Fig. 3

Allele-specific scRNA-seq analysis of XCR during iPSC reprogramming. A Experimental design to study allele-specific single-cell gene expression changes during reprogramming to iPSCs. B tSNE of gene expression levels (log2-transformed normalized counts) of the reprogramming dataset (n = 561 cells) colored by isolation time point. Each dot represents a cell. C tSNE visualization with cells colored by pseudotime along the reprogramming trajectory. Each dot represents a cell. D Normalized expression levels of representative pluripotency markers plotted along pseudotime. The fitted line was derived using the loess function. Grey areas represent the 95% confidence interval. E tSNE visualization with cells colored by the different reprogramming clusters. Each dot represents a cell. F Normalized expression of genes from selected cellular signatures in single cells during iPSC reprogramming. G UMAP of single-cell gene expression colored by dataset. Each dot represents a cell. H Expression of X-GFP transgene plotted along pseudotime trajectory. Fitted line derived using loess function. Grey areas around the fitted line represent the 95% confidence interval. I Expression of Xist plotted along pseudotime trajectory. Fitted line derived using loess function. The grey area around the fitted line represents the 95% confidence interval. J Ratio between expression from X-Mus allele and average autosomal expression in each single cell and modelled along pseudotime. The fitted line was derived using the loess function. The grey area around the fitted line represents the 95% confidence interval. K De novo kinetics of XCR reconstructed using loess regression to model the X-Mus to Cast allelic ratio calculated in each cell as a function of pseudotime for each gene. K-means clustering was used to classify by reactivation kinetics. Gene expression levels were normalized to library size (number of total counts per library) in D, F, H, and I