Fig. 4: HSCs undergo considerable gene expression changes during aging.
a UMAP visualization of single-cell RNA-seq data from stem- and progenitor cells, from juvenile, adult, and old mice (nJCD49b– = 115 cells, nJCD49b+ = 118 cells, nJLMPP = 34 cells, nJGMP = 11 cells, nACD49b– = 133 cells, nACD49b+ = 144 cells, nALMPP = 55 cells, nAGMP = 73 cells, nOCD49b– = 145 cells, nOCD49b+ = 135 cells, nOLMPP = 32 cells, nOGMP = 26 cells). Cells are colored by population (top) or age (bottom). b Heatmap of normalized expression for differentially expressed genes between juvenile and old HSCs. The top 50 differentially expressed genes up in juvenile and old, with padj < 0.01 and log2FC > 1 (LR test), are shown. c Gene set enrichment analysis for old compared to juvenile HSCs and the indicated custom gene sets from Svendsen et al.37 and Mann et al.35. d Proliferation and quiescence scores for all analyzed stem- and progenitor cells, regardless of age. e Proliferation and quiescence scores for juvenile, adult, and old HSC subsets. f Calculated HSC-score for stem- and progenitor cells from juvenile, adult, and old mice. All statistical analyses were performed two-sided, with Kruskal–Wallis with Dunn’s multiple comparison test in d and e and Mann–Whitney test in f. Only the HSC subsets were included in the statistical analysis in f. NES normalized enrichment score, J juvenile, A adult, O old. See also Supplementary Fig. 6. Source data are provided as a Source Data file.
