In order to select for X-chromosome CpG sites subject to XCI on the 27K DNA Methylation array, we first removed probes for sites in the pseudoautosomal regions of the X chromosome, and then selected the X-chromosome probes that were partially methylated (β values between 0.09–0.85) in at least 75% of the female tissue samples and unmethylated (β value less than 0.09) in at least 75% of the male tissue samples. 452 X chromosome DNA methylation probes representing 289 genes passed these filters, of which 293 probes for 199 genes were anti-correlated with gene expression (Table S5C). To identify probes subject to XCI on the 450K DNA Methylation array, we filtered for probes that were partially methylated (0.2<β<0.8) in 90% of female tissues tissues and unmethylated (β<0.2) 90% male tissues (Table S5D).
