RNA-Seq and Microarray Experiment Search

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Use a chromosome, point coordinate, or coordinate range:</li><ul><li>Chr1</li><li>Chr1:194732198</li><li>Chr1:194732198-294732198</li></ul> <li>Use asterisks (*) for wildcards at the end of partial words or genomic symbols:</li><ul><li>Pax*</li><li>embr* development</li><li>hippocamp* pyramid* cell layer</li></ul><li>Use quotation marks (" ") to indicate phrases:</li> <ul><li>"hair follicle" development</li><li>"amyotrophic lateral sclerosis"</li></ul><li>Use angle brackets to indicate superscript:</li><ul><li>Pax6<10Neu> for Pax6<sup>10Neu</sup></li></ul><li>Mix IDs, symbols, and keywords in a list:</li><ul><li>Nmt2, NM_013627, Acbd7, hair follicle development</li></ul></ul>Advanced searches are listed under the Search menu.<BR/>See <a href=\'https://www.informatics.jax.org/userhelp/QUICK_SEARCH_help.shtml\'>Using the Quick Search Tool</a> for more information.', STICKY, CAPTION, 'Quick Search Tips', CENTER, BELOW, WIDTH, 450, DELAY, 600, CLOSECLICK, CLOSETEXT, 'Close X');" 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class="yuimenuitemlabel">Function</a> <div id="navBarFunction" class="yuimenu"> <div class="bd"> <ul class="first-of-type"> <li class="yuimenuitem first-of-type"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/vocab/gene_ontology" onMouseOver="return overlib('Browse the Gene Ontology and mouse annotations in MGI.',ANCHOR, 'navBarFunction', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> GO Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/marker/" onMouseOver="return overlib('Search for genes and genome features by symbol, name, location, gene ontology classification or phenotype.',ANCHOR, 'navBarFunction', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Genes & Markers Query</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/batch" onMouseOver="return overlib('Obtain sets of MGI IDs for use in GO tools.',ANCHOR, 'navBarFunction', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Batch Query</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/function.shtml">More</a></li> </ul> </div> </div> </li>  <li class="yuimenuitem"><a class="yuimenuitemlabel">Strains / SNPs</a> <div id="navBarStrains" class="yuimenu"> <div class="bd"> <ul class="first-of-type"> <li class="yuimenuitem first-of-type"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/home/strain" onMouseOver="return overlib('Search for strains by name, synonyms, or attributes.',ANCHOR, 'navBarStrains', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();">Strain Query</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/snp" onMouseOver="return overlib('Search for SNPs by strain(s), SNP attributes, genomic position, or associated genes.',ANCHOR, 'navBarStrains', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> SNP Query</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" 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1.0,0.5,0,0.5);" onMouseOut="nd();"> Tumors</a></li>  <li class="yuimenuitem"><a class="yuimenuitemlabel">Sequence Searches</a> <div id="navBarSequences" class="yuimenu"> <div class="bd"> <ul class="first-of-type"> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://blast.ncbi.nlm.nih.gov/Blast.cgi" onMouseOver="return overlib('Search for sequence similarity using BLAST at NCBI.',ANCHOR, 'navBarSequences', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> BLAST at NCBI</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="http://jbrowse.informatics.jax.org/?data=data/GRCm39" onMouseOver="return overlib('Create a graphical display of genome features from regions of the mouse genome.',ANCHOR, 'navBarSequences', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> JBrowse Genome Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/batch" onMouseOver="return overlib('Input a list of gene IDs or symbols and retrieve 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</li>  <li class="yuimenuitem"><a class="yuimenuitemlabel">Ontologies</a> <div id="navBarVocabularies" class="yuimenu"> <div class="bd"> <ul class="first-of-type"> <li class="yuimenuitem first-of-type"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/vocab/gene_ontology" onMouseOver="return overlib('Browse the Gene Ontology and mouse annotations in MGI.',ANCHOR, 'navBarVocabularies', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> GO Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/disease" onMouseOver="return overlib('Browse for a human disease or condition term to find mouse models.',ANCHOR, 'navBarVocabularies', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Human Disease (DO) Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/vocab/mp_ontology" onMouseOver="return overlib('Search for a phenotype term to find relevant mutant genotypes.',ANCHOR, 'navBarVocabularies', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Mammalian Phenotype (MP) Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/vocab/gxd/anatomy/EMAPA:16039" onMouseOver="return overlib('Search or browse for anatomical structures; includes links to associated expression results.',ANCHOR, 'navBarVocabularies', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Mouse Developmental Anatomy Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/vocab/gxd/ma_ontology" onMouseOver="return overlib('An extensive ontology of anatomical structures for the postnatal mouse.',ANCHOR, 'navBarVocabularies', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Adult Mouse Anatomy Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/vocab/hp_ontology" onMouseOver="return overlib('Search for a human phenotype ontology term to find relevant human diseases.',ANCHOR, 'navBarVocabularies', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Human Phenotype (HPO) Browser</a></li> </ul> </div> </div> </li>  <li class="yuimenuitem"><a id="navBarBatch" class="yuimenuitemlabel" href="https://www.informatics.jax.org/batch" onMouseOver="return overlib('Input a list of gene IDs or symbols and retrieve other database IDs and gene attributes (e.g. phenotypes, GO).',ANCHOR, 'navBarBatch', ANCHORALIGN, 1.0,0.5,0,0.5);" onMouseOut="nd();"> Batch Query</a></li> <li class="yuimenuitem"><a id="navBarMine" class="yuimenuitemlabel" href="https://www.mousemine.org" onMouseOver="return overlib('Access MGI data via InterMine.',ANCHOR, 'navBarMine', ANCHORALIGN, 1.0,0.5,0,0.5);" onMouseOut="nd();"> MouseMine</a></li>  <li class="yuimenuitem"><a class="yuimenuitemlabel">Mouse Genome Browsers</a> <div id="navBarGenomeBrowsers" class="yuimenu"> <div class="bd"> <ul class="first-of-type"> <li class="yuimenuitem"><a id="navBarJBrowse" class="yuimenuitemlabel" href="http://jbrowse.informatics.jax.org/?data=data/GRCm39" onMouseOver="return overlib('Create a graphical display of genome features from regions of the mouse genome.',ANCHOR, 'navBarJBrowse', ANCHORALIGN, 1.0,0.5,0,0.5);" onMouseOut="nd();"> JBrowse Genome Browser</a></li> <li class="yuimenuitem"><a class="yuimenuitemlabel" href="https://www.informatics.jax.org/mgv/" onMouseOver="return overlib('Compare genome features of de novo sequenced mouse strains.',ANCHOR, 'navBarJBrowse', ANCHORALIGN, 'UR', 'UL');" onMouseOut="nd();"> Multiple Genome Viewer (MGV)</a></li> </ul> </div> </div> </li> </ul> </div> </div> </li>   <li class="yuimenubaritem"><a class="yuimenubaritemlabel" href="https://www.informatics.jax.org/downloads/reports/index.html">Download</a> <div id="navBarDownload" class="yuimenu"> <div class="bd"> <ul class="first-of-type"> <li class="yuimenuitem first-of-type"> <a class="yuimenuitemlabel" 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Tools</a></li> <li class="yuimenubaritem"><a class="yuimenubaritemlabel" href="https://www.informatics.jax.org/mgihome/support/mgi_inbox.shtml" title="Contact user support">Contact Us</a></li> <li class="yuimenubaritem"><a