Fig. 7
RNA-Seq analysis of the 56Fe ion-irradiated hippocampus at the 2-week time point. Heatmaps depict significantly-regulated genes (FDR-adjusted p < 0.05) at the 0.1 (a) and 0.2 (b) Gy dose. c Real-time PCR validation of significantly upregulated RNA-Seq regions at the 0.2 Gy 2wk time point (samples selected based on ranked p-value). Real-time PCR was conducted with absolute standard curves and 4 cDNA biological replicates. * denotes p < 0.05 and # denotes p < 0.1. d and e Overlap of top 1000 significantly-upregulated hmC regions and significantly-upregulated genes at the 0.1 (d) and 0.2 (e) Gy dose (within 50 kb of RefSeq TSS). At both doses, there was a highly significant overlap between regions with increased 5hmC and increased RNA transcription. f–i Gene ontology for the indicated significantly differentially-regulated regions (within 25 kb of RefSeq TSS). For the increased RNA transcription condition, there was more enrichment in pathways for the 0.2 (f) than the 0.1 (h) Gy dose. For the decreased RNA transcription condition, there was a highly significant enrichment for categories linked to neurodegenerative diseases, such as Alzheimer’s diseases, Parkinson’s disease, and Huntington’s disease, at the 0.1 (g) and 0.2 (i) Gy doses