Local and global differences in signaling programs of c-Kit mutant mice are revealed by single-cell transcriptional profiling and functional assays. (A) Log₂ fold-change of the percentage of cells in a cluster in the W⁴¹/W⁴¹ WT data divided by the percentage of cells mapped to that cluster in the WT data. Left-hand and right-hand bars indicate fold-changes for samples from 2 separate mice. Fold changes are only displayed for WT clusters with >100 cells. (B) Division kinetics of single WT and W⁴¹/W⁴¹ HSCs. (C) Colony size of single WT and W⁴¹/W⁴¹ HSCs at day 10. The results in panel B are derived from 5 WT and 5 W⁴¹/W⁴¹ mice, in which at total of at least 500 single HSCs were analyzed per genotype. The results in panel C are derived from 6 WT and 7 W⁴¹/W⁴¹ mice. A total of 598 WT and 629 W⁴¹/W⁴¹ HSCs were analyzed in panel C. The frequency of HSCs that formed colonies was 94% in WT and 95% in W⁴¹/W⁴¹ mice. The means and standard error of the mean of the mice are indicated. Unpaired 2-tailed Student t tests for each time point; *P < .05, **P < .01. Clone size estimates: VS, very small (<50 cells); S, small (50-5000 cells); M, medium (5000-10 000 cells); L, large (10 000-50 000); and XL, extra large (≥50 000 cells). (D-G) Violin plots showing the distribution of selected genes in WT and corresponding W⁴¹/W⁴¹ clusters, as measured by scRNA-seq. Distributions are shown for clusters containing >100 WT cells. Colors correspond to those in Figure 4. Data from WT and W⁴¹/W⁴¹ mice were normalized independently.