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/mm10/tadsEncode.ra src/hg/makeDb/trackDb/mouse/mm10/tadsEncode.ra index 91702fd3197..1a97c249929 100644 --- src/hg/makeDb/trackDb/mouse/mm10/tadsEncode.ra +++ src/hg/makeDb/trackDb/mouse/mm10/tadsEncode.ra @@ -1,176 +1,176 @@ track tadsEncode parent tads priority 2 compositeTrack faceted shortLabel ENCODE TADs longLabel ENCODE contact domains (TADs) across 16 mouse biosamples (Arrowhead/Hi-C) type bigBed 4 + 5 group regulation visibility pack metaDataUrl /gbdb/mm10/bbi/tad/tadsEncode_metadata.tsv primaryKey Accession colorSettingsUrl /gbdb/mm10/bbi/tad/organ_colors.json subtrackUrls Accession=https://www.encodeproject.org/experiments/$$/ maxCheckboxes 50 html tadsEncode track tadsEncode_ENCSR005UON parent tadsEncode on shortLabel CH12.LX longLabel ENCODE TADs in CH12.LX (ENCSR005UON) type bigBed 4 + 5 bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/CH12LX.bb color 6,218,147 visibility dense mouseOver <b>Biosample:</b> CH12.LX<br><b>Arrowhead corner score:</b> $cornerScore track tadsEncode_ENCSR097DFP parent tadsEncode on shortLabel Heart - longLabel ENCODE TADs in Heart (ENCSR097DFP) + longLabel ENCODE TADs in heart (ENCSR097DFP) type bigBed 4 + 5 bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/heart.bb color 116,50,165 visibility dense mouseOver <b>Biosample:</b> Heart<br><b>Arrowhead corner score:</b> $cornerScore track tadsEncode_ENCSR639NRL parent tadsEncode on shortLabel Left cerebral cortex - longLabel ENCODE TADs in Left cerebral cortex (ENCSR639NRL) + longLabel ENCODE TADs in left cerebral cortex (ENCSR639NRL) type bigBed 4 + 5 bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/leftcerebralcortex.bb color 155,155,18 visibility dense mouseOver <b>Biosample:</b> Left cerebral cortex<br><b>Arrowhead corner score:</b> $cornerScore track tadsEncode_ENCSR028GRK parent tadsEncode on - shortLabel Mouse embryonic stem + shortLabel Mouse ESC longLabel ENCODE TADs in Mouse embryonic stem cell (ENCSR028GRK) type bigBed 4 + 5 bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/mouseembryonicstemcell.bb color 118,158,101 visibility dense mouseOver <b>Biosample:</b> Mouse embryonic stem cell<br><b>Arrowhead corner score:</b> $cornerScore track tadsEncode_ENCSR820CZQ parent tadsEncode off shortLabel Adrenal gland - longLabel ENCODE TADs in Adrenal gland (ENCSR820CZQ) + longLabel ENCODE TADs in adrenal gland (ENCSR820CZQ) type bigBed 4 + 5 bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/adrenalgland.bb color 90,179,68 visibility dense mouseOver <b>Biosample:</b> Adrenal gland<br><b>Arrowhead corner score:</b> $cornerScore track tadsEncode_ENCSR549VZT parent tadsEncode off shortLabel CH12F3 longLabel ENCODE TADs in CH12F3 (ENCSR549VZT) type bigBed 4 + 5 bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/CH12F3.bb color 254,75,173 visibility dense mouseOver <b>Biosample:</b> CH12F3<br><b>Arrowhead corner score:</b> $cornerScore track tadsEncode_ENCSR051JZL parent tadsEncode off shortLabel ES-E14 longLabel ENCODE TADs in ES-E14 (ENCSR051JZL) type bigBed 4 + 5 bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/ESE14.bb color 118,158,101 visibility dense mouseOver <b>Biosample:</b> ES-E14<br><b>Arrowhead corner score:</b> $cornerScore track tadsEncode_ENCSR136LVP parent tadsEncode off shortLabel