Genome-wide chromatin state annotations from EpiMap and ROADMAP, classifying the genome into functional elements including active promoters, enhancers, transcribed regions, and quiescent states. Coverage spans tissues, primary cells, and cell lines across embryonic and adult samples, with broad representation of digestive, blood, brain, and lung tissues.
Data in this track hub were uniformly downloaded, processed, and harmonized by FILER2. Raw files were obtained from each source repository, converted to BED/bigBed format, lifted to the target genome assembly where necessary, and annotated with standardized metadata including cell type, tissue category, and assay type.
Source: http://www.roadmapepigenomics.org/
Publication: Integrative analysis of 111 reference human epigenomes
Citation: Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015;518(7539):317-330. doi:10.1038/nature14248
Funding: This work was supported by the NIH Common Fund as part of the NIH Roadmap Epigenomics Program through U01ES017155 (BB/AM), U01ES017154 (JC/MM), U01ES017166 (BR), U01ES017156 (JS), U01DA025956 (AM/AB), and by NHGRI through RC1HG005334, R01HG004037 (MK), RO1NS078839 (L-HT). This work was also supported by NIH fellowship grants F32HL110473 and K99HL119617 (S.L.), and NSF CAREER award 1254200 (J.E.). We acknowledge program leadership by members of the NIH Epigenomics Workgroup, especially John S. Satterlee, Frederick L. Tyson, Joni Rutter, Kimberly A. McAllister, Astrid Haugen, Christine Colvis (NCATS), James Battey (NIDCD), Linda Birnbaum (NIEHS), and Nora Volkow (NIDA). We acknowledge feedback from our External Scientific Panel members Marisa Bartolomei, Stephen Baylin, Stephan Beck, Aravinda Chakravarti, Laurie Jackson-Grusby, Jason Lieb, Steve Peckman, John Quackenbush, and Steve Stice. Sample procurement was supported by grants 5R24HD000836 (IAG) for staged fetal tissues; P30AG10161, R01AG15819, R01AG17917 (DAB) and U01AG46152 (PLD, DAB) for adult brain samples.
Source: https://personal.broadinstitute.org/cboix/epimap/ChromHMM/
Publication: Regulatory genomic circuitry of human disease loci by integrative epigenomics
Citation: Boix CA, James BT, Park YP, Meuleman W, Kellis M. Regulatory genomic circuitry of human disease loci by integrative epigenomics. Nature. 2021;590(7845):300-307. doi:10.1038/s41586-020-03145-z
Funding: We thank the ENCODE, Roadmap and GGR consortia for generating high-quality public datasets and rapidly disseminating their results to the broader community; D. Li and T. Wang, and I. Gabdank and J. S. Strattan for making our observed and imputed genome-wide tracks and chromatin-state annotations available through the WashU Epigenome Browser and the ENCODE portal, respectively; J. Ernst for advice, guidance and for developing the ChromImpute methodology and code base; P. Kheradpour for help with the motif enrichment analysis software; L. D. Ward for discussions on interactive visualizations of our predictions and HaploReg; C. Epstein, J. Schreiber, W. Noble, Z. Weng, M. Gerstein, ENCODE, Roadmap, GENCODE and GTEx consortia for feedback on early versions of this work; and I. Jungreis, X. Wang, L. Hou, L. Agudelo, S. Mohammadi, M. Wolf, A. Shi, K. Nguyen, M. Kousi, S. Kuosmanen, E. Schmauch and A. Amirabad for feedback on the work and the resource. This work was supported by the US National Institutes of Health grants HG008155, HG009446, HG009088, HG007234, HG007610, GM113708, MH109978, MH119509 and AG058002 (to M.K.) and the National Institutes of Health training grant GM087237 (to C.A.B.).