ca24bbc74b74174bec0fa1713fbb1250d1e5ef4e
gperez2
  Mon May 25 21:44:07 2026 -0700
Updating ENCODE4 Regulation track description pages for hg38 and mm10. refs #34923

- DNase/ATAC/Histone/CTCF (Indiv.): added experiment counts (3,201 hg38, 589 mm10) per code review feedback (refs #37577 note-7), updated Signal/Peak bullet header wording.
- TF rPeaks: added grayscale legend table, reworded peak shading description, colored the word "green" to match the motif decorator color.
- TF ChIP-seq (Indiv.): updates to opening paragraph, added Signal/Peak bullet block with grayscale legend to Description.
- ENCODE4 Regulation supertrack: added (Layered)/(Indiv.) explanation paragraph, bolded track names, fixed Indiv. capitalization and DNase/ATAC order to match shortLabels. hg38: alphabetized References, mirrored TF rPeaks grayscale wording, changed inline PMID citation to author/year.
- DNase, ATAC, H3K4me3, H3K27ac, CTCF (Layered): added "By default," to transparent overlay sentence in shared HTML.
- RNA-seq (Indiv.): updated experiment counts (523 hg38, 216 mm10), updated filter list to match hgTrackUi facet names, added Available Organs and Tissues table.
- Transcription (Layered): restructured Available Organs and Tissues table, added "By default," to transparent overlay sentence.

diff --git src/hg/makeDb/trackDb/encode4RegLayeredDisplay.shared.html src/hg/makeDb/trackDb/encode4RegLayeredDisplay.shared.html
index 4f516c2653a..26b356b4f7d 100644
--- src/hg/makeDb/trackDb/encode4RegLayeredDisplay.shared.html
+++ src/hg/makeDb/trackDb/encode4RegLayeredDisplay.shared.html
@@ -1,12 +1,12 @@
 <h2>Display Conventions and Configuration</h2>
 <p>
-This track uses a transparent overlay to visualize data from multiple organs or tissues within
+By default, this track uses a transparent overlay to visualize data from multiple organs or tissues within
 the same vertical space. For each organ or tissue, signals from all associated experiments were
 averaged to generate the displayed track. Each organ or tissue is assigned a distinct
 color following the
 <a href="https://wiki.wenglab.org/references/color-mappings/" target="_blank">ENCODE color
 mapping convention</a>,
 selected to be light and saturated to maintain clarity when overlaid. Initially, each layered
 track displays an overlay of five representative organs: blood, brain, kidney, liver, and
 muscle. Clicking on the track opens a details page where you can view and select organs or
 tissues.</p>