XO by SNP genotyping as evidenced by loss-of-heterozygosity in the pseudoautosomal regions (Figure S5A), and would be expected to have a male pattern of X chromosome DNA methylation. However, SIVF028, SIVF029, and CM8 had normal heterozygous XX SNP genotypes, indicating that they contained two different X chromosomes (Figure S5A). Therefore, the lack of DNA methylation on the X chromosome seen in these samples was due to absence of XCI, rather than deletion or uniparental disomy of the X chromosome. The remaining X-Clusters 4, 3 and 2 contained female hPSC samples, with those in X-Cluster 4 showing a uniform partially methylated pattern, and possessing a slightly higher level of methylation than the female somatic samples (X-Cluster 5). The X-Clusters 2 and 3 samples lacked DNA methylation in several non-contiguous regions of the X chromosome (Figure 5B); this was specific for hPSCs, and was not seen in tissues or primary cell cultures (Figure S5C).
