Extended Data Fig. 5: Transcriptional and chromatin accessibility changes in aged HSCs.

A, Proportions of the consensus peaks annotations in a donut chart. B, PCA plot for the ATAC-seq normalized read counts in the consensus peaks for the Ri-treatment experiment. C, Venn diagram for the number of common DARs in aged vs young and aged+Ri vs aged. D, Radar chart showing the minus logarithmic FDR for the significantly enriched GOs among the genes annotated to the DARs opening with Ri (permutation test, FDR < 0.1). E, PCA plot for the ATAC-seq normalized read counts in the aged vs young DARs for the young confined HSCs experiment. F, PCA plot for the RNA-seq normalized read counts in genes. Legend as in B. G, Volcano plots of differentially expressed (DE) genes in aged vs young and aged+Ri vs aged (moderated t-statistic, two-sided, unadjusted p < 0.001). Selected genes are shown. H, Venn diagram for the number of common DE genes in aged vs young and aged+Ri vs aged. I, Venn diagram for the number of common DE retrotranspon subfamilies in aged vs young and aged+Ri vs aged. Legend as in H. J–M, Enrichment plot and volcano plot for the acute inflammatory response GO term (J), the Interferome.org signature (K), the interferon-stimulated genes (L) and the aging signature (M) in aged+Ri vs aged. Permutation test. NES = normalized enrichment score. FDR = false discovery rate. Number of genes used for the analysis is also indicated.