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Generation and analysis of a mouse multitissue genome annotation atlas
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mouse multitissue genome annotation atlas</h1> <div class="contributors"> <ol class="contributor-list" id="contrib-group-1"> <li class="contributor" id="contrib-1" itemprop="author" itemscope="itemscope" itemtype="http://schema.org/Person"><span class="name" itemprop="name"><a class="name-search" href="/search?author1=Matthew+Adams&sortspec=date&submit=Submit">Matthew Adams</a></span><a id="xref-aff-1-1" class="xref-aff" href="#aff-1">1</a> and </li> <li class="last" id="contrib-2"><span class="name"><a class="name-search" href="/search?author1=Christopher+Vollmers&sortspec=date&submit=Submit">Christopher Vollmers</a></span><a id="xref-aff-2-1" class="xref-aff" href="#aff-2">2</a></li> </ol> <ol class="affiliation-list"> <li class="aff"><a id="aff-1" name="aff-1"></a><address><sup>1</sup>Department of Molecular, Cellular, and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064, USA; </address> </li> <li class="aff"><a id="aff-2" name="aff-2"></a><address><sup>2</sup>Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA </address> </li> </ol> </div> <li class="corresp" id="corresp-1">Corresponding author: <span class="em-link"><span class="em-addr">vollmers{at}ucsc.edu</span></span></li> <div class="section abstract" id="abstract-1" itemprop="description"> <h2>Abstract</h2> <p id="p-2">Generating an accurate and complete genome annotation for an organism is complex because the cells within each tissue can express a unique set of transcript isoforms from a unique set of genes. A comprehensive genome annotation should contain information on what tissues express what transcript isoforms at what level. This tissue-level isoform information can then inform a wide range of research questions as well as experiment designs. Long-read sequencing technology combined with advanced full-length cDNA library preparation methods has now achieved throughput and accuracy where generating these types of annotations is achievable. Here, we show this by generating a genome annotation of the mouse (<em>Mus musculus</em>). We used the nanopore-based R2C2 long-read sequencing method to generate 64 million highly accurate full-length cDNA consensus reads鈥攁veraging 5.4 million reads per tissue for a dozen tissues. Using the Mandalorion tool, we processed these reads to generate the Tissue-level Atlas of Mouse Isoforms which is available as a trackhub for the UCSC Genome Browser and contains at least one full-length isoform for the vast majority of expressed genes in each tissue. </p> </div> <div class="section fn-group" id="fn-group-1"> <h2>Footnotes</h2> <ul> <li class="fn-supplementary-material" id="fn-1"> <p id="p-80">[Supplemental material is available for this article.]</p> </li> <li class="fn" id="fn-2"> <p id="p-81">Article published online before print. Article, supplemental material, and publication date are at <a href="https://www.genome.org/cgi/doi/10.1101/gr.279217.124">https://www.genome.org/cgi/doi/10.1101/gr.279217.124</a>. </p> </li> <li class="fn" id="fn-3"> <p id="p-82">Freely available online through the <em>Genome Research</em> Open Access option. </p> </li> </ul> </div> <ul class="history-list"> <li xmlns:hwp="http://schema.highwire.org/Journal" class="received" hwp:start="2024-02-29"><span class="received-label">Received </span>February 29, 2024. </li> <li xmlns:hwp="http://schema.highwire.org/Journal" class="accepted" hwp:start="2024-09-11"><span class="accepted-label">Accepted </span>September 11, 2024. </li> </ul> <ul class="copyright-statement"> <li class="fn" id="copyright-statement-1"><a href="/site/misc/terms.xhtml">漏 2024 Adams and Vollmers; Published by Cold Spring Harbor Laboratory Press</a></li> </ul> <div class="license" id="license-1"> <p id="p-1">This article, published in <em>Genome Research</em>, is 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Published in Advance <span class="slug-ahead-of-print-date">October 23, 2024</span>, doi: <span title="10.1101/gr.279217.124" class="slug-doi">10.1101/gr.279217.124 </span> </span> <cite> <abbr title="Genome Research" class="slug-jnl-abbrev"> Genome Res.</abbr><span class="slug-pub-date" itemprop="datePublished"> 2024. </span> <span class="slug-vol"> 34: </span><span class="slug-pages"> 2108-2117 </span> </cite> <a href="/site/misc/terms.xhtml"> <nlm:copyright-statement xmlns:nlm="http://schema.highwire.org/NLM/Journal" xmlns:hwp="http://schema.highwire.org/Journal" hwp:id="copyright-statement-1"> <nlm:ext-link xmlns:l="http://schema.highwire.org/Linking" xmlns:xlink="http://www.w3.org/1999/xlink" l:rel="related" l:ref-type="uri" l:ref="http://genome.cshlp.org/site/misc/terms.xhtml" ext-link-type="uri" xlink:href="http://genome.cshlp.org/site/misc/terms.xhtml" hwp:id="ext-link-1">漏 2024 Adams and Vollmers; Published by Cold Spring Harbor Laboratory Press</nlm:ext-link> 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