Fig. 4: Altered accessibility of transcription factors in aged HSCs.

a Heatmap showing the z-scores of ATAC count values (DESeq2 normalized counts) in open (upper) and closed (lower) DARs in aged HSCs (4 biological replicates). Peaks were divided into 4 clusters using K-means clustering. Clusters and annotations are shown as in Fig. 2a. b Pie charts showing the percentage of each cluster subtype and annotation of open and closed DARs in aged HSCs. c UMAP plots illustrating the identification of cell clusters based on single cell ATAC peak profiling of young and aged HSCs. d Feature plots (left panels) and violin (right panels) plots showing the average chromatin accessibilities (normalized ATAC peak counts per million) at Aged HSC open (upper panels) and closed (lower panels) DARs. Average accessibilities were calculated using AddModuleScore function of Seurat. e Box plots showing fold expression of Aged HSC open DAR-linked genes in young and aged HSCs. Expression of DAR-linked genes is indicated as a fold expression relative to that in young HSCs (replication #1) using normalized read counts (DESeq2 normalized counts + 1). In total 381 Aged HSC open DAR-linked genes were examined in two biologically independent samples. Data derived from a single experiment are depicted. Boxes represent the 25–75 percentile ranges with the median of horizontal line. The ends of vertical lines represent minimum or maximum values. Paired Student’s one-tailed t tests were performed to calculate p values. f MA plots showing expression of DAR-linked genes in aged HSCs relative to that in young HSCs. The pink and blue dots represent up- and downregulated DAR-linked genes greater than twofold during aging, respectively. g Heatmap showing the z-scores of expression values (DESeq2 normalized counts) of representative DAR-linked genes that showed expression changes greater than twofold with q values <0.05 in aged HSCs. The distance between DARs and the nearest genes is listed in Supplementary Data 5i. Source data are provided as a Source Data file.