b7b9978c92a2376d6d9ef4f0a4974cb8167295f8
gperez2
  Wed Sep 30 14:17:50 2026 -0700
Updating the TAD tracks from the qa-track SKILL.md pass (hg19, hg38, mm10, mm39): shortLabel fixes for cut-off and duplicate ENCODE and 3DGB subtracks, lowercase biosamples in ENCODE longLabels, " bnd" dropped from Schmitt shortLabels, 3DGB subtracks set to pack with three mm10/mm39 defaults turned on, allButtonPair removed so the Schmitt matrix shows, and McArthur item labels hidden. Merged identical description pages into human/ and mouse/, plus description page cleanups (regenerated References, removed the "How to use these tracks" section, ENCODE pages now say 112 of 117 biosamples use Arrowhead). Also updated the ENCODE metadata columns and organ example in the hg38 makedoc. refs #21599

diff --git src/hg/makeDb/trackDb/mouse/mm39/tads3dgb.ra src/hg/makeDb/trackDb/mouse/mm39/tads3dgb.ra
index aabad2b28bc..ebccf7a79e2 100644
--- src/hg/makeDb/trackDb/mouse/mm39/tads3dgb.ra
+++ src/hg/makeDb/trackDb/mouse/mm39/tads3dgb.ra
@@ -2,314 +2,314 @@
 parent tads
 priority 3
 compositeTrack faceted
 shortLabel 3D Genome Browser
 longLabel TAD domains across 30 mouse Hi-C/Micro-C datasets (3DGB 2.0, lifted from mm10)
 type bigBed 4
 group regulation
 visibility hide
 metaDataUrl /gbdb/mm39/bbi/tad/tads3dgb_metadata.tsv
 primaryKey DatasetId
 colorSettingsUrl /gbdb/mm39/bbi/tad/organ_colors.json
 maxCheckboxes 50
 html tads3dgb
 
     track tads3dgb_418
-    parent tads3dgb off
+    parent tads3dgb on
     shortLabel mESC
     longLabel mESC TAD domains (Embryo, Hi-C, GSE35156, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/418.bb
     color 118,158,101
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> mESC (Embryo, Hi-C)
 
     track tads3dgb_424
-    parent tads3dgb off
+    parent tads3dgb on
     shortLabel CH12-LX
     longLabel CH12-LX TAD domains (Blood, Hi-C, GSE63525, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/424.bb
     color 254,75,173
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> CH12-LX (Blood, Hi-C)
 
     track tads3dgb_429
-    parent tads3dgb off
+    parent tads3dgb on
     shortLabel mESC WT MicroC
     longLabel mESC WT MicroC TAD domains (Embryo, Micro-C, GSE130275, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/429.bb
     color 118,158,101
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> mESC WT MicroC (Embryo, Micro-C)
 
     track tads3dgb_432
     parent tads3dgb off
     shortLabel mESC NELFB dTAB T0
     longLabel mESC NELFB dTAB T0 MicroC TAD domains (Embryo, Micro-C, GSE206131, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/432.bb
     color 118,158,101
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> mESC NELFB dTAB T0 MicroC (Embryo, Micro-C)
 
     track tads3dgb_445
     parent tads3dgb off
     shortLabel SSBP3 DMSO MicroC
     longLabel SSBP3 DMSO MicroC TAD domains (Blood, Micro-C, GSE288004, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/445.bb
     color 254,75,173
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> SSBP3 DMSO MicroC (Blood, Micro-C)
 
     track tads3dgb_446
     parent tads3dgb off
     shortLabel SSBP3 dTAGV1 MicroC
     longLabel SSBP3 dTAGV1 MicroC TAD domains (Blood, Micro-C, GSE288004, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/446.bb
     color 254,75,173
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> SSBP3 dTAGV1 MicroC (Blood, Micro-C)
 
     track tads3dgb_621
     parent tads3dgb off
     shortLabel Thymus Treg WT
     longLabel Thymus Treg WT TAD domains (Thymus, Hi-C, GSE301663, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/621.bb
     color 6,218,147
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> Thymus Treg WT (Thymus, Hi-C)
 
     track tads3dgb_622
     parent tads3dgb off
     shortLabel Thymus Treg KO
     longLabel Thymus Treg KO TAD domains (Thymus, Hi-C, GSE301663, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/622.bb
     color 6,218,147
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> Thymus Treg KO (Thymus, Hi-C)
 
     track tads3dgb_623
     parent tads3dgb off
     shortLabel 6KO scr rep1
     longLabel 6KO scr rep1 TAD domains (Embryo, Hi-C, GSE286893, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/623.bb
     color 118,158,101
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> 6KO scr rep1 (Embryo, Hi-C)
 
     track tads3dgb_625
     parent tads3dgb off
     shortLabel 6KO sh1A rep1
     longLabel 6KO sh1A rep1 TAD domains (Embryo, Hi-C, GSE286893, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/625.bb
     color 118,158,101
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> 6KO sh1A rep1 (Embryo, Hi-C)
 
     track tads3dgb_626
     parent tads3dgb off
     shortLabel 6KO sh1A rep2
     longLabel 6KO sh1A rep2 TAD domains (Embryo, Hi-C, GSE286893, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/626.bb
     color 118,158,101
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> 6KO sh1A rep2 (Embryo, Hi-C)
 
