Fig. 1: Transcriptional responses of murine HSPCs to whole-body irradiation.

A Schematic representation of the experimental design and gating strategies. Wild-type C57BL/6 (WT) and p53^−/− (p53KO) mice were subjected to 3-Gray whole-body irradiation and Lin−cKit⁺Sca1⁺CD150⁺ HSPCs were isolated from the bone marrow 3 h later for RNA-Seq transcriptional profiling. B Principal component analysis graph representing the gene expression profiles of each RNA-Seq sample and showing a major transcriptional response to genotoxic stress in WT-IR but not p53KO-IR HSPCs (PC2, 15.7% variability). C Heatmap displaying 327 significantly dysregulated genes in WT-IR or p53KO-IR relative to control WT HSPCs. The significance threshold is fold change ≥|2| and false discovery rate (FDR) ≤0.05. Relative expression levels to the average of WT group are used to generate the heatmap. Hierarchical clustering of the genes using Pearson correlation and complete linkage generated three distinct gene clusters. D Gene ontology (GO) enrichment analysis on genes from the three gene clusters described in C. Top 2–3 enriched biological process GO terms are displayed; the full list is available in Table S1C. E Gene set enrichment analysis (GSEA) [83] is performed with 4436 pre-established biological process gene signatures. Heatmap displays the normalized enrichment scores (NES) of upregulated and downregulated p53-dependent HSPC transcriptional signatures in response to irradiation, with NES ≥ | 1.8| in WT-IR versus WT RNA-Seq datasets.