages"><li class="warn icon"><span class="icon">This publication is provided for historical reference only and the information may be out of date.</span></li></ul></div><div class="bk_prnt"><p style="color:red;"><strong>This publication is provided for historical reference only and the information may be out of date.</strong></p></div><div class="iconblock clearfix whole_rhythm no_top_margin bk_noprnt"><a class="img_link icnblk_img" title="Table of Contents Page" href="/books/n/helpsrakb/"><img class="source-thumb" src="/corehtml/pmc/pmcgifs/bookshelf/thumbs/th-helpsrakb-lrg.png" alt="Cover of SRA Knowledge Base" height="100px" width="80px" /></a><div class="icnblk_cntnt eight_col"><h2>SRA Knowledge Base [Internet].</h2><a data-jig="ncbitoggler" href="#__NBK569243_dtls__">Show details</a><div style="display:none" class="ui-widget" id="__NBK569243_dtls__"><div>Bethesda (MD): <a href="https://www.ncbi.nlm.nih.gov/" ref="pagearea=page-banner&targetsite=external&targetcat=link&targettype=publisher">National Center for Biotechnology Information (US)</a>; 2011-.</div></div><div class="half_rhythm"><ul class="inline_list"><li style="margin-right:1em"><a class="bk_cntns" href="/books/n/helpsrakb/">Contents</a></li></ul></div></div><div class="icnblk_cntnt two_col"><div class="pagination bk_noprnt"><a class="active page_link prev" href="/books/n/helpsrakb/srch_SpecifStudType/" title="Previous page in this title">< Prev</a><a class="active page_link next" href="/books/n/helpsrakb/srch_by_platform/" title="Next page in this title">Next ></a></div></div></div></div></div>
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<div class="main-content lit-style" itemscope="itemscope" itemtype="http://schema.org/CreativeWork"><div class="meta-content fm-sec"><h1 id="_NBK569243_"><span class="title" itemprop="name">Searching for Specific Molecule Types</span></h1><p class="small">Created: <span itemprop="datePublished">August 22, 2011</span>; Last Update: <span itemprop="dateModified">March 18, 2014</span>.</p><p><em>Estimated reading time: 1 minute</em></p></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"><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><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><dt>3.</dt><dd><p class="no_top_margin">Click the “Search” button.</p></dd><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/#srch_Understand_SRA.what_do_the_differen">SRX/ERX/DRX</a> accessions) available in the SRA.</p></dd><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"><dt>a.</dt><dd><p class="no_top_margin">Links to each run in the experiment</p></dd><dt>b.</dt><dd><p class="no_top_margin">Experiment design information (if available)</p></dd><dt>c.</dt><dd><p class="no_top_margin">Submission accession and submitter name</p></dd><dt>d.</dt><dd><p class="no_top_margin">Study summary and abstract (if available)</p></dd><dt>e.</dt><dd><p class="no_top_margin">Experiment sample (SRS) information</p></dd><dt>f.</dt><dd><p class="no_top_margin">Links to a list of experiments (SRX)</p></dd><dt>g.</dt><dd><p class="no_top_margin">Library information (if available)</p></dd><dt>h.</dt><dd><p class="no_top_margin">Platform information</p></dd><dt>i.</dt><dd><p class="no_top_margin">Processing information (base calls and quality scores)</p></dd><dt>j.</dt><dd><p class="no_top_margin">Spot descriptor information</p></dd><dt>k.</dt><dd><p class="no_top_margin">Links to related information</p></dd></dl></dd><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"><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><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><dt>c.</dt><dd><p class="no_top_margin"><b>Click on one of the</b>
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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></dd></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>
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