c6b77b666eeacc402d28f9d9585458e7960d70a5
lrnassar
  Wed Jan 14 17:32:42 2026 -0800
Capitalizing and fixing the referenced gene models to reference the correct mouse release vs. the human GENCODE release on both. Refs #36908

diff --git src/hg/makeDb/trackDb/mouse/mm10/clsLongReadRna.html src/hg/makeDb/trackDb/mouse/mm10/clsLongReadRna.html
index 8f75d75869d..a562e3c750c 100644
--- src/hg/makeDb/trackDb/mouse/mm10/clsLongReadRna.html
+++ src/hg/makeDb/trackDb/mouse/mm10/clsLongReadRna.html
@@ -27,35 +27,35 @@
 <b>Views:</b><br>
 <ul>
   <li><b>Targets:</b> Capture target regions</li>
   <li><b>Models:</b> Transcript models generated from reads and merging</li>
   <li><b>Sample models:</b> Transcript models by sample in which they were observed </li>
   <li><b>Per-experiment reads:</b> Read mappings per experiment</li>
   <li><b>Per-experiment Models:</b> Transcript models generated from the experiments</li>
 </ul></p>
 
 <p><b>Model Color Coding</b> <br>
 <p>
 Model annotations are color-coded based on their incorporation into GENCODE VM36
 and the assigned GENCODE VM36 BioType.  Note that VM36 is not on the mm10 assembly.
 </p>
 <ul>
-  <li style="color: rgb(12,12,120);"><b>coding</b></li>
-  <li style="color: rgb(0,100,0);"><b>non-coding</b></li>
-  <li style="color: rgb(255,51,255);"><b>pseudogene</b></li>
-  <li style="color: rgb(254,0,0);"><b>to be experimentally confirmed (TEC)</b></li>
-  <li style="color: rgb(255,160,122);"><b>Not incorporated into GENCODE V47</b></li>
+  <li style="color: rgb(12,12,120);"><b>Coding</b></li>
+  <li style="color: rgb(0,100,0);"><b>Non-coding</b></li>
+  <li style="color: rgb(255,51,255);"><b>Pseudogene</b></li>
+  <li style="color: rgb(254,0,0);"><b>To be experimentally confirmed (TEC)</b></li>
+  <li style="color: rgb(255,160,122);"><b>Not incorporated into GENCODE M36</b></li>
 </ul>
 
 <h2>Methods</h2>
 <p>
 This project, led by the 
 <a href="https://www.gencodegenes.org/" target="_blank">GENCODE consortium</a>,
 employed the Capture Long-read Sequencing (CLS) protocol to enrich transcripts from targeted genomic regions. It used a large capture array with orthologous probes in human and mouse genomes, targeting non-GENCODE lncRNA annotations and regions suspected of unannotated transcription. CapTrap-Seq, a cDNA library preparation protocol, was used to enrich for full-length RNA molecules (5′ to 3′).
 </p>
 
 <p>
 Matched adult and embryonic tissues from human and mouse were selected to maximize transcriptome complexity. Libraries were sequenced pre- and post-capture using PacBio and Oxford Nanopore Technologies (ONT) long-read platforms, as well as short-read technologies.
 </p>
 
 <p>
 Transcript isoform models were built from reads using the LyRic analysis software. These were merged using intron chains, with transcription start and end sites anchored using CAGE and poly(A) data.