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<div class="search"><form method="get" action="/sra/"><div class="search_form"><label for="database" class="offscreen_noflow">Search database</label><select id="database"><optgroup label="Recent"><option value="sra" selected="selected">SRA</option><option value="nuccore">Nucleotide</option><option value="books">Books</option><option value="pubmed" class="last">PubMed</option></optgroup><optgroup label="All"><option value="gquery">All Databases</option><option value="assembly">Assembly</option><option value="biocollections">Biocollections</option><option value="bioproject">BioProject</option><option value="biosample">BioSample</option><option value="books">Books</option><option value="clinvar">ClinVar</option><option value="cdd">Conserved Domains</option><option value="gap">dbGaP</option><option value="dbvar">dbVar</option><option value="gene">Gene</option><option value="genome">Genome</option><option value="gds">GEO DataSets</option><option value="geoprofiles">GEO Profiles</option><option value="gtr">GTR</option><option value="ipg">Identical Protein Groups</option><option value="medgen">MedGen</option><option value="mesh">MeSH</option><option value="nlmcatalog">NLM Catalog</option><option value="nuccore">Nucleotide</option><option value="omim">OMIM</option><option value="pmc">PMC</option><option value="protein">Protein</option><option value="proteinclusters">Protein Clusters</option><option value="protfam">Protein Family Models</option><option value="pcassay">PubChem BioAssay</option><option value="pccompound">PubChem Compound</option><option value="pcsubstance">PubChem Substance</option><option value="pubmed">PubMed</option><option value="snp">SNP</option><option value="sra">SRA</option><option value="structure">Structure</option><option value="taxonomy">Taxonomy</option><option value="toolkit">ToolKit</option><option value="toolkitall">ToolKitAll</option><option value="toolkitbookgh">ToolKitBookgh</option></optgroup></select><div class="nowrap"><label for="term" class="offscreen_noflow" accesskey="/">Search term</label><div class="nowrap"><input type="text" name="term" id="term" title="Search SRA" value="" class="jig-ncbiclearbutton jig-ncbiautocomplete" data-jigconfig="isEnabled:false,disableUrl:'NcbiSearchBarAutoComplCtrl'" autocomplete="off" data-sbconfig="ds:'no',pjs:'no',afs:'yes'" /></div><button id="search" type="submit" class="button_search nowrap" cmd="go">Search</button></div></div></form><ul class=" inline_list searchlinks"><li>
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<a title="SRA Submission Quick Start" href="/sra/docs/submit">Submission Quick Start</a></li>
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<a title="SRA Search and Download Guide" href="/sra/docs/sradownload">Search and Download</a>
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<a title="Archive Documentation" href="/sra/docs/sra-data-storage-model/">Archive Documentation</a>
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<li><a title="Data Storage Model" href="/sra/docs/sra-data-storage-model/">Data Storage Model</a></li>
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<li><a title="Root Cause Analysis: Summary and Report" href="/sra/docs/rca/">Root Cause Analysis: Summary and Report</a></li>
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<div class="container">
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<div class="col1">
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<h1 id="search-in-sra-entrez">Search in SRA Entrez</h1>
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<div class="jig-ncbiinpagenav" data-all-heading-levels="["h2"]" data-top-of-page-t-o-c="true">
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<h2 id="introduction">Introduction</h2>
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<div class="warning-message"> <img src="/core/assets/sra/images/tack.png" alt="Tack" height="20" /> <span class="strong">EXPERIMENT</span> (accession in the form of SRX\#) is a minimum publishable unit in SRA. SRA database's queries result in a list of SRA experiments that meet your search criteria.
