26c4835e47a40f162ae82c0ea20e1997f42bc4ad gperez2 Tue Apr 21 16:35:37 2026 -0700 Moving shared HTML content in mouseDevTimecourse track description pages into shared include files using Claude. refs #37414 diff --git src/hg/makeDb/trackDb/mouse/mm39/mouseDevTimecourse.html src/hg/makeDb/trackDb/mouse/mm39/mouseDevTimecourse.html index bbcd5f6b2c8..6de077f1175 100644 --- src/hg/makeDb/trackDb/mouse/mm39/mouseDevTimecourse.html +++ src/hg/makeDb/trackDb/mouse/mm39/mouseDevTimecourse.html @@ -1,136 +1,71 @@ <h2>Description</h2> <p> This track set displays bulk RNA-seq gene expression data from a mouse developmental time course, covering 17 tissues across up to 8 time points (embryonic days 10.5 through 16.5 and postnatal day 0). Expression values (FPKM and TPM) were generated by RSEM from alignments to the mm10 reference genome using GENCODE M21 annotations and lifted over to the mm39 reference genome.</p> <p> The data were produced as part of the <a href="https://www.encodeproject.org/" target="_blank">ENCODE</a> project at the <a href="http://woldlab.caltech.edu/" target="_blank">Wold Lab</a>, Caltech. Each tissue and time point has two biological replicates, each displayed as its own bar.</p> <p>The two sub tracks are:</p> <ul> <li><b>timecourse M21 TPM</b> – TPM values using GENCODE M21 annotations, lifted over from mm10</li> <li><b>timecourse M21 FPKM</b> – FPKM values using GENCODE M21 annotations, lifted over from mm10</li> </ul> -<h2>Display Conventions and Configuration</h2> -<p> -Each sub track is displayed as a -<a href="/goldenPath/help/barChart.html" target="_blank">bigBarChart</a>. -Bar charts show expression levels for each sample, colored by tissue -type. The tracks can be faceted by tissue and timepoint using the track -configuration controls.</p> - -<p>Bars are colored by tissue:</p> -<table border="1" cellpadding="4" cellspacing="0"> - <tr><th>Color</th><th>Tissue</th></tr> - <tr><td style="background-color:#0118FA;width:30px;"> </td><td>adrenal gland</td></tr> - <tr><td style="background-color:#C0C0C0;width:30px;"> </td><td>embryonic facial prominence</td></tr> - <tr><td style="background-color:#00FFFF;width:30px;"> </td><td>forebrain</td></tr> - <tr><td style="background-color:#FF8380;width:30px;"> </td><td>heart</td></tr> - <tr><td style="background-color:#8B8A1D;width:30px;"> </td><td>hindbrain</td></tr> - <tr><td style="background-color:#CAC379;width:30px;"> </td><td>intestine</td></tr> - <tr><td style="background-color:#00FF00;width:30px;"> </td><td>kidney</td></tr> - <tr><td style="background-color:#FFFA2C;width:30px;"> </td><td>limb</td></tr> - <tr><td style="background-color:#C39CFB;width:30px;"> </td><td>liver</td></tr> - <tr><td style="background-color:#7762F0;width:30px;"> </td><td>lung</td></tr> - <tr><td style="background-color:#717E8D;width:30px;"> </td><td>midbrain</td></tr> - <tr><td style="background-color:#A71206;width:30px;"> </td><td>neural tube</td></tr> - <tr><td style="background-color:#35B5E2;width:30px;"> </td><td>skeletal muscle tissue</td></tr> - <tr><td style="background-color:#9834E7;width:30px;"> </td><td>spleen</td></tr> - <tr><td style="background-color:#995432;width:30px;"> </td><td>stomach</td></tr> - <tr><td style="background-color:#483F84;width:30px;"> </td><td>thymus</td></tr> - <tr><td style="background-color:#ff0000;width:30px;"> </td><td>urinary bladder</td></tr> -</table> - -<p style="margin-top:1em;">Within each tissue, bars are grouped by developmental time point: -e10.5, e11.5, e12.5, e13.5, e14.5, e15.5, e16.5, and P0. Not all -tissues are available at all time points.</p> +<!--#insert file="../../mouseDevTimecourseDisplay.shared.html"--> <h2>Methods</h2> <p> RNA-seq reads were processed using the <a href="https://www.encodeproject.org/pipelines/ENCPL002LSE/" target="_blank">ENCODE long RNA-seq pipeline</a>. Reads were aligned to the mm10 genome using STAR (Dobin <em>et al</em>., 2013) and quantified at the gene level using RSEM (Li and Dewey, 2011) with the GENCODE M21 annotation set. The FPKM or TPM column from the RSEM gene quantification files across all tissues and replicates was concatenated into a single matrix. This matrix was then converted into the UCSC <a href="/goldenPath/help/barChart.html#example6" target="_blank">faceted bigBarChart</a> format (bed, categories, and facet files). The bed file was converted to the mm39 genome using liftOver and then converted into a bigBarChart bigBed file.</p> <h2>Data Access</h2> <p> The data in this track can be explored interactively with the <a href="../cgi-bin/hgTables">Table Browser</a> or the <a href="../cgi-bin/hgIntegrator">Data Integrator</a>. For programmatic access, the track can be accessed using the Genome Browser's <a href="/goldenPath/help/api.html" target="_blank">REST API</a>.</p> <p> The bigBarChart bigBed files underlying this track can be downloaded from <a href="https://hgdownload.soe.ucsc.edu/gbdb/mm39/mouseDevTimecourse/" target="_blank">our download server</a>. Individual regions or the whole genome annotation can be obtained using our tool <tt>bigBedToBed</tt>, which can be compiled from the source code or downloaded as a precompiled binary for your system. Instructions for downloading source code and binaries can be found <a href="https://hgdownload.soe.ucsc.edu/downloads.html#utilities_downloads" target="_blank">here</a>.</p> <p>The original data files and experimental metadata are available from the <a href="https://www.encodeproject.org/publications/e0d01543-9965-4edb-933c-778a40575cd9/" target="_blank">ENCODE Portal</a>.</p> <p>Please refer to our <a href="../FAQ/FAQdownloads.html#download36" target="_blank">Data Access FAQ</a> for more information.</p> -<h2>Credits</h2> -<p> -Peng He (<!-- above address is Peng.He at ucsf.edu --><A HREF="mailto:Peng.He@ucsf.edu">Peng.He@ucsf.edu</A>) -was the lead author for this project and performed the data analysis. -Diane Trout (<!-- above address is diane at caltech.edu --><A HREF="mailto:diane@caltech.edu">diane@caltech.edu</A>) -at the Wold Lab, Caltech, was responsible for data management. The data -were produced as part of the ENCODE Consortium.</p> - -<h2>References</h2> -<p> -Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, -Chaisson M, Gingeras TR. -<a href="https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/bts635" -target="_blank"> -STAR: ultrafast universal RNA-seq aligner</a>. -<em>Bioinformatics</em>. 2013 Jan 1;29(1):15-21. -PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/23104886" -target="_blank">23104886</a>; PMC: <a -href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3530905/" -target="_blank">PMC3530905</a> -</p> - -<p> -Li B, Dewey CN. -<a href="https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-323" -target="_blank"> -RSEM: accurate transcript quantification from RNA-Seq data with or -without a reference genome</a>. -<em>BMC Bioinformatics</em>. 2011 Aug 4;12:323. -PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/21816040" -target="_blank">21816040</a>; PMC: <a -href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3163565/" -target="_blank">PMC3163565</a> -</p> +<!--#insert file="../../mouseDevTimecourseCreditsAndReferences.shared.html"-->