scRNA-seq of bone marrow basophil/mast cell progenitors reveals transcriptional profile distinct from GMPs. (A) Schematic showing process of isolating BMCP and GMP cells for parallel single-cell sequencing and culture experiments (Figure 2). Table indicates numbers of cells that passed quality and median number of genes detected in scRNA-seq samples. (B) Diffusion map calculated on 4267 highly variable genes from scRNA-seq data colored by cell type. (C) Diffusion map colored by clusters assigned by hierarchical clustering. (D) Heatmap displaying Z-score transformed expression of 15 most significantly differentially expressed genes specific to each cluster. Genes in top rows are upregulated in cluster 1 vs cluster 2, genes in middle rows are upregulated in cluster 2 when compared with cells in clusters 1 and 3, and genes in bottom rows are upregulated in cluster 3 cells when compared with cells in clusters 1 and 2. The colored bars at the top of the heatmap indicate cluster and cell type identity of cells in the columns. (E) Expression of groups of genes from heatmap in panel D in the droplet-based scRNA-seq data. A geometric mean score of counts was calculated for each cell across the genes in a group. The color of cells indicates the value of this score, with gray being the lowest value and red the highest value. Insets in left and center panels show magnifications of regions in black boxes. DC, diffusion component.