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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml"><head>
<script>
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<title>Yeast CRISPRi | Search</title>
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<strong>Yeast</strong> CRISPRi
<!-- <img style="width: 200px" src="images/logo.svg" alt="Yeast CRISPRi Home"/> -->
</h3>
<ul class="nav nav-pills navbar-right">
<li role="presentation" id="nav-search" class="active" data-id="search-page"><a class="hand"><i class="fa fa-search hide"></i> Search</a></li>
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<!--START ABOUT PAGE-->
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<h2>Yeast CRISPRi guide selection and evaluation</h2>
<hr>
<p>This site helps to select effective guide RNAs for dCas9-mediated transcriptional repression, and evaluate existing designs for efficacy. The estimates are based on the work of Smith et al. (2016), that derived several yeast-specific guide RNA design rules for CRISPRi, and publically available nucleosome occupancy, ATAC-seq, and transcription start site data.</p>
<h3>Citation</h3>
If you use the yeast CRISPRi resource in your work, please cite the following:
<p>Smith, J.D., Suresh, S., Schlecht, U., Wu, M., Wagih, O., Peltz, G., Davis, R.W., Steinmetz, L.M., Parts, L. and Onge, R.P.S., 2016. Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design. <em>Genome biology</em>, 17(1), p.1.</p>
<p><a href="http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0900-9" target="_blank">Link to article</a></p>
<h3>Contact information</h3>
<p>For questions or comments, please get in touch with one of us</p>
<dl class="dl-horizontal">
<dt>Justin Smith</dt>
<dd><a href="http://www.google.com/recaptcha/mailhide/d?k=01OOxvylBECEcbhnEXT2FeFg==&c=kC10m0pkCBKDnmNLPQe0TF84j7cu6fA5jKdBhYlNMkU=" onclick="window.open('http://www.google.com/recaptcha/mailhide/d?k\07501OOxvylBECEcbhnEXT2FeFg\75\75\46c\75kC10m0pkCBKDnmNLPQe0TF84j7cu6fA5jKdBhYlNMkU\075', '', 'toolbar=0,scrollbars=0,location=0,statusbar=0,menubar=0,resizable=0,width=500,height=300'); return false;" title="Reveal this e-mail address">j...</a>@gmail.com</dd>
<dt>Omar Wagih</dt>
<dd><a href="http://www.google.com/recaptcha/mailhide/d?k=016S5i6CBkBjmH6P2b3aewUQ==&c=VoSkrjvAKI4hqNEKA6QFTQ==" onclick="window.open('http://www.google.com/recaptcha/mailhide/d?k\075016S5i6CBkBjmH6P2b3aewUQ\75\75\46c\75VoSkrjvAKI4hqNEKA6QFTQ\75\075', '', 'toolbar=0,scrollbars=0,location=0,statusbar=0,menubar=0,resizable=0,width=500,height=300'); return false;" title="Reveal this e-mail address">w...</a>@ebi.ac.uk</dd>
<dt>Leopold Parts</dt>
<dd><a href="http://www.google.com/recaptcha/mailhide/d?k=01OOxvylBECEcbhnEXT2FeFg==&c=iFBnMhsYrALdwhsEMJqvzx5Xz-8yJMJKV-9-v0jqqY8=" onclick="window.open('http://www.google.com/recaptcha/mailhide/d?k\07501OOxvylBECEcbhnEXT2FeFg\75\75\46c\75iFBnMhsYrALdwhsEMJqvzx5Xz-8yJMJKV-9-v0jqqY8\075', '', 'toolbar=0,scrollbars=0,location=0,statusbar=0,menubar=0,resizable=0,width=500,height=300'); return false;" title="Reveal this e-mail address">l...</a>@sanger.ac.uk</dd>
<dt>Robet P. St. Onge</dt>
<dd><a href="http://www.google.com/recaptcha/mailhide/d?k=01V3fPybU16OiWkGbvrwoc2Q==&c=qaICZkAn6LMgWUX1DEEjkhDtq7NIWwNPej6EyOQuQZk=" onclick="window.open('http://www.google.com/recaptcha/mailhide/d?k\07501V3fPybU16OiWkGbvrwoc2Q\75\75\46c\75qaICZkAn6LMgWUX1DEEjkhDtq7NIWwNPej6EyOQuQZk\075', '', 'toolbar=0,scrollbars=0,location=0,statusbar=0,menubar=0,resizable=0,width=500,height=300'); return false;" title="Reveal this e-mail address">b...</a>@stanford.edu</dd>
</dl>
</div>
</div>
</div><!--END ABOUT PAGE-->
<!--START ABOUT PAGE-->
<div id="help-page" style="display:none">
<div class="row">
<div class="col-lg-12">
<h2>Help page</h2>
<hr>
<h3>Description of features</h3>
<dl class="dl-horizontal">
<dt>Nucleosome</dt>
<dd>Posterior probability of nucleosome occupancy as defined in Schep et al. (2015) Genome Research</dd>
<dt>ATAC-seq</dt>
<dd>Read count from Schep et al. ATAC-seq experiment, averaged in a sliding window of 50bp, and normalised to the largest value in a 1000bp window. This features encodes how open the chromatin is relative to the rest of the region.</dd>
<!--
<dt>PAM+1-C, PAM+9-C</dt>
<dd>1 if the targeted sequence has a "C" at position 1 or 9, 0 otherwise. Smith et al. (2015) observed a lower median guide efficacy for guides with a C in this position. While statistically significant, this effect was not validated by independent experiments, so these features are given as secondary suggestions.</dd> -->
</dl>
</div>
</div>
</div><!--END ABOUT PAGE-->
<!--START SEARCH PAGE-->
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<div class="col-lg-4">
<ul class="list-group">
<li class="list-group-item">
<span class="badge" id="guide-length">–</span>
Length
</li>
<li class="list-group-item">