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</div>
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<h3 id="anatomy-of-the-sra-search-result">Anatomy of the SRA search results' web page</h3>
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<div class="shadowing"><a data-jig="ncbipopper" data-resizable="true" href="#target-1"><img src="/core/assets/sra/images/sra_search_results.png" alt="SRA Search results" width="500" /></a></div>
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<div xmlns="" id="target-1"><img src="/core/assets/sra/images/sra_search_results.png" alt="SRA Search results" /></div>
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<h2 id="basic-search-in-sra">Basic search in SRA</h2>
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<h3 id="boolean-operators">Boolean operators</h3>
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<p>You can modify your search results by including the following terms in your query:</p>
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<ol>
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<li><span class="strong">OR</span> finds records that contain at least one of the terms,</li>
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<li><span class="strong">AND</span> (serves as a default operator) narrows the search results by finding only records that contain all terms,</li>
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<li><span class="strong">NOT</span> in front of the search term narrows the search by excluding records matching this term.</li>
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</ol>
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<p>Parentheses are used to construct complex queries, for example: <a target="_blank" title="Complex query example" href="/sra?term=%28%28tumor%5BAll%20Fields%5D%20AND%20head%5BAll%20Fields%5D%29%20OR%20%28tumor%5BAll%20Fields%5D%20AND%20neck%5BAll%20Fields%5D%29%29%20NOT%20%22cell%20line%22%5BAll%20Fields%5D">((tumor AND head) OR (tumor AND neck)) NOT "cell line"</a>.</p>
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<p>Search result page always has a <span class="strong">Search details</span> section that shows underlying query or <span class="strong">query translation</span>, which will help you interpret your results and refine your query.</p>
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<h3 id="search-by-accession">Search by accession</h3>
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<p>There are four hierarchical levels of SRA entities and their accessions:</p>
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<ol>
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<li><span class="strong">STUDY</span> with accessions in the form of SRP#, ERP#, or DRP#</li>
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<li><span class="strong">SAMPLE</span> with accessions in the form of SRS#, ERS#, or DRS#</li>
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<li><span class="strong">EXPERIMENT</span> with accessions in the form of SRX#, ERX#, or DRX#</li>
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<li><span class="strong">RUN</span> with accessions in the form of SRR#, ERR#, or DRR#</li>
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</ol>
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<p>The first letter in the accession makes a notation of the source database - SRA, EBI, or DDBJ correspondingly.</p>
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<p>Examples of searches by accession:</p>
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<ul>
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<li>Find one specific study: <a target="_blank" title="Find 1 specific study, new window" href="/sra/?term=SRP006081">SRP006081</a></li>
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<li>Find studies with consecutive accessions using wild card: <a target="_blank" title="Find studies with consecutive accessions using wild card, new window" href="/sra/?term=SRP00608*">SRP00608*</a></li>
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<li>Find two specific studies: <a target="_blank" title="Find 2 specific studies, new window" href="/sra/?term=SRP006081+OR+SRP006083">SRP006081 OR SRP006083</a></li>
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</ul>
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<h3 id="search-by-words-or-phrases-using">Search by words or phrases using NCBI's Entrez search engine</h3>
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<p>To search by words simply type them in the search text field, for example: <a target="_blank" title="cancer cell line search, new window" href="/sra/?term=cancer+cell+line">cancer cell line</a>.</p>
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<p>To search by exact word combination (phrase) enclose it in quotation marks, for example: <a target="_blank" title="Cancer cell line search, new window" href="/sra/?term=%22cancer+cell+line%22">"cancer cell line"</a>.</p>
