To assess the stability of XCI in our samples, we identified 293 CpGs on the X chromosome (using the 27K DNA Methylation array) that were methylated in a manner consistent with XCI in tissue samples (Experimental Procedures). Hierarchical clustering on the samples yielded five major sample clusters (X-Cluster 1 – X-Cluster 5), which are displayed with the CpGs ordered according to chromosomal location in Figure 5A–B. All of the female somatic samples were in X-Cluster 5, and had partial DNA methylation across the entire X chromosome, consistent with the expected somatic female X-inactivated (XaXi) state. X-Cluster 1 contained all of the male somatic and male hPSC samples (which were, as expected, unmethylated throughout the X chromosome), as well as one parthenogenetic hESC line (LLC15) and samples from four female hESC lines (SIVF024, SIVF028, SIVF029, and CM8) (Figure 5A–B). SIVF024 was 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
