Fig. 3

Dynamics of gene silencing on the Xi during XCI using allele-specific RNA-seq. a Distribution of relative expression of genes from the 129 versus the Cast allele during EB formation of ES_Tsix-stop. A log2 ratio of 0 represents equal biallelic gene expression from the 129 and Cast alleles, while positive and negative ratios represent higher expression from the 129 or Cast allele, respectively. b Distribution of absolute gene expressions from the 129 and Cast alleles (absolute allelic expression values in RPKM; see Materials and methods” for further details) in the ES_Tsix-stop ESCs during EB formation. c Median of the relative expression of genes from the 129 versus the Cast allele during EB formation of ES_Tsix-stop for highly and lowly expressed genes on chromosome X (same as the medians shown for the boxplots for chromosome X in Additional file 1: Figure S5b). For highly expressed genes we included genes showing a mean RPKM >2 over the time course (338 genes), while lowly expressed genes showed a mean RPKM ≤2 over the time course (81 genes). See Additional file 1: Figure S5 for further details