class="yuimenubaritemlabel" href="https://www.informatics.jax.org/mgihome/homepages/browser_compatibility.shtml" title="Browser compatibility">Browsers</a></li> </ul> </div> </div>  </div> <div id="templateBodyInsert">   <iframe id="yui-history-iframe" src="/fewi/blank.html"></iframe> <input id="yui-history-field" type="hidden">  <div id="titleBarWrapperGxd" userdoc="EXPRESSION_htexp_index_help.shtml" style="min-width: 1000px"> <a href="https://www.informatics.jax.org/expression.shtml"><img class="gxdLogo" src="https://www.informatics.jax.org/webshare/images/gxd_logo.png" height="75"></a> <div id="pageHeaderWrapper" style='display:inline-block; margin-top: 20px;'> <span class="titleBarMainTitleGxd">RNA-Seq and Microarray Experiment Search</span> <br/><span class="titleBarSubTitleGxd">Using GXD Metadata Annotations</span> </div> </div> <div id="outerGxd"> <div id="toggleQF" class="summaryControl" style="display:none"><span id="toggleImg" class="qfExpand" style="margin-right:15px; margin-top:0px;" onClick="toggleQueryForm()"></span><span id="toggleLink" class="filterButton" onClick="toggleQueryForm()">Click to modify search</span></div> <div id="qwrap">  <style> #locations { float:left; padding:4px; height:28px; width:260px; background-color: #FFFFFF; } #gxdQueryForm table tr td table tr td ul li span { font-size: 10px; font-style: italic; } #gxdQueryForm table tr td table tr td span { font-size: 10px; font-style: italic; } span.smallGrey { font-size: 75%; color: #999999; } #assayTypes1 > li, #assayTypes2 > li, #geneticBackground > li { list-style-type: none; list-style-image: none; margin-left:20px; } .detected { margin-left: 6px; margin-right: 3px; } #theilerStage, #age {width:75%;} /* style for ageStage tab widget (+ some extra stuff to make it look like a YUI tabView) */ .tab-nav { float: left; /*margin-right: 2px; */ padding: 5px 10px; cursor: pointer; } .tab-content { clear: both; text-align:center; border: 1px solid gray; border-top-width: 0; padding: .25em .5em; } .inactive-tab { border: 1px solid #A3A3A3; border-bottom-color: black; background: linear-gradient(white, white 35%, #d8d8d8 65%, #d8d8d8) ; margin-top: 4px; } .inactive-tab:hover { background: #bfdaff; outline:0; } .active-tab, .active-tab a:hover { border: 1px solid gray; border-top-color: black; border-bottom-width: 0; padding-bottom: 10px; } .active-content { display: block; } .inactive-content { display: none; } .buttonRow { background-color: white } .redNot{ font-size:110%; color:red; font-weight:bold; } .hide { display:none; } .anatomyAC { padding:2px 0px 12px 20px; width:300px; text-align:left; } #ageStage { display: inline-block;  min-width: 100px; } #gxdStructureHelp { font-family: Verdana,Arial,Helvetica; font-size: 12px; font-weight: normal; }  #ageStageDiv {width:21em;} #theilerStage {margin-left:0px;margin-right:12px;height:9.5em} #age {margin-left:7px;margin-right:7px;height:9.5em} #ageStageTd {height:12em;} <![endif]--> </style> <div id="standard-qf"> <form id="queryForm" class="gxdQf" action="https://www.informatics.jax.org/gxd/htexp_index/summary" method="GET">  <table class="pad5 borderedTable" width="100%"> <tr class="buttonRow"> <td align="left" colspan="2"> <input class="buttonLabel" value="Search" type="submit" id="submit1" onClick="logSubmission()">    <input type="reset" id="reset1">    Find experiments where expression was assayed in... </td> </tr> <tr class="stripe1"> <td class="cat1Gxd">Anatomical<br/>structure</td> <td><input type="text" size="40" name="structure" id="structureAC" placeholder="any anatomical structure" value="" /> </td> </tr> <tr class="stripe2"> <td class="cat2Gxd">Developmental<br/>stage</td> <td> <div id="ageStage"> <div class="tab-header"> <div class="tab-nav active-tab" id="stagesTab">Use Theiler Stages</div> <div class="tab-nav inactive-tab" id="agesTab">Use Ages (dpc)</div> </div> <div id="ageStageDiv" class="tab-content"> <div class="active-content"> <a