Extended Data Fig. 8: Characterizing age-related changes in mouse HSCs.

a, UMAP showing gene scores of cell type marker genes Cd3d, Elane, Hlf, and Gata1, respectively. b, Percentage of old cells in the 100-cell nearest neighbourhood for FACS sorted HSCs (left) or lineage- cells (right). c-d, UMAP showing (c) RNA and (d) ATAC levels of aging marker genes (Clu, Selp, Nupr1) in HSCs. e, Volcano plot of differential RNA testing (old-versus-young). P-values were calculated using a two-sided Wald test by DESeq2. f, UMAP showing example pseudo-bulks. Black dots represent member cells within each pseudo-bulk. g, Heatmap showing clustering of pseudo-bulks (columns) and Spectra gene programs (rows). Pseudo-bulks were grouped into 5 major HSC subpopulations as labelled at the top. h-i, UMAP showing expression of gene signatures for Mk-biased and multi-lineage HSCs. Gene signatures were obtained from ref. ⁴¹. j-m, Box plots showing expression of example Spectra gene programs across HSC subpopulations (n = 100 pseudo-bulks). Boxes show first, second, and third quartiles. Whiskers show the farthest point falling within the first quartile − 1.5 IQR or third quartile + 1.5 IQR. P-values were derived using a two-sided t-test.