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/tads3dgb.html src/hg/makeDb/trackDb/mouse/mm10/tads3dgb.html deleted file mode 100644 index eae971bf42c..00000000000 --- src/hg/makeDb/trackDb/mouse/mm10/tads3dgb.html +++ /dev/null @@ -1,66 +0,0 @@ -

Description

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-This composite shows TAD domains from the -3D Genome Browser -(3DGB) 2.0, across 30 mouse Hi-C and Micro-C datasets. Each subtrack is one 3DGB -dataset, displayed exactly as called and published by 3DGB. They are browsable with a -faceted selector (organ, cell type, assay, year, study); the displayed domain -intervals are 3DGB's own, with no UCSC re-calling, merging, or recurrence scoring. -

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-The calls are native to mm10. On mm39 they are shown lifted from mm10 (noted in each track's -long label). By default all subtracks are off; use the faceted selector to enable datasets. -

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Display Conventions and Configuration

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-Each subtrack is drawn as boxes spanning the self-interacting domains and is -colored by organ. These datasets are not a cross-comparable consensus; each -represents one dataset's own TAD calls. Because calls are made on binned Hi-C data (3DGB calls -TADs at 25 kb), domain edges are uncertain to roughly the bin size, and domains do not tile -the genome end to end. -

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-The facets are Organ, Cell type, Assay, Year, and Study. -(The human 3DGB track additionally offers Condition, Treatment, and Provenance facets; those -were manually curated for the human datasets and are not provided here.) -

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Methods

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-TAD domains were called by the 3D Genome Browser pipeline and are displayed verbatim. UCSC -performed only a format normalization (reshaping the published per-dataset BED-like file to a -plain four-column bigBed) and, for mm39, a liftOver from mm10; no domain coordinates -were changed and no re-calling was performed. The dataset metadata used for the faceted -selector was copied directly from the 3D Genome Browser. -

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Data Access

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-The raw data can be explored interactively with the -Table Browser or the -Data Integrator. For programmatic access, the -track can be accessed using the Genome Browser's -REST API. -The underlying bigBed files can be downloaded from our -download server. -The complete original datasets are available from the -3D Genome Browser. -

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Credits

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-Thanks to the 3D Genome Browser team (Yue lab, Northwestern University). The 3D Genome Browser -data are distributed under a -CC BY-NC 4.0 -license (free for non-commercial use). Please cite the 3D Genome Browser, and the original -studies, when using these data. -

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References

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-Yu S, Fu Y, Wong JH, Wang J, Zhao H, Zhao J, Yue F. -The 3D Genome Browser 2.0: an enhanced online platform for visualizing and analyzing 3D -genome architecture. Nucleic Acids Res. 2026;54(D1):D48-D54. -doi:10.1093/nar/gkaf1109 -