17b7d3c37be41135afaf8e91e365e3847af96ca5 lrnassar Mon Jun 22 10:56:56 2026 -0700 Add TAD (topologically associating domains) track set on hg19, hg38, mm10, mm39. refs #21599 New "tads" superTrack collecting published TAD calls, alpha-gated via include tad.ra alpha in each assembly's trackDb.ra. hg38 (all five sources): Dixon 2012 domains, Schmitt 2016 boundaries, McArthur & Capra 2021 boundary stability, ENCODE contact domains (faceted composite over 117 biosamples), and 3D Genome Browser 2.0 domains (faceted composite over 464 datasets). hg19: the three sources with hg19-compatible data (Dixon, Schmitt, McArthur). mm10/mm39 (domains only; the boundary sources have no mouse data): Dixon, ENCODE (faceted, 16 biosamples), and 3D Genome Browser (faceted, 30 datasets); mm39 lifted from mm10, lift noted in the long labels. Faceted composites are organ-colored from a TAD-owned organ_colors.json symlinked into /gbdb/<asm>/bbi/tad/. Build scripts and autoSql are version-controlled under makeDb/scripts/tad/ and symlinked into the per-source build dirs. Provenance and fetch for every dataset are documented in the makedocs (doc/hg38/tad.txt, doc/mm10/tad.txt, doc/mm39/tad.txt, and the hg19 TAD section in doc/hg19.txt). diff --git src/hg/makeDb/trackDb/mouse/mm39/tads3dgb.ra src/hg/makeDb/trackDb/mouse/mm39/tads3dgb.ra new file mode 100644 index 00000000000..27397205942 --- /dev/null +++ src/hg/makeDb/trackDb/mouse/mm39/tads3dgb.ra @@ -0,0 +1,315 @@ +track tads3dgb +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 + 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 + mouseOver 3DGB TAD domain: mESC (Embryo, Hi-C) + + track tads3dgb_424 + parent tads3dgb off + 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 + mouseOver 3DGB TAD domain: CH12-LX (Blood, Hi-C) + + track tads3dgb_429 + parent tads3dgb off + 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: 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 + mouseOver 3DGB TAD domain: TSC R2 (Embryo, Hi-C) +