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/mm10/mouseDevTimecourse.html src/hg/makeDb/trackDb/mouse/mm10/mouseDevTimecourse.html index 547e75f0913..10ec3772785 100644 --- src/hg/makeDb/trackDb/mouse/mm10/mouseDevTimecourse.html +++ src/hg/makeDb/trackDb/mouse/mm10/mouseDevTimecourse.html @@ -13,63 +13,31 @@ Caltech. Each tissue and time point has two biological replicates, each displayed as its own bar.</p> <p>The four sub tracks are:</p> <ul> <li><b>timecourse M4 TPM</b> – TPM values using GENCODE M4 annotations</li> <li><b>timecourse M4 FPKM</b> – FPKM values using GENCODE M4 annotations</li> <li><b>timecourse M21 TPM</b> – TPM values using GENCODE M21 annotations</li> <li><b>timecourse M21 FPKM</b> – FPKM values using GENCODE M21 annotations</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 and quantified at the gene level using RSEM. For each annotation set (GENCODE M4 and M21), 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), and the bed file was converted into a bigBarChart bigBed file.</p> @@ -88,49 +56,16 @@ 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"-->