Gastrocnemius - longLabel ENCODE TADs in Gastrocnemius (ENCSR136LVP) + longLabel ENCODE TADs in gastrocnemius (ENCSR136LVP) type bigBed 4 + 5 bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/gastrocnemius.bb color 137,135,170 visibility dense mouseOver <b>Biosample:</b> Gastrocnemius<br><b>Arrowhead corner score:</b> $cornerScore track tadsEncode_ENCSR471ZWB parent tadsEncode off shortLabel Mature B cell - longLabel ENCODE TADs in Mature B cell (ENCSR471ZWB) + longLabel ENCODE TADs in mature B cell (ENCSR471ZWB) type bigBed 4 + 5 bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/matureBcell.bb color 254,75,173 visibility dense mouseOver <b>Biosample:</b> Mature B cell<br><b>Arrowhead corner score:</b> $cornerScore track tadsEncode_ENCSR357JYI parent tadsEncode off - shortLabel Mouse trophoblast stem + shortLabel Mouse trophoblast SC longLabel ENCODE TADs in Mouse trophoblast stem cell (ENCSR357JYI) type bigBed 4 + 5 bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/mousetrophoblaststemcell.bb color 104,171,71 visibility dense mouseOver <b>Biosample:</b> Mouse trophoblast stem cell<br><b>Arrowhead corner score:</b> $cornerScore track tadsEncode_ENCSR080JTU parent tadsEncode off shortLabel Patski longLabel ENCODE TADs in Patski (ENCSR080JTU) type bigBed 4 + 5 bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/Patski.bb color 92,161,153 visibility dense mouseOver <b>Biosample:</b> Patski<br><b>Arrowhead corner score:</b> $cornerScore track tadsEncode_ENCSR516LTA parent tadsEncode off shortLabel Regulatory T cell - longLabel ENCODE TADs in Regulatory T cell (ENCSR516LTA) + longLabel ENCODE TADs in regulatory T cell (ENCSR516LTA) type bigBed 4 + 5 bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/regulatoryTcell.bb color 254,75,173 visibility dense mouseOver <b>Biosample:</b> Regulatory T cell<br><b>Arrowhead corner score:</b> $cornerScore track tadsEncode_ENCSR858EVG parent tadsEncode off shortLabel T-helper 1 cell longLabel ENCODE TADs in T-helper 1 cell (ENCSR858EVG) type bigBed 4 + 5 bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/Thelper1cell.bb color 254,75,173 visibility dense mouseOver <b>Biosample:</b> T-helper 1 cell<br><b>Arrowhead corner score:</b> $cornerScore track tadsEncode_ENCSR072ORZ parent tadsEncode off shortLabel T-helper 17 cell longLabel ENCODE TADs in T-helper 17 cell (ENCSR072ORZ) type bigBed 4 + 5 bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/Thelper17cell.bb color 254,75,173 visibility dense mouseOver <b>Biosample:</b> T-helper 17 cell<br><b>Arrowhead corner score:</b> $cornerScore track tadsEncode_ENCSR407MXC parent tadsEncode off shortLabel T-helper 2 cell longLabel ENCODE TADs in T-helper 2 cell (ENCSR407MXC) type bigBed 4 + 5 bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/Thelper2cell.bb color 254,75,173 visibility dense mouseOver <b>Biosample:</b> T-helper 2 cell<br><b>Arrowhead corner score:</b> $cornerScore track tadsEncode_ENCSR799QDS parent tadsEncode off - shortLabel v-Abl transformed + shortLabel v-Abl pro-B cell longLabel ENCODE TADs in v-Abl transformed pro-B cells (ENCSR799QDS) type bigBed 4 + 5 bigDataUrl /gbdb/mm10/bbi/tad/tadsEncode/vAbltransformedproBcells.bb color 254,75,173 visibility dense mouseOver <b>Biosample:</b> v-Abl transformed pro-B cells<br><b>Arrowhead corner score:</b> $cornerScore