Fig. 2. Allele-specific analysis of Xist expression.

a Scatter plot showing Xist UMI counts mapping to the B6 and Cast chromosome in individual cells. Cell coloring indicates the Xist pattern classification, where Xist detection from only one allele is termed monoallelic (MA, orange, green). Detection of both chromosomes is termed biallelic (BA, pink), if at least 20% of UMI counts come from each allele, or termed skewed (light pink) if one allele contributes <20% of reads. b Relative distribution of Xist patterns as in (a) across time. c RNA FISH of Xist under the same conditions as in (a, b). The bar graph (left) shows quantification of three biological replicates over time (100 cells were counted for each). An example image at day 2 of differentiation (right) is shown, where dotted lines indicate the outline of cell nuclei stained with Dapi (blue). d Violin plot comparing Xist allelic expression levels from the B6 (green) and Cast chromosomes (orange) in Xist-MA cells. The horizontal line indicates the median value and p values of a Mann–Whitney U two-sided test are shown. Source data are provided as a Source Data file.