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<!DOCTYPE HTML>
<!--
Phantom by HTML5 UP
html5up.net | @ajlkn
Free for personal and commercial use under the CCA 3.0 license (html5up.net/license)
-->
<html>
<head>
<title>Services & Pricing</title>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1, user-scalable=no" />
<link rel="stylesheet" href="assets/css/main.css" />
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<link rel="apple-touch-icon" sizes="114x114" href="images/tab.png" />
<noscript><link rel="stylesheet" href="assets/css/noscript.css" /></noscript>
</head>
<div class="alert">
<!-- <span class="closebtn" onclick="this.parentElement.style.display='none';">×</span> -->
<b> TREx is now part of Biotechnology Resource Center. Please <a class="customHyper" href="https://www.biotech.cornell.edu/core-facilities-brc/facilities/transcriptional-regulation-expression-facility-trex"> click here </a> to visit the BRC affiliated site. </b> <br/>
The TREx Lab is currently OPEN and is taking sample submissions by appointment only. <br />Please review our NEW <a class="customHyper" href="announcements.html"> <b><em>SAMPLE SUBMISSION GUIDELINES</em> </b> </a> for more information or <a class="customHyper" target="_blank" href="https://cores.lifesciences.cornell.edu/userdev/placeorder.php"> <b> <em> Click Here </em></b> </a> to place an order.<br />
To schedule a virtual meeting and or get in touch via e-mail: <a class="customHyper" href="home.html#Virtual"> <b><em>Click Here</em> </b> </a> <br />
<!-- <a class="customHyper" href="https://www.cornell.edu/coronavirus/" target="_blank"> <b> Novel Coronavirus (COVID-19) Resources and Updates </b> </a> /-->
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<span class="symbol"><img src="images/Asset.png" alt="" /></span>
</a>
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<nav>
<ul>
<li><a href="#menu">Menu</a></li>
</ul>
</nav>
</div>
</header>
<!-- Menu -->
<nav id="menu">
<h2>Menu</h2>
<ul>
<li><a href="index.html">Home</a></li> <li><a href="home.html">About Us</a></li>
<li><a href="services.html">Service & Pricing </a></li>
<li><a href="analysis.html">Analysis</a></li>
<li><a href="forms.html">Resources </a></li>
<li><a href="announcements.html">Announcements </a></li>
<li><a href="faqs.html">FAQs </a></li>
</ul>
</nav>
<!-- Main -->
<div id="main">
<div class="inner">
<h1>Transcriptional Regulation & Expression Facility</h1>
<hr>
<h1>Services & Pricing :</h1>
<p> To place an order, please <a class="customHyper" target="_blank" href="https://cores.lifesciences.cornell.edu/userdev/placeorder.php"> click here </a> to lauch the sample submision portal <i> (BRC account required)</i>.</p>
<section>
<div class="row">
<div class="col-6 col-12-medium">
<blockquote>
<b> Pricing Info: </b> <br>
<a href="https://www.biotech.cornell.edu/core-facilities-brc/services/rna-seq-standard-package" target="_blank"> RNA-Seq </a> <br>
<a href="https://www.biotech.cornell.edu/core-facilities-brc/services/small-rna-sequencing-standard-package" target="_blank"> smRNA-Seq </a> <br>
<!-- <a href="https://www.biotech.cornell.edu/core-facilities-brc/services/atac-seq-standard-package" target="_blank"> ATAC-Seq </a> <br> -->
</div>
</blockquote>
<div class="col-6 col-12-medium">
<blockquote>
<b> General guidelines and Other info:</b> <br>
<a href="#req"> RNA Input Requirements</a><br>
<a href="#data-dist"> Data Distribution </a><br>
<a> </a>
<!-- <a href="#cp"> Custom Services </a><br> -->
</blockquote>
</div>
</div>
<!-- <div class="box alt">
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<hr>
<h2 id="rna-seq"> RNA-Seq Standard package </h2>
<ul>
<li><b>Sample Submission:</b> 10ng — 1ug purified RNA (see <a href="#req"> RNA input requirements</a>).
'Bioanalyzer QC' is highly recommended. <br>Contact us for information about RNA QC options.</li>
<li><b>Library Preparation:</b> NEBNext Ultra II [Directional] RNA
PolyA* enrichment (included) or ribosomal RNA depletion (extra cost; <br>we can deplete animal and/or bacterial rRNA).<br>
Directional (stranded, default) or non-directional (non-stranded, recommended for input < 20ng total RNA).</li>
<li><b>Sequencing:</b> Minimum 20M raw reads.
Deeper sequencing is available on request (extra cost).</li>
<li><b>Standard analysis:</b>
Read preprocessing, mapping to reference genome, data QC reports including mapping rate and sample
clustering analyses, differential gene expression analysis (DESeq2).
Alternative analysis modes including pathogen discovery are also available; contact us for information.
