MOESM2 of Perturbed maintenance of transcriptional repression on the inactive X-chromosome in the mouse brain after Xist deletion

Additional file 2. mRNA levels and DNA methylation of X-linked genes are altered upon Xist deletion. A MeCP2-EGFP mRNA levels measured by RT-qPCR in the RNA extracted from brains of Nestin-Cre Xistmut/MeCP2-GFP Xist2lox females with Xist deletion in the brain (Cre+) relative to the MeCP2-EGFP mRNA level in MeCP2-EGFP/MeCP2-EGFP females that carry the reporter gene on the Xa (Xa) (n = 3 for each group, error bars indicate SD, *** p < 0.001, Student’s t test). B Scatter plot of RNA expression levels for genes on autosomes (black) and X-chromosome (red). The genes on X-chromosome exhibit an upward shift relative to autosomes. C Cumulative expression plots of fold expression changes in mRNA level among controls (Control 1/average (Controls 2 and 3) for genes on autosomes (black) and X-chromosome (red). The two curves are overlapping (p = 0.31, Wilcoxon rank-sum test). D Scatter plot of methylation levels in promoter proximal regions of the genes on autosomes (black) and X-chromosome (red). The genes on X-chromosome exhibit a downward shift relative to autosomes.