a, f, k, ForceAtlas2 layouts of mouse E9.5 embryos, mouse ES cell and human iPS cell single-cell k-NN graphs, coloured by cluster identity and collection time points, as indicated. b, g, l, Confusion matrices plot the overlap of cluster and time-point assignments, row-normalized. c, h, m, Top 20 positively enriched transcripts for Louvain clusters relative to all other clusters in each dataset, as detected by a two-sided Wilcoxon rank-sum test. Reported transcripts are ranked by FDR-corrected P values (Benjamini–Hochberg). Exact sample sizes are given in Supplementary Table 1. d, i, n, ForceAtlas2 layouts of single-cell k-NN graphs, overlaid with log-normalized transcript counts for indicated genes. e, j, o, Top, colours indicate pseudotemporal orderings. Bottom, heat map of selected markers of paraxial mesoderm differentiation. Approximate locations of cluster centres are indicated.