Fig. 4: Dynamic allele usage of X-linked genes in human developing tissue.

a Force-directed graph of snRNA-seq data from iPSCs and organoids (d30) using the A-ctrl and the hoik1 iPSC lines showing cluster and lineage annotations. Diffusion pseudotime is indicated in the dashed box. Number of cells total: 18.638, A-ctrl: 901, hoik1: 17.737. b Degree of biallelic expression of X-linked genes. c Expression of XIST in snRNA-seq data. d PAGA plot showing XIST expression and the degree of biallelic expression. e Dot plot showing in individual cells (all cells included in the embedding in Fig. 4a) the correlation between XIST expression and biallelic score. The color code indicates the expression level of the progenitor marker SOX2. f Fitted line plots indicating the reactivation score (left) and the full escapee score (right) in XIST positive cells along diffusion pseudotime. 95% confidence interval is shown as a transparent band in the respective same color. On the X-axis the expression levels of selected marker genes are shown along pseudotime. g Force-directed graph embedding of published scRNA-seq data³⁴ showing the clusters of six female human developing spinal cord samples. Number of cells total: 39.210. Inset shows diffusion pseudotime. h Degree of biallelic expression (upper plot) and XIST mRNA level (lower plot). In a, b, c, g, h FA: force atlas. i Heatmap depicting the Z-score of biallelic expression of all non-pseudoautosomal genes detected to be biallelically expressed in distinct differentiation lineages. npc (neural progenitor cells), gaba (GABAergic neurons), glut (glutamatergic neurons), mn (motoneurons), pm (paraxial mesoderm), pns (peripheral nervous system), fp-rp (floorplate-roofplate), mg (microglia), bl (blood cells), endo (endothelial cells), fibro (fibroblasts), summarized in Supplementary Data 4. j Line plot showing biallelic expression of non-pseudoautosomal genes along pseudotime in the CNS lineage (central nervous system, clusters 0, 1, 5, 7, 9, 10, 11, 12). 95% confidence interval is shown as a transparent band in the respective same color. On the X-axis the expression levels of selected marker genes are shown along pseudotime. k Density plot showing biallelic expression and XIST expression in the same cells separated by developmental age. CS Carnegie Stage.