Transcriptional profiling of 44 802 single hematopoietic stem and progenitor cells reveals a differentiation landscape with 8 lineage entry points. (A) Diagram indicating relative maturity of cells captured in LSK and LK sorting gates. (B) Sorting gate used to isolate LSK and LK cells based on c-Kit and Sca-1 surface expression for droplet-based scRNA-seq. Table indicates numbers of cells that passed quality control and median number of genes detected in scRNA-seq samples. (C) Force-directed graph embedding of scRNA-seq data on LSK and LK cells. Individual cells are connected to their 7 nearest neighbors based on similarities in their transcriptional profiles, and the resulting nearest-neighbor graph is used to calculate 2-dimensional coordinates. Top panel shows LSK cells highlighted in red, with LK cells in gray in the background. Similarly, the bottom panel highlights LK cells in purple, with LSK cells in gray behind. (D) Expression of marker genes plotted on the force-directed graph embedding. Gene expression is plotted on a log(normalized count + 1) scale, with gray equal to no counts and dark red representing the maximum value detected. (E) Expression of marker genes plotted on the force-directed graph embedding using a log(normalized count + 1) scale, with gray equal to no counts and dark red representing the maximum value detected. Insets in the bottom left of each panel display magnified branch of interest. Panels display genes relating to (i) eosinophil, (ii) mast cell and basophil, (iii) mast cell, and (iv) basophil lineages, respectively. Bone marrow cells were harvested simultaneously and pooled from 6 mice.