Fig. 1

a Top Genome browser shot illustrating part of the target selection process for the DyMe-Seq assay design. DNAme—DNA methylation; REMC H3K27ac/H3K4me3—union peak set of H3K27ac or H3K4me3 ChIP-Seq data across 70 and 71 distinct cell types each from the Roadmap Epigenome Project; CGI—CpG island; TFBS—transcription factor binding site data across ENCODE transcription factors and cell types; DNAse—Union of DNAse I hypersensitivity sites across 92 cell types form the ENCODE project; Probes—footprint of the final hybrid capture probe set. Right Flowchart of filters and prioritization steps during the target selection process. Bottom Origin of regions selected for the DyMe-Seq targets by dataset. b Total number (y-axis, left chart) or percentage (y-axis, right chart) of distinct genomic features (x-axis) theoretically covered by the DyMe-Seq assay. Prom—promoter, CGI—CpG island, CGIShore—CpG island shore, H3K27ac—union of all H3K27ac peaks identified in 70 distinct cell types from the Epigenome Roadmap project, DNAase I—DNAse I hypersensitive clusters across ENCODE cell types, TFBS—transcription factor binding sites identified across all ENCODE TF chromatin immunoprecipitation sequencing (ChIP-Seq) experiments. c Percentage of regions covered by DyMe-Seq that overlap with different genomic features. Prom—promoter, CGI—CpG island, CGIShore—CpG island shore, H3K27ac—union of all H3K27ac peaks identified in 70 distinct cell types from the Epigenome Roadmap project, H3K4me3—union of all H3K27ac peaks identified in 70/71 distinct cell types from the Epigenome Roadmap project, DNAase I—DNAse I hypersensitive clusters across ENCODE cell types, TFBS—transcription factor binding sites identified across all ENCODE TF chromatin immunoprecipitation sequencing (ChIP-Seq) experiments. d CpG level overlap between DyMe-Seq and commonly used array or sequencing based methylation profiling methods. The y-axis is the percentage of CpGs targeted by the respective assays that are also part of the by DyMe-Seq target set. 27K, 450K and EPIC—Illumina Methylation bead arrays, RRBS—reduced representation bisulfite sequencing, CpGiant—off-the-shelf SeqCap Epi targeted bisulfite sequencing assay from Roche-NimbleGen. SureSelect—off-the-shelf targeted bisulfite-sequencing assay from Agilent