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<h2 id="advanced-search-in-the-sra-advan">Advanced search in the SRA Advanced Search Builder</h2>
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<p>To start advanced search in SRA click on the link <a target="_blank" title="Advanced SRA search, new window" href="/sra/advanced">Advanced</a> located below the universal search field.</p>
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<div class="shadowing"><img src="/core/assets/sra/images/advanced_search.png" alt="Advanced search" /></div>
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<p>This will open the SRA Advanced Search Builder.</p>
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<div class="shadowing"><a data-jig="ncbipopper" data-resizable="true" href="#target-3"><img src="/core/assets/sra/images/sra_search_builder.png" alt="SRA Advanced Search Builder" width="500" /></a></div>
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<div id="target-3"><img src="/core/assets/sra/images/sra_search_builder.png" alt="SRA Advanced Search Builder" /></div>
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<h3 id="filter">Filter</h3>
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<p><span class="strong">Filter</span> in SRA primarily allows you to find SRA records that are cross-referenced with other NCBI databases:
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PubMed, PubMed Central (PMC), Nucleotide, Assembly, and others.</p>
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<h4 id="find-available-filters">Find available "Filters"</h4>
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<ol>
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<li>Go to <a target="_blank" title="SRA Advanced Search Builder" href="/sra/advanced">SRA Advanced Search Builder</a>.</li>
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<li>Select "Filter" in the pull-down menu, click on <strong>Show index list</strong> link, and select available filter.</li>
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<li>Click the "Search" button.</li>
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</ol>
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<h4 id="find-all-drosophila-melanogaster">Find all <em>Drosophila melanogaster</em> SRA experiments that were referenced by articles in PubMed Central (PMC)</h4>
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<p><a target="_blank" title="Drosophila melanogaster records in SRA-PMC" href="/sra?term=%22sra%20pmc%22%5BFilter%5D%20AND%20%22Drosophila%20melanogaster%22%5BOrganism%5D">"sra pmc"[Filter] AND "Drosophila melanogaster"[organism]</a>.</p>
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<p>Experiments found by this query contain link to the research article(s) in PMC where the sequencing data were published. Note that all articles in PMC (vs PubMed) are free-text articles and many of them are Open Access.</p>
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<div class="shadowing"><img src="/core/assets/sra/images/related_information.png" alt="Record related information" /></div>
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<h3 id="properties">Properties</h3>
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<p>SRA collects and stores various metadata that pertain to technical side of NextGen sequencing.</p>
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<p><span class="strong">Properties</span> in SRA primarily allows you to narrow search results by controlled-vocabulary library's annotations.</p>
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<h4 id="find-available-properties">Find available "Properties"</h4>
|
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<ol>
|
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<li>Go to <a target="_blank" title="SRA Advanced Search Builder" href="/sra/advanced">SRA Advanced Search Builder</a>.</li>
|
|
<li>Select <strong>Properties</strong>in the pull-down menu, click on <strong>Show index list</strong> link, and select available property.</li>
|
|
<li>Click the "Search" button.</li>
|
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</ol>
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<h4 id="find-sra-records">Find SRA records</h4>
|
|
<ul>
|
|
<li>By 'Instrument': <a target="_blank" title="search by propery instrument, new window" href="/sra?term=%22instrument%20illumina%20genome%20analyzer%20iix%22%5BProperties%5D">"instrument illumina genome analyzer iix"[Properties]</a></li>
|
|
<li>By 'Library layout': <a target="_blank" title="search by library layout, new window" href="/sra?term=%22library%20layout%20paired%22%5BProperties%5D">"library layout paired"[Properties]</a></li>
|
|
<li>By 'Platform': <a target="_blank" title="search by platform, new window" href="/sra?term=%22platform%20helicos%22%5BProperties%5D">"platform helicos"[Properties]</a></li>
|
|
</ul>
|
|
<h2 id="advanced-search-via-other-ncbi-d">Advanced search via other NCBI databases</h2>
|
|
<div class="warning-message"> <img src="/core/assets/sra/images/tack.png" alt="Tack" height="20" /> Use connections between SRA and other NCBI databases to find SRA records linked to information specific to other databases!
