Fig. 3. Chromosome-wide gene silencing dynamics.

a Violin plot showing the distribution of the allelic expression ratio for the entire X chromosome excluding Xist, as the fraction of X-chromosomal reads mapping to the B6 chromosome, in Xist-positive (pink) and Xist-negative cells (black). Horizontal lines indicate the median values. b Scatter plots showing spliced (top) and unspliced (bottom) reads mapping to the X chromosome on the B6 and Cast alleles. Cells are colored by Xist expression pattern as in Fig. 2a and indicated in the gray box on the right. c The first two principal components, computed on the allelic expression ratio for all X-linked genes with the color indicating the chromosome-wide allelic fraction. Arrows indicate the predicted change of the X-linked allelic fraction based on RNA velocity analysis. d Scatter plot showing the X-chromosomal allelic fraction vs. Xist’s allelic fraction, for cells with >5 allele-specific Xist UMI counts. e Box plot showing the X:A expression ratio in cells assigned to different Xist classes, as indicated in the gray box above the plot, based on allele-specific mapping as in Fig. 2a. 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. Dots represent individual cells and cell numbers are indicated on top. Source data are provided as a Source Data file.