Fig. 7. Experimental validation of differential silencing dynamics.
a To measure allele-specific silencing dynamics, the X inactivation center (Xic), which contains the Xist locus, was deleted on either the Cast (top) or on the B6 allele (bottom). Upon differentiation, the entire cell population will thus initiate XCI on the B6 and Cast allele, respectively, allowing quantification of allele-specific silencing dynamics by bulk RNA-sequencing, as shown in (b–d). b–d RNA-seq differentiation time course of the cell lines shown in (a). b Xist expression. Horizontal bars represent the mean of three biological replicates, dots the individual measurements, significance (p values) of the difference between the two cell lines according to a two-sample two-sided unpaired Student’s t test is indicated. c Xi:Xa expression ratios for all X-linked genes outside the deleted region (n = 660 genes) averaged across n = 3 biological replicates. Significance (p values) of the difference between the two cell lines according to a two-sample two-sided paired Student’s t test is indicated. The central mark indicates the median, and the bottom and top edges of the box indicate the first and third quartiles, respectively. The top and bottom whiskers extend the boxes to a maximum of 1.5 times the interquartile range. Outliers are not shown. d Xi:Xa expression ratios for differentially silenced genes, as identified in Fig. 6, normalized to the average ratio on the pre-XCI state (day 0, dashed line). Horizontal bars represent the mean of three biological replicates, dots the individual measurements. In addition, p values of a two-sample unpaired two-sided Student’s t test comparing the two cell lines are shown. Source data are provided as a Source Data file.