We hypothesized that the different pluripotent cells might harbor different patterns of genomic DNA methylation; thus, we performed Comprehensive High-throughput Array-based Relative Methylation (CHARM) analysis, which interrogates ~4.6 million CpG sites, including almost all CpG islands and nearby sequences termed shores2021, but does not assess non-CpG methylation. We determined the number of differentially methylated regions (DMRs) between pair-wise comparisons, using a threshold area cutoff of 2, corresponding to a 5% false discovery rate (FDR22; Supplementary Table 1a). By this analysis, ntESC were most similar to fESC (only 229 DMRs), whereas F-iPSC differed most extensively (5304 DMRs). Relative to fESC, hypermethylated DMRs predominated for F-iPSC (3349=63%) and B-iPSC (516=74%). Highlighting their functional differences, 5202 DMRs were identified between B-iPSC and F-iPSC. We confirmed the results of CHARM analysis by bisulfite pyrosequencing of multiple loci (Supplementary Fig. 2).
