Fig. 3

RNA-sequencing of optic nerve head microglia from D2 and radiation therapy treated D2 mice. Following RNA-sequencing of microglia form D2 and radiation therapy treated (RAD-D2) optic nerve heads, samples were grouped by unsupervised hierarchical clustering (a; blue = strong correlation, red = weak correlation), creating D2 and RAD-D2 clusters (* denotes outlier excluded from subsequent analysis). b Genes were binned by log₂ fold change (bin width 0.2) and coloured to show DE genes (red; q < 0.05). A simple summary is shown in the inset of b. (c) Scatter plot of all genes by mean log₂ counts per million (CPM) for D2 (x) against RAD-D2 (y), showing DE genes (pink, q < 0.05; red, q < 0.001; non DE genes in grey) with top 20 DE genes annotated. Ingenuity pathway analysis (d) showed dysregulation of a number of sensome and inflammatory pathways, and metabolism pathways, representing a correction of the D2 phenotype in RAD treated animals. Top 20 pathways sorted by z-score are shown, with the threshold for significant activation or inhibition marked. Relevant to metabolism and signaling (e) mt-RNA:nu-RNA ratios are shown. DE gene expression (red, q < 0.05) in mitochondrial transcripts in nu-RNA and mt-RNA are shown. Genes involved in OXPHOS and glycolysis/gluconeogenesis (GNG) are compared. f Overlap of DE genes from D2 vs. D2-Gpnmb⁺ and D2 vs. RAD-D2 datasets. In e^†PPRs = pattern recognition receptors