href="https://www.informatics.jax.org/glossary/theiler" target="_blank"><img style="margin-bottom:82px;" id="" src="https://www.informatics.jax.org/webshare/images/help_icon.png" /></a> <select id="theilerStage" name="theilerStage" multiple="multiple" size="7"><option value="0" selected="selected">Any developmental stage</option><option value="1">TS 1 (0.0-2.5 dpc)</option><option value="2">TS 2 (1.0-2.5 dpc)</option><option value="3">TS 3 (1.0-3.5 dpc)</option><option value="4">TS 4 (2.0-4.0 dpc)</option><option value="5">TS 5 (3.0-5.5 dpc)</option><option value="6">TS 6 (4.0-5.5 dpc)</option><option value="7">TS 7 (4.5-6.0 dpc)</option><option value="8">TS 8 (5.0-6.5 dpc)</option><option value="9">TS 9 (6.25-7.25 dpc)</option><option value="10">TS 10 (6.5-7.75 dpc)</option><option value="11">TS 11 (7.25-8.0 dpc)</option><option value="12">TS 12 (7.5-8.75 dpc)</option><option value="13">TS 13 (8.0-9.25 dpc)</option><option value="14">TS 14 (8.5-9.75 dpc)</option><option value="15">TS 15 (9.0-10.25 dpc)</option><option value="16">TS 16 (9.5-10.75 dpc)</option><option value="17">TS 17 (10.0-11.25 dpc)</option><option value="18">TS 18 (10.5-11.25 dpc)</option><option value="19">TS 19 (11.0-12.25 dpc)</option><option value="20">TS 20 (11.5-13.0 dpc)</option><option value="21">TS 21 (12.5-14.0 dpc)</option><option value="22">TS 22 (13.5-15.0 dpc)</option><option value="23">TS 23 (15 dpc)</option><option value="24">TS 24 (16 dpc)</option><option value="25">TS 25 (17 dpc)</option><option value="26">TS 26 (18 dpc)</option><option value="27">TS 27 (newborn)</option><option value="28">TS 28 (postnatal)</option></select><input type="hidden" name="_theilerStage" value="1"/> </div> <div class="inactive-content"> <select id="age" name="age" multiple="multiple" size="7"><option value="ANY" 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value="13.5">E13.5</option><option value="14">E14.0</option><option value="14.5">E14.5</option><option value="15">E15.0</option><option value="15.5">E15.5</option><option value="16">E16.0</option><option value="16.5">E16.5</option><option value="17">E17.0</option><option value="17.5">E17.5</option><option value="18">E18.0</option><option value="18.5">E18.5</option><option value="19">E19.0</option><option value="19.5">E19.5</option><option value="20">E20.0</option><option value="20.5">E20.5</option></select><input type="hidden" name="_age" value="1"/> </div> </div> </div> </td> </tr> <tr class="stripe1"> <td class="cat1Gxd">Mutant</td> <td>Samples mutated in <input id="mutatedIn" name="mutatedIn" style="width:135px;" class="formWidth" type="text" value=""/></td> </tr> <tr class="stripe2"> <td class="cat2Gxd">Strain</td> <td><input type="text" size="40" name="strain" id="strainNameAC" placeholder="name" value="" /><br/> <span style="font-size: 85%">Use * for wildcard.</span> </td> </tr> 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<label><input name="textScope" type="checkbox" value="Title" checked="checked" /> In Title</label>   <label><input name="textScope" type="checkbox" value="Description" checked="checked" /> In Description</label>   </td> </tr> <tr class="stripe2"> <td class="cat2Gxd">ArrayExpress or GEO ID</td> <td> <input id="arrayExpressID" name="arrayExpressID" style="width:270px;" class="formWidth" type="text" value=""/><br/> </td> </tr> <tr class="buttonRow"> <td colspan="3" align="left"> <input class="buttonLabel" value="Search" type="submit" id="submit2" onClick="logSubmission()">    <input type="reset" id="reset2"> </td> </tr> </table> </form> </div> </div> </div> <br clear="all" /> <div id="summaryControl" class="summaryControl" style="display: none"> <div id="resultbar" class="goldbar">Results</div> <link rel="stylesheet" type="text/css" href="https://www.informatics.jax.org/assets/css/gxd/gxd_summary.css" /> <style> table.experimentWrapper { border: 1px solid gray; border-collapse: collapse; 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