src/hg/makeDb/trackDb/mouse/mm10/developmentTimecourseSignalMm10.html 78988553dd9b460c26f0b9f21f15a1aacfad9dab

78988553dd9b460c26f0b9f21f15a1aacfad9dab
lrnassar
  Fri Aug 21 15:44:40 2026 -0700
Polish pass on the mouseDevTimecourse tracks after a Playwright QA sweep. refs #37001

Sentence-case the tissue names and the facet column titles, so the barChart
facet filter reads "Tissue / Spleen" rather than "tissue / spleen" and the
bigWig matrix reads "Spleen". Only the first character is upper-cased. Added
sentenceCaseTissues.sh, which does the .facets and .categories files and is
idempotent, since the hub still ships lower-case and this has to be replayed
after any refetch. The count and color column names are deliberately left
lower-case: barChartUi.c requires a field literally named "count" to load the
file at all, and facetedTable.c keys its merge logic on "count", "color" and
"val". Renaming the faceted columns means trackDb matches, so the stanzas now
read barChartFacets Tissue,Timepoint.

Set priority on the container children so the default-visible M21 TPM sorts
first and the signal composite sorts last. The composite needs an explicit
value; without one it inherits the superTrack's 0.6 and floats to the top.

Fix the All reads view, which was inert. Every all-reads subtrack shipped
parent off, so switching the view to full revealed nothing. The view's own
visibility already gates drawing, so the subtrack state should not encode the
view as well. The default image is unchanged at 78 unique-reads rep1 tracks,
and switching the view to full now yields 156. This also makes the Rep 2
toggle symmetric across the two views.

Rename the bigWig subGroup3 display label from Age to Timepoint, matching the
barChart facet and the .facets column. The group name stays "age" because
dimensions and sortOrder reference it by name.

Add relatedTracks cross-links between the mm10 container and Tabula Muris.
Not Tabula Muris Senis, which is not on the RR.

Description pages: reorder the mm10 subtrack list to match the new display
order, "sub tracks" to "subtracks", capitalise the colour legend tissue names,
and correct the mm39 Il11ra2 note - the gene appears three times, two of them
stacked at one position and sharing a details page, with the third 497 kb away.

Makedocs record the casing step, its ordering constraint relative to the
reorder and colour steps, and the count/color naming constraint.

diff --git src/hg/makeDb/trackDb/mouse/mm10/developmentTimecourseSignalMm10.html src/hg/makeDb/trackDb/mouse/mm10/developmentTimecourseSignalMm10.html
index 37fd305c88f..8cc8e4c7b66 100644
--- src/hg/makeDb/trackDb/mouse/mm10/developmentTimecourseSignalMm10.html
+++ src/hg/makeDb/trackDb/mouse/mm10/developmentTimecourseSignalMm10.html
@@ -1,101 +1,101 @@
 <h2>Description</h2>
 <p>
 This track displays RNA-seq signal (read coverage) from the same mouse
 developmental time course bulk RNA-seq experiment shown in the
 <a href="../cgi-bin/hgTrackUi?db=mm10&amp;g=mouseDevTimecourse">ENCODE
 Expression</a> bigBarChart tracks, covering 17 tissues across up to 8 time
 points (embryonic days 10.5 through 16.5 and postnatal day 0). While the
 bigBarChart tracks show gene-level TPM and FPKM summary values, this track
 shows the underlying per-base signal that those values were derived from.</p>
 
 <p>
 For each of the 156 samples (78 tissue/time point combinations, each with
 two biological replicates), two signal tracks are provided: one from reads
 that align uniquely to the genome (Unique reads), and one that includes
 all aligned reads, including reads that map to multiple locations (All
 reads).</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.</p>
 
 <h2>Display Conventions and Configuration</h2>
 <p>
 Tracks are organized into two views, <b>Unique reads</b> and <b>All
 reads</b>. Within each view, subtracks are arranged in a matrix by
 developmental time point and tissue, with a <b>Replicate</b> filter (Rep 1,
 Rep 2). By default, only the Unique reads view and Rep 1 are visible; use
 the track configuration matrix to turn on other tissues, time points,
 replicates, or the All reads view.</p>
 