</li>
<br>
To place an order, please <a class="customHyper" target="_blank" href="https://cores.lifesciences.cornell.edu/userdev/placeorder.php"> click here </a> to lauch the sample submision portal <i> (BRC account required)</i>.</p>
</ul>
<hr>
<h2 id="smrna-seq"> Small-RNA-Seq Standard package </h2>
<ul>
<li><b>Sample Submission:</b> 100ng - 1ug purified RNA (lower input is sufficient for cell-free RNA; see <a href="#req"> RNA input requirements</a>).<br>
'Bioanalyzer QC' is highly recommended; contact us for information about RNA QC options.
<li><b>Library Preparation:</b> NEBNext Small RNA. </li>
<li><b>Sequencing:</b>
Minimum 10M raw reads.
Deeper sequencing is available on request (extra cost).
</li>
<li><b>Standard analysis:</b>
Read preprocessing, quantification of annotated microRNAs (miRdeep2 using miRBase annotations), data QC
reports including total microRNA counts and sample clustering analyses, differential microRNA detection analysis (DESeq2).<br>
<i>Optional: </i> Reads can be mapped to a reference genome on request.
</li>
<br>
To place an order, please <a class="customHyper" target="_blank" href="https://cores.lifesciences.cornell.edu/userdev/placeorder.php"> click here </a> to lauch the sample submision portal <i> (BRC account required)</i>.</p>
</ul>
<hr>
<!-- <h2 id="atac-seq"> ATAC-Seq Standard package </h2>
<ul>
<li><b>Sample Submission:</b> At least 25k permeabalized nuclei, frozen in storage media.
Please contact us for reccommended sample preparation protocol.</li>
<li><b>Library Preparation:</b>Illumina TDE1 enzyme. </li>
<li><b>Sequencing:</b>
Minimum 20M (PE 2X150) raw reads.
Deeper sequencing is available and may be needed to attain recommended coverage (extra cost).
</li>
<li><b>Standard analysis:</b>
Read preprocessing, mapping to reference genome, peak calling and annotation, data QC reports including mapping/duplication rates and "fraction of reads in peaks" (FRIP), differential accessibility analysis (DESeq2).
Motif enrichment analysis is available upon request.
</li>
<br>
To place an order, please <a class="customHyper" target="_blank" href="https://cores.lifesciences.cornell.edu/userdev/placeorder.php"> click here </a> to lauch the sample submision portal <i> (BRC account required)</i>.</p>
</ul>
<hr> -->
<h2 id="req">RNA Input Requirements </h2> <br>
<div class="box alt">
<div class="row gtr-uniform">
<!-- <div class="col-12"><span class="image fit"><img src="images/rna-input.png" alt="" /></span></div> -->
</div>
<table >
<!-- <blockquote><h2 id="req">RNA Input Requirements </h2></blockquote> -->
<tbody>
<tr>
<td><i>Library Type</i></td>
<td><i>Transcriptome</i></td>
<td><i>Recommended</i></td>
<td><i>Minimum</i></td>
<tr>
<tr>
<td>RNAseq - directional </td>
<td>polyA+
<br> rRNA-depleted
</td>
<td>
≥ 500ng total RNA, RIN > 8
<br> 100ng - 1µg total RNA
</td>
<td>
10ng total RNA, RIN > 7
<br> 10ng total RNA
</td>
<tr>
<tr>
<td>RNAseq - non-directional </td>
<td>polyA+
<br>
<br> rRNA-depleted
</td>
<td>
use directional RNAseq or 50-100ng
<br> total RNA, RIN > 8
<br> same as directional RNAseq
</td>
<td>
1ng total RNA, RIN > 8
<br>
<br>
10ng total RNA
</td>
<tr>
<tr>
<td>small-RNAseq</td>
<td>small RNAs
</td>
<td>
≥ 500ng total RNA or
<br> 10ng cell-free RNA (e.g. serum)
</td>
<td>
100ng total RNA or
<br> 10pg cell-free RNA (e.g. serum)
</td>
<tr>
</tbody>
</table>
<hr>
<h2 id="cp">Custom Services</h2>
<p> Custom services are available on a limited basis for additional cost. Please contact us for more information.
<ul>
<li>DNase Treatment and RNA Cleanup</li>
<li>Nanodrop/Qubit Quantification</li>
<li>RNA QC on Fragment Analyzer</li>
</ul>
</p>
<hr>
<h2 id="data-dist">Data Distribution</h2>
<ul>
<li>Data analysis reports (html and xlsx formats) including data QC, raw count tables, and differential expression analysis results will be distributed when a project is complete via Box, Google Drive, and/or email. </li>
<li>Large data files are available on request and will be distributed via Globus or on the BRC Bioinformatics network (user account required).</li>
<li>Raw reads (fastq files) will be archived for at least 5 years by the TREx Facility.</li>
<li>Mapped reads (bam files) will be retained only as required for standard analysis and will be purged on a quarterly basis.</li>
<li>The first distribution of large data files is included in the standard package rates. <br> Repeat requests for distribution of large data files may incur additional fees.</li>
</ul>
</div>
</section>
</div>
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<li>© TREx 2022. All rights reserved</li>
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