Fig. 2

a Pearson correlation coefficient (PCC) of three distinct cell types profiled by whole genome bisulfite sequencing (WGBS, W-) and/or DyMe-Seq (D-). The PCC was calculated across all 200-bp tiles of the target region set, excluding all tiles not covered by at least 10 reads in all samples. b Scatter plot of CpG methylation levels across 200-bp tiles of the DyMe-Seq target set for two replicates of human embryonic stem cells (hESCs), each profiled with more than 1 billion reads (left) and one hESC WGBS replicate (x-axis) and an independent replicate of hESCs profiled by DyMe-Seq (y-axis) using approx. 40 million high-quality aligned reads. R indicates the Pearson correlation coefficient between the two samples. c IGV screenshot for the STAT5 locus (chr17:40,397,503-40,503,980), a key gene involved in T-cell function. From top to bottom: H3K27ac distribution in hESCs and CD8 T cells, methylation level distribution of all covered CpGs for hESCs profiled by WGBS and DyMe-Seq as well as CD8 T cells profiled by WGBS and DyMe-Seq. Each blue dot represents a single CpG, and the position on the y-axis indicates its methylation level (scale 0–100%). Black bars represent DMRs identified between hESCs and CD8 based on the WGBS or DyMe-Seq using one replicate each. DMRs are defined as tiles of our target region set that exhibit a significant methylation difference (q value ≤0.05, BH-corrected Fisher’s exact test p value) exceeding 20%. Dynamically methylated tiles within 200 bp of each other were then merged into larger DMRs. Red bars indicate positions of DyMe-Seq targets across this locus. d Pie chart indicating the number of DMRs identified between hESCs and CD8 in the WGBS data that were not recovered by DyMe-Seq (WGBS only) or found with both (Shared). e Percentage of WGBS defined hESC-CD8 DMRs overlapping with selected genomic features. f Pie charts showing the fraction of WGBS hESC-CD8 feature DMRs that are recovered in the WGBS only or found in both WGBS and DyMe-Seq