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Fig. 3 | Genome Biology

Fig. 3

From: Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation

Fig. 3

X inactivation-associated structural changes in Tsix-stop cells during differentiation. A Heatmaps of X-chromosome (left) and chromosome 1 (right) allelic contact decay profiles (CDPs) for the 129 (red bar) and cast (blue bar) alleles for 1390 Tsix-stop cells (rows) with at least 50 contacts per allele (along both chrX and chr1). Cells are sorted by time point (d0, d3, d7, d11, and NPCs, separated by black horizontal lines and with cell counts shown by the n number) and then by the presence of a bipartite Xi, if detectable. (Note that XCI is skewed towards the 129 allele in Tsix-stop cells.) The heatmap color scale reflects z-scaled counts within contact distance ranges shown along the x-axis. Contact counts were binned within exponentially increasing contact distances ranges (2^x where x was incremented by 0.125). These bins were then aggregated further to reduce noise by combining the counts within 10 non-overlapping bins at a time. B Line plots of the CDPs described in A for chrX parental alleles (129 in red, cast in blue) in Tsix-stop at the indicated time points during differentiation from ESCs (d0) to embryoid bodies (d11), as well as neural precursor cells (NPCs) for cells classified as not having the Xi bipartite structure (top row) and those that do exhibit CDPs indicative of an Xi on their 129 allele (bottom row). The average allelic CDP is plotted over the plots of CDPs for each individual cell. Spearman correlation values between the two mean allelic CDPs (i) and median of the Spearman correlation values between allelic CDPs for each cell (ii) are given in the top left corner of each plot. C Distributions of the difference between the long-range to mid-range differences (LMDs) of each allele (as described in Fig. 2 I and the “Methods” section) for each cell as described in A for chrX (green) and chr1 (black). The dashed lines represent a threshold chosen below which cells were called as having an Xi bipartite structure based on the chrX allelic CDP LMD differences. This threshold represents a 10% false-positive rate (FPR) based on the distribution for chr1 allelic CDP LMD differences. See Additional file 1: Table S2

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