Fig. 1: Age-related decline in multilineage HSCs marked by low Kit expression.
A–H Multiome single-cell RNA and ATAC sequencing was performed on HSC (Lineage-Sca-1+cKit+ CD34-CD48-Flt3-CD150+) cells isolated from 2-mo (young) or 24-mo (old) female C57BL/6 mice. nTOTAL = 12,350 cells. A Volcano plot of DGE analysis between MLin-HSC vs. q-HSC subsets in young HSCs, highlighting bona fide HSC markers. B Violin plot for imputed Kit gene expression by annotated HSC subsets (as described in Fig. S2C). C Frequency of computationally defined HSC subtypes in Kithi and Kitlo subsets in young HSCs. D, E Combined Uniform manifold approximation and projection (UMAP) of young and old HSCs after Harmony batch correction, annotated by age (D) and annotated HSC subsets (q-HSC: Quiescent HSCs; Mgk-HSCs: Platelet-biased HSCs; Mlin-HSC: Multilineage HSCs; p-HSC: Proliferative HSCs; Int-HSC: Intermediate HSCs) (E). F Frequency of HSC subtypes in young and old HSCs. G Heatmap showing MAGIC-imputed gene expression values of bona fide HSC markers ordered by increasing Kit expression. H Violin plot for imputed Kit gene expression by age. Statistical analysis was performed using the Wilcoxon test. I Scaled change in frequency for each Kit HSC subset with age. J FACS analysis showing the frequency of Kithi and Kitlo HSCs by age. All data are from n = 6 mice/group (young = 6; old = 6). Error bars represent mean ± SEM. **P < 0.01, ***P < 0.001. P-values calculated by two-way ANOVA. Source data are provided as a Source Data file, Source Data Fig. 1.
