This track collection 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.
The calls are native to mm10. On mm39 they are shown lifted from mm10 (noted in each track's long label). By default a small set of reference datasets is shown (mESC, CH12-LX, and mESC WT MicroC). Use the faceted selector to enable other datasets.
Each subtrack is colored by organ. These datasets are not a cross-comparable consensus. Each represents one dataset's own TAD calls. Because 3DGB calls TADs from Hi-C data analyzed in fixed-size 20 or 25 kb bins, domain edges are only accurate to roughly one bin, and domains do not cover the whole genome.
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.)
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, removing lifted domains that came out more than twice their mm10 size (this happens when a domain spans a gap or a rearranged region between the two assemblies). No re-calling was performed, and the mm10 coordinates are unchanged from the 3DGB files. The dataset metadata used for the faceted selector was copied directly from the 3D Genome Browser.
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.
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.
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 Jan 6;54(D1):D48-D54. DOI: 10.1093/nar/gkaf1109; PMID: 41206958; PMC: PMC12807788