Fig. 6: Transcriptional response of DAR-linked genes to cytokine stimulation.

a Box plots showing fold expression of DAR-linked genes in young and aged HSCs after cytokine stimulation. Young and aged HSCs were stimulated with a mixture of cytokines (SCF, TPO, GM-CSF, IL-1, IL-6, and IL-11) in vitro and subjected to RNA-seq analysis at the indicated time points. Expression of Aged HSC open DAR-linked genes is indicated as a fold expression relative to that in young HSCs (0 h) using normalized read counts (DESeq2 normalized counts + 1). In total 381 Aged HSC open DAR-linked genes were examined. 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. b Heatmap showing the expression values (DEseq2 normalized counts) of representative genes that showed a significant upregulation greater than threefold (Young 3 h vs. Young 0 h) in (a). c Box plots showing fold expression of the genes linked to STAT or ATF motif-containing DARs in (a). STAT-motif and ATF-motif-containing DAR-linked genes (103 and 116 genes, respectively) were examined. 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. d Box plots showing normalized ATAC counts (counts per million, CPM) before and after cytokine stimulation of young and aged HSCs at Aged HSC open and closed DARs. Aged open DARs (428) and aged close DARs (119) were examined. 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. e Box plots showing normalized ATAC counts (CPM) before and after cytokine stimulation of young and aged HSCs at Aged HSC open DARs containing STAT or ATF binding motif. STAT-motif and ATF-motif-containing Aged HSC open DARs (108 and 117 DARs, respectively) were examined. 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. Source data are provided as a Source Data file.