     track tads3dgb_627
     parent tads3dgb off
     shortLabel 6KO scr DS rep1
     longLabel 6KO scr DS rep1 TAD domains (Embryo, Hi-C, GSE286893, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/627.bb
     color 118,158,101
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> 6KO scr DS rep1 (Embryo, Hi-C)
 
     track tads3dgb_628
     parent tads3dgb off
     shortLabel 6KO scr DS rep2
     longLabel 6KO scr DS rep2 TAD domains (Embryo, Hi-C, GSE286893, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/628.bb
     color 118,158,101
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> 6KO scr DS rep2 (Embryo, Hi-C)
 
     track tads3dgb_629
     parent tads3dgb off
     shortLabel 6KO sh1A DS rep1
     longLabel 6KO sh1A DS rep1 TAD domains (Embryo, Hi-C, GSE286893, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/629.bb
     color 118,158,101
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> 6KO sh1A DS rep1 (Embryo, Hi-C)
 
     track tads3dgb_630
     parent tads3dgb off
     shortLabel 6KO sh1A DS rep2
     longLabel 6KO sh1A DS rep2 TAD domains (Embryo, Hi-C, GSE286893, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/630.bb
     color 118,158,101
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> 6KO sh1A DS rep2 (Embryo, Hi-C)
 
     track tads3dgb_631
     parent tads3dgb off
     shortLabel Spleen WT
     longLabel Spleen WT TAD domains (Blood, Hi-C, GSE302478, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/631.bb
     color 254,75,173
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> Spleen WT (Blood, Hi-C)
 
     track tads3dgb_632
     parent tads3dgb off
     shortLabel Spleen KO
     longLabel Spleen KO TAD domains (Blood, Hi-C, GSE302478, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/632.bb
     color 254,75,173
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> Spleen KO (Blood, Hi-C)
 
     track tads3dgb_645
     parent tads3dgb off
     shortLabel EBKO DNs All
     longLabel EBKO DNs All TAD domains (Thymus, Hi-C, GSE296309, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/645.bb
     color 6,218,147
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> EBKO DNs All (Thymus, Hi-C)
 
     track tads3dgb_673
     parent tads3dgb off
     shortLabel mESC rep1
     longLabel mESC rep1 TAD domains (Embryo, Hi-C, GSE215449, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/673.bb
     color 118,158,101
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> mESC rep1 (Embryo, Hi-C)
 
     track tads3dgb_674
     parent tads3dgb off
     shortLabel mESC rep2
     longLabel mESC rep2 TAD domains (Embryo, Hi-C, GSE215449, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/674.bb
     color 118,158,101
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> mESC rep2 (Embryo, Hi-C)
 
     track tads3dgb_675
     parent tads3dgb off
     shortLabel 2i rep1
     longLabel 2i rep1 TAD domains (Embryo, Hi-C, GSE215449, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/675.bb
     color 118,158,101
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> 2i rep1 (Embryo, Hi-C)
 
     track tads3dgb_676
     parent tads3dgb off
     shortLabel 2i rep2
     longLabel 2i rep2 TAD domains (Embryo, Hi-C, GSE215449, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/676.bb
     color 118,158,101
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> 2i rep2 (Embryo, Hi-C)
 
     track tads3dgb_677
     parent tads3dgb off
     shortLabel EPSC rep1
     longLabel EPSC rep1 TAD domains (Embryo, Hi-C, GSE215449, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/677.bb
     color 118,158,101
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> EPSC rep1 (Embryo, Hi-C)
 
     track tads3dgb_678
     parent tads3dgb off
     shortLabel EPSC rep2
     longLabel EPSC rep2 TAD domains (Embryo, Hi-C, GSE215449, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/678.bb
     color 118,158,101
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> EPSC rep2 (Embryo, Hi-C)
 
     track tads3dgb_679
     parent tads3dgb off
     shortLabel RA rep1
     longLabel RA rep1 TAD domains (Embryo, Hi-C, GSE215449, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/679.bb
     color 118,158,101
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> RA rep1 (Embryo, Hi-C)
 
     track tads3dgb_680
     parent tads3dgb off
     shortLabel RA rep2
     longLabel RA rep2 TAD domains (Embryo, Hi-C, GSE215449, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/680.bb
     color 118,158,101
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> RA rep2 (Embryo, Hi-C)
 
     track tads3dgb_712
     parent tads3dgb off
     shortLabel XEN R1
     longLabel XEN R1 TAD domains (Embryo, Hi-C, GSE213645, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/712.bb
     color 118,158,101
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> XEN R1 (Embryo, Hi-C)
 
     track tads3dgb_713
     parent tads3dgb off
     shortLabel XEN R2
     longLabel XEN R2 TAD domains (Embryo, Hi-C, GSE213645, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/713.bb
     color 118,158,101
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> XEN R2 (Embryo, Hi-C)
 
     track tads3dgb_714
     parent tads3dgb off
     shortLabel TSC R1
     longLabel TSC R1 TAD domains (Embryo, Hi-C, GSE213645, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/714.bb
     color 118,158,101
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> TSC R1 (Embryo, Hi-C)
 
     track tads3dgb_715
     parent tads3dgb off
     shortLabel TSC R2
     longLabel TSC R2 TAD domains (Embryo, Hi-C, GSE213645, lifted from mm10)
     type bigBed 4
     bigDataUrl /gbdb/mm39/bbi/tad/tads3dgb/715.bb
     color 118,158,101
-    visibility dense
+    visibility pack
     mouseOver <b>3DGB TAD domain:</b> TSC R2 (Embryo, Hi-C)