Fig. 2

Integration of heterogeneous scRNA-seq experiments reveals stage-specific transcriptomic signatures associated with cell type commitment in mammalian development. a The heatmap displays the percentage of variance explained for each Factor (rows) in each group (pool of mouse embryos at a specific developmental stage, columns). b, c Characterization of Factor 1 as extra-embryonic (ExE) endoderm formation (b) and Factor 4 as Mesoderm commitment (c). In each panel, the top left plot shows the distribution of Factor values for each batch of embryos. Cells are colored by cell type. Line plots (top right) show the distribution of gene weights, with the top five genes with largest (absolute) weight highlighted. The bottom beeswarm plots represent the distribution of Factor values, with cells colored by the expression of the genes with highest weight. d Line plots show the percentage of variance explained (averaged across the two biological replicates) for each Factor as a function of time. The value of each replicate is shown as gray dots. e Dimensionality reduction using t-SNE on the inferred factors. Cells are colored by cell type