|
|
</div>
|
|
<p>For example, metadata that describe biological aspects of sequencing experiments are archived by the NCBI BioProject and BioSample databases. How can we use these databases to find specific SRA records?</p>
|
|
<div class="warning-message"> <img src="/core/assets/sra/images/tack.png" alt="Tack" height="20" /> Advanced Search Builder works similarly in all NCBI databases. However, each database has a unique set of fields, properties, and filters.
|
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</div>
|
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<h3 id="bioproject">BioProject</h3>
|
|
<h4 id="1-find-projects-where-organism-i">1. Find projects where organism is <em>Homo sapiens</em> and where project has a reference to genome assembly information in the NCBI <a title="Assembly" href="/assembly/">Assembly</a> database.</h4>
|
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<ul>
|
|
<li>Go to the NCBI <a target="_blank" title="BioProject" href="/bioproject/">BioProject</a> database</li>
|
|
<li>Click on <a target="_blank" title="BioProject Advanced Search Builder" href="/bioproject/advanced">Advanced</a> link under search text field</li>
|
|
<li>In pull-down menu of the first row select <strong>Filter</strong>, click <strong>Show index list</strong>, and select <strong>bioproject sra</strong></li>
|
|
<li>In pull-down menu of the second row select <strong>Organism</strong> and in adjacent text field type <em>Homo sapiens</em></li>
|
|
<li>Click the <strong>Search</strong> button and view search results: <a target="_blank" title="search in BioProject, new window" href="/bioproject?term=%22bioproject%20sra%22%5BFilter%5D%20AND%20%22Homo%20sapiens%22%5BOrganism%5D">"bioproject sra"[Filter] AND Homo sapiens[Organism]</a></li>
|
|
</ul>
|
|
<h4 id="2-narrow-your-search-to-projects">2. Narrow your search to projects that have reference to research article(s) in PubMed</h4>
|
|
<ul>
|
|
<li>Add "bioproject pubmed"[Filter]: <a target="_blank" title="search in BioProject, new window" href="/bioproject?term=%22bioproject%20sra%22%5BFilter%5D%20AND%20%22Homo%20sapiens%22%5BOrganism%5D%20AND%20%22bioproject%20pubmed%22%5BFilter%5D">"bioproject sra"[Filter] AND Homo sapiens[Organism] AND "bioproject pubmed"[Filter]</a></li>
|
|
</ul>
|
|
<h4 id="3-restrict-search-to-human-cells">3. Restrict search to human cells and tissues (eliminate metagenomes)</h4>
|
|
<ul>
|
|
<li>Add "scope monoisolate"[Properties]: <a target="_blank" title="search in BioProject, new window" href="/bioproject?term=%22bioproject%20sra%22%5BFilter%5D%20AND%20%22Homo%20sapiens%22%5BOrganism%5D%20AND%20%22bioproject%20pubmed%22%5BFilter%5D%20AND%20%22scope%20monoisolate%22%5BProperties%5D">"bioproject sra"[Filter] AND Homo sapiens[Organism] AND "bioproject pubmed"[Filter] AND "scope monoisolate"[Properties]</a></li>
|
|
</ul>
|
|
<h4 id="4-pull-all-sra-experiments-that-">4. Pull all SRA experiments that are linked to resulting subset of BioProjects</h4>
|
|
<ul>
|
|
<li>On the left side of the page with the search results locate <strong>Find related data</strong> section, select <strong>SRA</strong> in the <strong>Database</strong> pull-down menu and click the button <strong>Find items</strong>.</li>
|
|
</ul>
|
|
<h3 id="biosample">BioSample</h3>
|
|
<h4 id="1-find-samples-where-organism-ha">1. Find samples where organism has attribute "Strain" and value "BALB/c"</h4>
|
|
<ul>
|
|
<li>Go to the NCBI <a target="_blank" title="BioSample" href="/biosample/">BioSample</a> database</li>
|
|
<li>Click on <a target="_blank" title="BioSample Advanced Search Builder" href="/biosample/advanced">Advanced</a> link under search text field</li>
|
|
<li>In pull-down menu of the first row select <strong>Attribute Name</strong>, type <strong>str</strong> in the adjacent text field, click <strong>Show index list</strong>, and select <strong>strain</strong></li>
|
|
<li>In the text field of the second row type <strong>BALB/c*</strong> (the wild card <strong>*</strong> will allow for inclusion of all values that have <strong>BALB/c</strong> in them, for example, <strong>BALB/cJ</strong>)</li>
|
|
<li>Click the <strong>Search</strong> button and view search results: <a target="_blank" title="search in BioSample, new window" href="/biosample?term=%22strain%22%5BAttribute%20Name%5D%20AND%20BALB%2Fc%2A">"strain"[Attribute Name] AND BALB/c*</a></li>
|
|
</ul>
|
|
<h4 id="2-restrict-the-search-results-to">2. Restrict the search results to samples that also have Attribute "Tissue"</h4>
|
|
<ul>
|
|
<li>Add "tissue"[Attribute Name]: <a title="search in BioSample, new window" href="/biosample/?term=%22strain%22%5BAttribute+Name%5D+AND+BALB%2Fc%2A+AND+%22tissue%22%5BAttribute+Name%5D">"strain"[Attribute Name] AND BALB/c* AND "tissue"[Attribute Name]</a></li>
|
|
</ul>
|
|
<h4 id="3-pull-all-sra-experiments-that-">3. Pull all SRA experiments that are linked to resulting subset of samples</h4>
|
|
<ul>
|
|
