828e8fde956c566c299dd09ccde15f217de365a3
lrnassar
  Wed Jan 7 16:54:30 2026 -0800
Final touches to the track, feedback from Zhiping. Reordering the registry tracks to be alphbetical by longLabel, but still keep data types together and updating the refences to the nature article that has now published. Refs #34109

diff --git src/hg/makeDb/trackDb/human/hg38/cCREsSuper.html src/hg/makeDb/trackDb/human/hg38/cCREsSuper.html
index bbdd09b6d6b..06b29d749eb 100644
--- src/hg/makeDb/trackDb/human/hg38/cCREsSuper.html
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@@ -1,32 +1,53 @@
 <H2>Description</H2>
 <p>
 This track collection displays candidate Cis-Regulatory Elements (cCREs) generated by the 
 ENCODE Consortium during Phase 4 (ENCODE4) and Phase 3 (ENCODE3), with the ENCODE3 track 
 retained for archival purposes. The tracks include both integrated (biosample-agnostic) and 
 biosample-specific annotations derived from core epigenomic assays.</p>
 
 <ul>
 <li><b>ENCODE4 cCREs</b>: This track presents the ENCODE Registry of 2,348,854 
 cCREs identified and classified using data 
 from all phases of the ENCODE Project (Phases 1–4). The registry integrates chromatin accessibility 
 and ChIP-seq signals across thousands of biosamples. All cCREs are consolidated into a single, 
 cell type-agnostic annotation track displayed here.</li>
 <br>
 <li><b>ENCODE4 Core Collection</b>: This track displays biosample-specific cCREs alongside 
 genome-wide epigenomic signals for the ENCODE4 Core Collection, consisting of 170 biosamples 
 comprehensively profiled using four core assays: DNase-seq, ChIP-seq for H3K4me3 and 
 H3K27ac (histone modifications), and ChIP-seq for CTCF. These data support detailed 
 analysis of regulatory activity in individual biosamples.</li>
 <br>
 <li><b>ENCODE3 cCREs</b>: This track provides the version of the cCRE Registry generated 
 at the end of ENCODE3, using data available up to that phase. The methodology was 
 refined and the dataset greatly expanded during ENCODE4. For instance, the Core 
 Collection would have included only 25 biosamples under ENCODE3 criteria. While ENCODE3 
 tracks are preserved for reproducibility, ENCODE4 tracks are recommended for all 
 current analyses, as they also incorporate ENCODE3 data.</li>
 </ul>
 
 <H2>Display conventions, data access, and credits</H2>
 <p>
 For information on track configuration, data description, data access, methods, and data provenance, 
 see the individual track description pages via their links above</p>
+
+<h2>References</h2>
+<p>
+ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T,
+Davis CA, Dobin A <em>et al</em>.
+<a href="https://doi.org/10.1038/s41586-020-2493-4" target="_blank">
+Expanded encyclopaedias of DNA elements in the human and mouse genomes</a>.
+<em>Nature</em>. 2020 Jul;583(7818):699-710.
+PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/32728249" target="_blank">32728249</a>; PMC: <a
+href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7410828/" target="_blank">PMC7410828</a>
+</p>
+<p>
+Moore JE, Pratt HE, Fan K, Phalke N, Fisher J, Elhajjajy SI, Andrews G, Gao M, Shedd N, Fu Y <em>et
+al</em>.
+<a href="https://www.nature.com/articles/s41586-025-09909-9" target="_blank">
+An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional
+Regulation</a>.
+<em>Nature</em>. 2026 January 7.
+PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/39763870" target="_blank">39763870</a>; PMC: <a
+href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11703161/" target="_blank">PMC11703161</a>
+</p>