We jointly processed and analyzed our 111 reference epigenomes with 16 additional epigenomes from ENCODE9,23. We generated genome-wide normalized coverage tracks, peaks and broad enriched domains for ChIP-seq and DNase-seq7,32, normalized gene expression values for RNA-seq33, and fractional methylation levels for each CpG site31,34-35. We computed several quality control measures (Fig. 2, Table S1) including: number of distinct uniquely mapped reads; the fraction of mapped reads overlapping areas of enrichment18,36; genome-wide strand cross-correlation37 (Fig. 2e-g); inter-replicate correlation; multidimensional scaling of datasets from different production centers (Fig. S1); correlation across pairs of datasets (Extended Data 1e); consistency between assays carried out in multiple mapping centers (Table S2); and read mapping quality for bisulfite-treated reads38-39. Outlier datasets were flagged, removed or replaced, and lower-coverage datasets were combined when possible (See Methods).