<li>On the left side of the search results page locate <strong>Find related data</strong> section, select <strong>SRA</strong> in the <strong>Database</strong> pull-down menu and click the button <strong>Find items</strong></li>
|
|
</ul>
|
|
<h4 id="4-restrict-search-results-to-sra">4. Restrict search results to SRA experiments where sequencing was performed on Illumina HiSeq 2000</h4>
|
|
<ul>
|
|
<li>Go to <a target="_blank" title="SRA Advanced Search Builder" href="/sra/advanced">SRA Advanced Search Builder</a> by clicking on the link <strong>Advanced</strong> under search text field</li>
|
|
<li>In pull-down menu of the first row select <strong>Properties</strong>, click <strong>Show index list</strong>, and select <strong>instrument illumina hiseq 2000</strong></li>
|
|
<li>In the text field of the second row type number of your search, from the <strong>History</strong> section below, with query <strong>SRA Links for BioSample</strong> (<code>Search ("strain"[Attribute Name]) AND BALB/c* AND "tissue"[Attribute Name]</code>) in the form of <code>#{number}</code></li>
|
|
<li>Click the button <strong>Search</strong> and view search results. </li>
|
|
</ul>
|
|
<h2 id="sra-cloudbased-search">SRA Cloud-based search</h2>
|
|
<ul>
|
|
<li><a title="SRA cloud-based search" href="/sra/docs/sra-cloud-based-examples">Cloud-based Search</a> </li>
|
|
<li><a title="SRA in BigQuery" href="/sra/docs/sra-bigquery-examples">Search in BigQuery</a> </li>
|
|
<li><a title="SRA in Athena" href="/sra/docs/sra-athena-examples">Search in Athena</a> </li>
|
|
</ul>
|
|
<hr />
|
|
<h2 id="contact-sra">Contact SRA</h2>
|
|
<p>Contact SRA staff for assistance at <a href="mailto:sra@ncbi.nlm.nih.gov?subject=SRA%20question&body=Dear%20SRA%20staff">sra@ncbi.nlm.nih.gov</a> </p>
|
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</div>
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</div>
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<!--/.col1-->
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<div class="col2">
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<div id="shared-content-1">
|
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<h2 data-heading="h2" data-no-toc="true">Getting Started</h2>
|
|
<ul>
|
|
<li><a title="SRA Getting Started" href="/sra/docs/">Getting Started</a></li>
|
|
</ul>
|
|
<h2 data-heading="h2" data-no-toc="true">Downloading SRA Data</h2>
|
|
<ul>
|
|
<li><a title="Download SRA sequences from Entrez search results" href="/sra/docs/sradownload">Download Guide</a> </li>
|
|
<li><a title="dbGAP Download Guide" href="/sra/docs/sra-dbgap-download">dbGaP Download Guide</a> </li>
|
|
<li><a title="Data Delivery to cloud bucket" href="/sra/docs/data-delivery">Data Delivery to Cloud</a> </li>
|
|
<li><a title="Access Trace Data" href="/sra/docs/trace-data">Access Trace Data</a> </li>
|
|
</ul>
|
|
<h2 data-heading="h2" data-no-toc="true">Search SRA</h2>
|
|
<ul>
|
|
<li><a title="Search in SRA" href="/sra/docs/srasearch">Search in SRA Entrez</a> </li>
|
|
<li><a title="SRA cloud-based search" href="/sra/docs/sra-cloud-based-examples">Cloud-based Search</a> </li>
|
|
<li><a title="SRA in BigQuery" href="/sra/docs/sra-bigquery-examples">Search in BigQuery</a> </li>
|
|
<li><a title="SRA in Athena" href="/sra/docs/sra-athena-examples">Search in Athena</a> </li>
|
|
</ul>
|
|
<h2 data-heading="h2" data-no-toc="true">Browsing</h2>
|
|
<ul>
|
|
<li><a target="_blank" title="SRA Run Selector" href="/Traces/study/">SRA Run Selector</a> </li>
|
|
<li><a target="_blank" title="Browse Samples, new window" href="/Traces/sra/sra.cgi?view=samples">Samples</a> </li>
|
|
<li><a target="_blank" title="Browse Analyses, new window" href="/Traces/sra/sra.cgi?view=analysis">Analyses</a> </li>
|
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<li><a target="_blank" title="Run Browser" href="/Traces/sra/sra.cgi?view=run_browser">Data for a single RUN</a> </li>
|
|
</ul>
|
|
<h2 data-heading="h2" data-no-toc="true">SRA-BLAST</h2>
|
|
<ul>
|
|
<li><a target="_blank" title="SRA Blast Step by Step" href="https://ftp.ncbi.nlm.nih.gov/pub/factsheets/HowTo_LocalSRABlast_StepByStep.pdf">SRA BLAST How To</a> </li>
|
|
</ul>
|
|
<h3 id="use-cases">Use cases</h3>
|
|
<ul>
|
|
<li><a target="_blank" title="The Tasmanian Devil and Cancer as an Infectious Disease: Analysis of transcriptome data, new window" href="https://ncbiinsights.ncbi.nlm.nih.gov/2013/02/27/the-tasmanian-devil-and-cancer-as-an-infectious-disease-analysis-of-transcriptome-data/">Transcriptome analysis<img src="/core/assets/sra/images/offsite.png" alt="offsite image" width="15" /></a></li>
|
|
<li><a target="_blank" title="Exploring next-gen sequencing experiments with SRA-BLAST, new window" href="/books/NBK431007/">Metagenome analysis<img src="/core/assets/sra/images/offsite.png" alt="offsite image" width="15" /></a></li>
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</ul>
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</div>
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</div>
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