The genome-wide frequency of DNA methylation at both CG and non-CG (mCH, where H = A, C or T) sites indicated that iPSCs resemble ES cells and are distinct from somatic cells. All ES cell and iPSC lines were methylated at CG dinucleotides at a higher frequency compared to the somatic cell lines (Fig. 1b), consistent with the global partially methylated state previously observed in the IMR90 fibroblast genome18. Similarly, whereas somatic cells contained negligible levels of cytosine methylation in the non-CG context, all pluripotent cells harboured significant mCH at a similar frequency (Fig. 1c), accounting for 20–30% of detected DNA methylation events in the genome. As observed in ES cells18, all iPSC genomes showed enrichment for mCH in genes (Fig. 1d). On a genome scale the DNA methylomes of ES cells and iPSCs are similar to one another and highly distinct from the primary somatic cell lines, including the adult stem cell ADS line, and this relationship agrees with clustering of cell types based on transcriptional activity (Fig. 1e and Supplementary Fig. 1a, b). Analysis of DNA methylation patterns
