Ifnar1 deletion has only modest effects on immature progenitor populations when the populations are defined by single-cell transcriptomes rather than surface marker phenotypes. (A) Heatmap identifying 13 distinct clusters after iterative clustering via ICGS2. The clusters are numbered (ranging, 1-29), as defined by the ICGS2 algorithm. The clustering reflects aggregates of separately sorted LK and LSK cells from Ifnar1^+/− and Ifnar1^–/–-mice. Genotypes and cell types are indicated by color coding in the second horizontal bar above the heatmap. (B) HSC, MPP, and committed progenitor populations were defined based on surface markers as per supplemental Table 2. The frequencies of each phenotypically defined population within the LK samples are shown for Ifnar1^+/− and Ifnar1^–/–-mice. (C,D) UMAP plots showing clustering results for Ifnar1^+/− and Ifnar1^–/–-LK and LSK cells. Differentiation states are indicated based on marker gene expression for each cluster. Clusters are color coded to match panel A. Cluster 16, a T-cell–biased MPP population, is indicated by the hashed circle. (E) Percentages of LK cells in clusters 4, 16, 25, and 29 with the indicated surface marker phenotypes. (F) Percentages of LK cells in HSC cluster 4 or MPP clusters 16, 25, and 29 in Ifnar1^+/− and Ifnar1^–/–-mice. (G) Percentages of LK cells in myeloid clusters 7, 8, and 15 in Ifnar1^+/− and Ifnar1^–/–-mice. (H) Summary of changes in HSC, MPP, and pGM frequencies when the populations are defined by surface marker phenotype as compared with single-cell transcriptomes. ∗P < .05; ∗∗P < .01; ∗∗∗P < .001 by the χ² test.