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. Author manuscript; available in PMC: 2017 Jan 5.
Published in final edited form as: Cell Rep. 2016 Dec 16;18(1):54–67. doi: 10.1016/j.celrep.2016.11.054

Figure 2. CGI methylation distinguishes XeXa, XaXa, and XiXa ESCs.

Figure 2

A) Heatmap of unsupervised hierarchical clustering of RRBS-based methylation levels for CpGs within X-linked CGIs in indicated female and male ESC lines and control fibroblasts. Methylation level of 1 indicates 100% methylation and 0 absence of methylation. CpGs with constitutively low (<0.15) and high (>0.85) methylation were excluded to highlight Xi-linked intermediate methylation.

B) Violin plots of the distribution of methylation levels of CpGs in X-linked CGIs in indicated cell lines. White square=median, black diamond=mean.

C) As in (B), except for methylation levels of X-linked CpGs outside CGIs.

D) Plot of standard deviation (SD) of methylation of all X-linked CpGs and the subsets within and outside of CGIs, respectively, relative to CpG density in the 200-nucleotide window around each CpG considered, in female ESC lines with different XCI states. The number of CpGs analyzed is given.

E) Boxplot of SD values defined in (D) for X-linked CpGs within and outside of CGIs and significance testing of the difference.

See also Figure S4.