Differential effects of IFN-α treatment on VF and VF;Dm^Δ/Δ LT-HSCs. (A) Experimental setup for single-cell RNA seq of FACS sorted LT-HSCs. (B) Expression of selected lineage and cycling genes in reduced dimension plots. TSNE, t-distributed stochastic neighbor embedding. (C) Clustering of cells is based on the gene expression in reduced dimension plot (D) Shifts in cell identity induced by IFN-α treatment in reduced dimension plots (left); and the relative cell abundance per cell type across genotypes and treatments (right). (E) Heat map analysis of IFN response genes expression (Reactome R-MMU-91353) in quiescent LT-HSCs. Normalized expression of genes in pseudobulk samples was plotted. (F) Gene set enrichment analysis of Hallmark gene sets comparing IFN-α–treated VF and VF;Dm^Δ/Δ quiescent LT-HSCs (qLT-HSCs). (G) Fold change in the normalized expression of Cxcl9 and Cxcl10 genes derived from number of reads (counts per million) in pseudobulk analysis. Expression in vehicle–treated VF cells was set to 1. (H) PROGENy analysis in quiescent LT-HSCs. ANOVA with subsequent Tukey posttest was used. ∗∗P < .01; ∗∗∗P < .001; ∗∗∗∗P < .0001. FACS, fluorescence-activated cell sorting.