To facilitate and spearhead these efforts, the NIH Roadmap Epigenomics Program was established, with the goal of elucidating how epigenetic processes contribute to human biology and disease. One of the major components of this program consists of the Reference Epigenome Mapping Centers15, which systematically characterized the epigenomic landscapes of representative primary human tissues and cells. We used a diversity of assays, including chromatin immunoprecipitation (ChIP)9-10,16-17, DNA digestion by deoxyribonuclease I (DNase)7,18, bisulfite treatment 1-2,19-20, methylated DNA immunoprecipitation (MeDIP)21, methylation-sensitive restriction enzyme digestion (MRE)22, and RNA profiling8, each followed by massively-parallel short-read sequencing (-seq). The resulting datasets were assembled into publicly-accessible websites and databases, which serve as a broadly useful resource for the scientific and biomedical community. Here, we report the integrative analysis of 111 reference epigenomes (Fig. 1, Extended Data 1a-d), which we analyze jointly with an additional 16 epigenomes previously reported by the ENCyclopedia Of DNA Elements (ENCODE) project9,23.
