Figure 1. XIE reflected in high X-specific variance in female hPSCs.

(A) β values distribution of probes on the X in female (red) and male (blue) samples.

(B) Principal-component analysis (PCA) of female (red) and male (blue) samples using only X-linked probes with Brown-Forsythe p ≤ 0.01.

(C and D) Density plots of probe β variance on X and autosomes, respectively, with red lines for female samples, and blue for male samples (Kolmogorov-Smirnov [KS] distance indicated, with KS p values of 5.6e–15 and 0.78 for C and D, respectively).

(E) PCA of DMPs across female samples colored by their k-means assigned cluster (see Method details). Gray lines link different passages of the same cell line. Shaded areas represent the 95% confidence ellipse for each cluster.

(F and G) Projection of C19 and C23 iPSC validation samples, using PCs from (E), labeled by passage numbers, and colored as in (E).

(H) Fraction of DMPs demethylated to within 10% of expected DNAme loss captured in each passage of C19 and C23 iPSCs.

(I) DNAme heatmap of high variance X probes in female hPSCs. Samples within each k-means cluster (A–F) are ordered by mean X DNAme. Probes (rows) are grouped by transition (lowest q ≤ 0.05), and β value change (↑ up, ↓ down, or ~ fluctuating irrespective of transition). Cluster transitions are numbered (1–5). Cell lines with data from multiple passages are described below the heatmap, with arrows drawn between samples and the passage numbers marked.

(J) DNAme heatmap for C19 (dark gray) and C23 (light gray) iPSC samples, ordered by cluster and passage as annotated below heatmap.