Figure 1.

DNA methylation is higher on the X chromosome in placentas from female bearing pregnancies. DNA methylation levels were assessed at 8346 CpG sites on the X chromosome. DNA methylation of placental tissue from three publicly available data sets (GSE44667, GSE54399 and GSE57767) for a total of 19 male and 22 female term uncomplicated placentas was assessed. Probes that had missing values for samples were discarded, leaving 8346 X chromosome probes for all samples. Normalization was performed using the beta-mixture quantile normalization (BMIQ) method, which corrects for the two different designs of probes, followed by quantile normalization (Teschendorff et al. 2013). Batch effects were corrected using the Combat function implemented in the ChAMP Bioconductor package (Leek et al. 2012, Morris et al. 2014). Sample sex was identified using the minfi package in which the median value of theβvalues for probes that mapped uniquely for the X and Y chromosome, respectively, were first determined (Aryee et al. 2014). This resulted in the identification of 19 male and 22 female placentas. The overall DNA methylation for the X chromosome in each sample was calculated by taking the overall meanβvalue of all the probes that map to the X chromosome.