This track collection shows TAD boundaries across 21 human samples (7 cell lines and 14 primary tissues) from Schmitt et al., 2016. A boundary is the insulating region that separates two adjacent topologically associating domains. These are boundaries, not domains; for domain intervals see the Dixon 2012 TADs track.
Each boundary is a bin of about 40 kb, the fixed segment size used in the Hi-C analysis. The bin width reflects the localization precision of the analysis, not a measured physical width. Subtracks are grouped by sample type (cell line vs. primary tissue) and organ system, and colored by organ system. Because the same boundary is reported independently per sample, turning on multiple subtracks shows boundary conservation directly: a boundary present in many samples is stable across cell types, while one present in few is cell-type specific. By default, 5 samples are shown: GM12878, H1, IMR90, dorsolateral prefrontal cortex, and liver.
Boundaries were called with the insulation-score method at 40 kb resolution (1 Mb insulation square, 200 kb delta window) as described in Schmitt et al., 2016 (Supplementary Table S3). Per-sample boundary bins were obtained on assembly hg19; for this assembly they were used natively or lifted with the UCSC liftOver tool, with a small fraction of bins that did not map cleanly dropped. Lifted bins that came out more than twice their original size were also removed, because this happens when a bin spans a gap or a rearranged region between the two assemblies.
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.
Schmitt AD, Hu M, Jung I, Xu Z, Qiu Y, Tan CL, Li Y, Lin S, Lin Y, Barr CL et al. A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome. Cell Rep. 2016 Nov 15;17(8):2042-2059. DOI: 10.1016/j.celrep.2016.10.061; PMID: 27851967; PMC: PMC5478386