Single-cell transcriptomic and epigenomic analyses of aged LT-HSCs. (A) UMAP embedding showing 21 Seurat clusters identified after unsupervised clustering. The legend on the right shows the annotation of the single clusters. (B) Stacked bar graph showing the distribution of the transcriptional annotated clusters in young and old HSPCs. (C) On the left, UMAP embedding showing four annotated Seurat subclusters identified after unsupervised clustering of cluster 0. On the right, stacked bar graph showing the distribution of the four transcriptional subclusters in young and old HSCs. (D) Heatmap showing the top 20 differentially upregulated and downregulated genes between young and old HSCs-MPP or LT-HSCs. (E) Expression of LT-HSCs module score on young and old LT-HSCs. The module score was computed based on a set of marker genes associated to LT-HSCs properties derived from previous publications. (F) Heatmap showing average log2FC of genes related to DNA replication stress between young and old HSPCs or LT-HSCs. Genes found statistically significant in at least one of the two cell populations with log2FC < −0.1 and >0.1 were shown. (G) Heatmap showing the signature strength of the six ATAC-seq signatures from NMF analysis of indicated BM HSPCs subpopulations from young (three donors, 21–28 years, n = 16 subpopulations) and old (four donors, 52–79 years, n = 15 subpopulations). (H) Signature strength assessment in CD49f⁺ HSCs from young compared with old donors for six NMF signatures. (I) Heatmap of the TF motif enrichment of signature 1 and signature 2 shows three main clusters: enriched in signature 1 only (old CD49f⁺ HSCs motifs), shared motifs and signature 2 only motifs (young CD49f⁺ HSCs motifs). (J) Log P value enrichment of indicated motifs enriched in young CD49f⁺ HSCs. Dotted red lines mark −log (0.05), indicating statistical significance. (K) Log P value enrichment of indicated motifs enriched in old CD49f+HSCs. Dotted red lines mark −log (0.05), indicating statistical significance. (L) DEGs in young and old LT-HSCs at transcriptomic level. * < 0.05; *** < 0.001.