 <p>Tracks are colored by tissue, with a gradient that darkens as the time point advances through the eight developmental time points (e10.5, e11.5, e12.5, e13.5, e14.5, e15.5, e16.5, and P0), matching the colors used in the ENCODE Expression bigBarChart tracks. Not all tissues are available at all time points.</p>
 <table border="1" cellpadding="4" cellspacing="0">
 <tr><th>Tissue</th><th>Colors by time point (earliest to latest)</th></tr>
-<tr><td>thymus</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#C8B400;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
-<tr><td>spleen</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#A0856C;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
-<tr><td>liver</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#e0e0e0;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e11.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#cfcfcf;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e12.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#b5b5b5;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e13.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#9a9a9a;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#7f7f7f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#666666;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e16.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#4d4d4d;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
-<tr><td>heart</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#f7c6c6;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e10.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#f19999;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e11.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#ec6b6b;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e12.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#e64545;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e13.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#d93030;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#b71f1f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#8f1515;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e16.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#6f0f0f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
-<tr><td>skeletal muscle tissue</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#FF6B6B;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
-<tr><td>urinary bladder</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#FF8C00;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
-<tr><td>adrenal gland</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#000000;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
-<tr><td>kidney</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#f6c38a;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#f0a14d;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#d17a2c;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e16.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#a95c1b;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
-<tr><td>lung</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#fff59a;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#fff066;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#e6d84a;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e16.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#bfae2f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
-<tr><td>stomach</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#d7f7a6;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#bdf06f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#8fcd3c;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e16.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#5f8f1f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
-<tr><td>intestine</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#b6f7da;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#7eecc0;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#44c494;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e16.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#2f8f6c;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
-<tr><td>limb</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#f6c3e8;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e10.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#f19cd9;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e11.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#ea73c9;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e12.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#e04ab8;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e13.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#b92d8f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#7f1f63;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div></td></tr>
-<tr><td>embryonic facial prominence</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#f2b3c8;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e10.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#e979a0;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e11.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#de4f7e;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e12.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#c92d63;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e13.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#9f1f4d;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#6f1435;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div></td></tr>
-<tr><td>forebrain</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#e1c6f7;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e10.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#cfa1f2;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e11.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#b36ae6;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e12.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#8f3fd9;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e13.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#6a28b8;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#4b1a8f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#34105f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e16.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#22093f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
-<tr><td>midbrain</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#c6d8ff;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e10.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#9fbaff;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e11.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#6f96ff;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e12.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#3f70ff;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e13.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#1f4de6;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#1637b8;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#0f267f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e16.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#08184f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
-<tr><td>hindbrain</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#c6dbf0;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e10.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#9bbce6;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e11.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#6a9cd9;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e12.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#3f7ec4;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e13.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#285fa3;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#1a457f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#0f2f5f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e16.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#081c3f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
-<tr><td>neural tube</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#d6fbff;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e11.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#a6f0ff;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e12.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#6fdcff;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e13.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#3fbfe6;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#2a8fb8;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#1a5f6f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
+<tr><td>Thymus</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#C8B400;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
+<tr><td>Spleen</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#A0856C;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
+<tr><td>Liver</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#e0e0e0;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e11.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#cfcfcf;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e12.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#b5b5b5;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e13.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#9a9a9a;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#7f7f7f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#666666;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e16.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#4d4d4d;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
+<tr><td>Heart</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#f7c6c6;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e10.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#f19999;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e11.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#ec6b6b;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e12.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#e64545;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e13.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#d93030;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#b71f1f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#8f1515;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e16.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#6f0f0f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
+<tr><td>Skeletal muscle tissue</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#FF6B6B;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
+<tr><td>Urinary bladder</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#FF8C00;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
+<tr><td>Adrenal gland</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#000000;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
+<tr><td>Kidney</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#f6c38a;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#f0a14d;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#d17a2c;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e16.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#a95c1b;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
+<tr><td>Lung</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#fff59a;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#fff066;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#e6d84a;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e16.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#bfae2f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
+<tr><td>Stomach</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#d7f7a6;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#bdf06f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#8fcd3c;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e16.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#5f8f1f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
+<tr><td>Intestine</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#b6f7da;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#7eecc0;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#44c494;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e16.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#2f8f6c;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
+<tr><td>Limb</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#f6c3e8;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e10.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#f19cd9;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e11.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#ea73c9;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e12.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#e04ab8;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e13.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#b92d8f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#7f1f63;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div></td></tr>
+<tr><td>Embryonic facial prominence</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#f2b3c8;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e10.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#e979a0;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e11.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#de4f7e;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e12.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#c92d63;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e13.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#9f1f4d;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#6f1435;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div></td></tr>
+<tr><td>Forebrain</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#e1c6f7;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e10.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#cfa1f2;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e11.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#b36ae6;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e12.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#8f3fd9;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e13.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#6a28b8;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#4b1a8f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#34105f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e16.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#22093f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
+<tr><td>Midbrain</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#c6d8ff;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e10.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#9fbaff;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e11.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#6f96ff;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e12.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#3f70ff;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e13.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#1f4de6;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#1637b8;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#0f267f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e16.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#08184f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
+<tr><td>Hindbrain</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#c6dbf0;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e10.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#9bbce6;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e11.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#6a9cd9;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e12.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#3f7ec4;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e13.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#285fa3;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#1a457f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#0f2f5f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e16.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#081c3f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
+<tr><td>Neural tube</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#d6fbff;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e11.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#a6f0ff;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e12.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#6fdcff;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e13.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#3fbfe6;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#2a8fb8;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#1a5f6f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>
 </table>
 
 <h2>Methods</h2>
 <p>
 RNA-seq reads were processed using the ENCODE
 <a href="https://www.encodeproject.org/pipelines/ENCPL862USL/"
 target="_blank">Bulk RNA-seq pipeline</a>. Reads were aligned to
 the mm10 genome using STAR (Dobin <em>et al</em>., 2013), which reports
 signal separately for reads that align uniquely to the genome and for all
 aligned reads, including reads that map to multiple locations. These
 bigWig signal files were obtained from the ENCODE Portal for each sample
 and replicate.</p>
 
 <p>
 The steps and <a href="https://github.com/ucscGenomeBrowser/kent/tree/master/src/hg/makeDb/scripts/mouseDevTimecourse"
 target="_blank">scripts</a> used to build this track are documented in our
 <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/doc/mm10.txt"
 target="_blank">makedoc</a>, and the track configuration is in
 <a href="https://github.com/ucscGenomeBrowser/kent/blob/master/src/hg/makeDb/trackDb/mouse/mm10/developmentTimecourseSignalMm10.ra"
 target="_blank">developmentTimecourseSignalMm10.ra</a>.</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&apos;s
 <a href="/goldenPath/help/api.html" target="_blank">REST API</a>.</p>
 
 <p>
 The bigWig files underlying this track can be downloaded from
 <a href="https://hgdownload.soe.ucsc.edu/gbdb/mm10/mouseDevTimecourse/"
 target="_blank">our download server</a>. Individual regions or the whole
 genome annotation can be obtained using our tool <tt>bigWigToWig</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>
 
 <!--#insert file="../../mouseDevTimecourseCreditsAndReferences.shared.html"-->