Each of the 127 epigenomes included consolidated ChIP-seq datasets for a core set of histone modifications - H3K4me1, H3K4me3, H3K27me3, H3K36me3, H3K9me3 as well as a corresponding whole-cell extract sequenced control. 98 epigenomes and 62 epigenomes had consolidated H3K27ac and H3K9ac histone ChIP-seq datasets respectively. A smaller subset of epigenomes had ChIP-seq datasets for additional histone marks, giving a total of 1319 consolidated datasets (Table S1, QCSummary sheet). 53 epigenomes had DNA accessibility (DNase-seq) datasets. 56 epigenomes had mRNA-seq gene expression data. For the 127 consolidated epigenomes, a total of 104 DNA methylation datasets across 95 epigenomes involved either bisulfite treatment (WGBS or RRBS assays) or a combination of MeDIP-seq and MRE-seq assays. In addition to the 1936 datasets analyzed here across 111 reference epigenomes, the NIH Roadmap Epigenomics Project has generated an additional 869 genome-wide datasets, linked from GEO, the Human Epigenome Atlas, and NCBI, and also publicly and freely available.
