This track collection shows TAD domains ("contact domains") called by the ENCODE uniform Hi-C pipeline across 16 mouse biosamples. Contact domains are regions that preferentially self-interact, called by the Arrowhead algorithm (Juicer). Each subtrack is one biosample, browsable with a faceted selector (filter by organ, biosample type, assay, life stage, and call type).
The calls are native to mm10. On mm39 they are shown lifted from mm10 (noted in each track's long label); the "Calls" facet records the native call assembly.
Subtracks are colored by organ. Mousing over a domain shows the biosample and the Arrowhead corner score. The details page also reports Arrowhead's upper/lower variance and sign scores. Scores are rounded to three decimal places. Use the faceted selector on the track configuration page to choose biosamples by Organ, Biosample type, Assay (intact or in situ Hi-C), Life stage, and Calls. These calls use a different algorithm and finer resolution (5 kb) than the Dixon domains, produce smaller domains, and are not directly comparable to them.
Contact domains were produced by the ENCODE uniform Hi-C processing pipeline (Aiden lab, built on Juicer), which calls domains with Arrowhead. For each biosample, one representative experiment was selected (preferring an untreated baseline over a perturbed experiment where both were available) and its contact-domain files were pooled: each Juicer/Arrowhead paired-anchor BEDPE record (both anchors describing the same domain interval) was reduced to a single domain interval, the five Arrowhead scores retained, and replicate calls whose endpoints fell within one 5 kb bin merged (keeping the higher corner score). For mm39, the mm10 domains were lifted with liftOver, and lifted domains that came out more than twice their mm10 size were removed, because this happens when a domain spans a gap or a rearranged region between the two assemblies. The chosen ENCODE experiment accession is given in each subtrack's long label and links to the ENCODE portal.
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 dataset is available at the ENCODE portal.
Durand NC, Shamim MS, Machol I, Rao SS, Huntley MH, Lander ES, Aiden EL. Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. Cell Syst. 2016 Jul;3(1):95-8. DOI: 10.1016/j.cels.2016.07.002; PMID: 27467249; PMC: PMC5846465
ENCODE Project Consortium, Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR et al. Perspectives on ENCODE. Nature. 2020 Jul;583(7818):693-698. DOI: 10.1038/s41586-020-2449-8; PMID: 32728248; PMC: PMC7410827
Rao SS, Huntley MH, Durand NC, Stamenova EK, Bochkov ID, Robinson JT, Sanborn AL, Machol I, Omer AD, Lander ES et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell. 2014 Dec 18;159(7):1665-80. DOI: 10.1016/j.cell.2014.11.021; PMID: 25497547; PMC: PMC5635824