Single-cell RNA-seq quality control metrics and lineage assignment. (A–C) t-SNE (distributed stochastic neighbor embedding) plots from ABM and E13.5 FL samples overlaid with number of genes detected per cell (A); genotype of each cell (B); and unsupervised graph-based clustering (C). (D) Heatmap of the average expression of Haemopedia lineage signature genes in each cluster defined for ABM (i) or E13.5 (ii) samples. Only genes that were detected in the samples are shown. Cluster numbers as in C. Lineages assigned to each cluster using lineage signatures defined from Haemopedia mouse RNA-seq (iii). (E–G) Expression of lineage specific genes for each individual cell across tSNE plot: Kit (progenitor cell associated gene; E); Itgb3, Pf4, Gp9, and Mpl (Mk-associated genes; F); and Gypa, an erythroid associated gene whose expression was enriched in Nfe2^−/− Mk cluster, and Tspo2, which is also an erythroid associated gene but was not detected in the Mk clusters (G).