Fig. 4

Progressive establishment of the distinctive Xi architecture during differentiation. A As in Fig. 3B, but for F121 cells with additional panels showing the allelic CDPs for those cells that do exhibit CDPs indicative of an Xi bipartite structure on their cast allele (bottom row; XCI is partially skewed towards the 129 allele in F121 cells at d0–11 and completely skewed to the 129 allele in NPCs). See Additional file 1: Fig. S3C for F121 heatmaps. B As in Fig. 3C, but for F121 cells. C Plots of the proportion (%) of Tsix-stop cells with a 129 allele (red) and cast (blue) allele with an Xi bipartite structure. D As in C but for F121 cells. E Plots of the proportion (%) of Tsix-stop cells (light green) and F121 cells (light blue) with an Xi bipartite structure. F Pseudobulk allelic contact maps combining the cells that were classified as having a chrX homolog exhibiting an Xi bipartite structure (XCI cells) for EB cells (d3, d7, and d11 cells from both F121 and Tsix-stop time course experiments combined). Below each contact map is a plot of the contact score (see the “Methods” section) showing the dip in contacts across the Dxz4 locus (vertical red dashed line). G As in F, but for Tsix-stop and F121 NPCs classified as having an Xi. 450 cells were sampled from a potential 1077 inactivated NPCs in order to make the contact maps more comparable to those in F