<span class="badge" id="pam-location">–</span>
PAM location
</li>
<li class="list-group-item">
<span class="badge" id="orf-tss">–</span>
ORF TSS
</li>
</ul>
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<div class="col-lg-4">
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<li class="list-group-item hide">
<span class="badge" id="pam-19">–</span>
PAM +1/+9 C
</li>
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<span class="badge" id="atac-seq">–</span>
ATAC-seq
</li>
</ul>
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<li class="list-group-item">
<span class="badge bx-green" id="nucleosome">0.11</span>
Nucleosome
</li>
<li class="list-group-item">
<span class="badge bx-green" id="pam-location-rel">124</span>
PAM distance to TSS
</li>
</ul>
</div>
</div><!--END ROW-->
</div>
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<form>
<fieldset>
<legend>Search by gene</legend>
<div class="form-group" id="gene-form-group">
<label for="gene-search" class="hide">gene</label>
<input multiple type="search" class="form-control input-lg" id="gene-search" name="gene-search" placeholder="Type gene name or ORF to search">
<span id="missing-genes" class="help-block hide"><i class="fa fa-exclamation-circle"></i> No gene names or ORFs found, please try again.</span>
<span id="too-many-genes" class="help-block hide"><i class="fa fa-exclamation-circle"></i> You have selected too many genes, please limit the number of genes to 50.</span>
</div>
<a class="btn btn-default btn-sm" id="gene-search-btn">Search</a>
<a class="btn btn-primary btn-sm" id="gene-search-example-btn">Example</a>
</fieldset>
<br>
<fieldset>
<legend>Search by sequence</legend>
<div class="form-group" id="seq-form-group">
<label for="seq-data" class="hide">Some text</label>
<textarea id="seq-data" class="form-control input-lg" rows="5" placeholder="Enter sequences in FASTA format"></textarea>
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<fieldset>
<legend>Filters</legend>
<h4 style="font-weight:600; font-size:16px">Nucleosome</h4>
<input id="ex8" data-slider-id="ex1Slider" type="text" class="slider span2" value="" data-slider-handle="square" data-slider-min="0" data-slider-max="100" data-slider-step="1" data-slider-value="100" data-slider-orientation="horizontal" data-slider-selection="before" data-slider-tooltip="show" style="max-width:100%">
</fieldset>
</form>
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</div><!--row1 end-->
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<center>
<a class="hand btn btn-default btn-sm" id="update-search"><i class="fa fa-repeat"></i> Update query</a>
<a class="hand btn btn-primary btn-sm" id="download-table"><i class="fa fa-arrow-down"></i> Download table</a>
</center>
<br>
<div class="col-xs-12" >
<!-- START DYNATABLE -->
<table id="data-table" class="table table-hover2 table-striped2">
<thead>
<!--1-->
<th data-dynatable-column="ORF_url">
<abbr data-toggle="tooltip" data-placement="top" title="Target open reading frame">ORF</abbr>
</th>
<!--2-->
<th data-dynatable-column="Gene_name_url">
<abbr data-toggle="tooltip" data-placement="top" title="Target gene name">Gene name</abbr>
</th>
<!--3-->
<th data-dynatable-column="Chrm">
<abbr data-toggle="tooltip" data-placement="top" title="Chromosome of target gene">Chrom.</abbr>
</th>
<!--4-->
<th data-dynatable-column="Seq">
<abbr data-toggle="tooltip" data-placement="top" title="Specifcity sequence">Sequence</abbr>
</th>
<!--5-->
<th data-dynatable-column="PAM_mid_pretty" data-dynatable-sorts="PAM_mid">
<abbr data-toggle="tooltip" data-placement="top" title="Midpoint location of the PAM">PAM loc.</abbr>
</th>
<!--6-->
<th class="hide" data-dynatable-column="Target_mid">Target midpoint</th>
<!--7-->
<th class="hide" data-dynatable-column="Midpoint_TSS_dist" >Midpoint TSS dist</th>
<!--8-->
<th data-dynatable-column="Nucleosome">
<abbr data-toggle="tooltip" data-placement="top" title="Nucleosome occupancy score">Nucl.</abbr>
</th>
<!--9-->
<th data-dynatable-column="Chromatin">
<abbr data-toggle="tooltip" data-placement="top" title="Normalized chromatin accessibility">ATAC-seq</abbr>
</th>
<!--10-->
<th class="hide" data-dynatable-column="1C">
<abbr data-toggle="tooltip" data-placement="top" title="Value is equal 1 if targeted sequence has a 'C' at position +1, 0 otherwise">+1C</abbr>
</th>
<!--11-->
<th class="hide" data-dynatable-column="9C">
<abbr data-toggle="tooltip" data-placement="top" title="Value is equal 1 if targeted sequence has a 'C' at position +9, 0 otherwise">+9C</abbr>
</th>
<!--12-->
<th class="hide" data-dynatable-column="Length">Guide length</th>
<!--13-->
<th data-dynatable-column="score_viz" data-dynatable-sorts="score">
<abbr data-toggle="tooltip" data-placement="top" title="Quality score">Score</abbr>
</th>
<th data-dynatable-column="expand_arrow">
</th>
</thead>
<tbody>
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