Fig. 1

RNA-sequencing of optic nerve head microglia from D2 and D2-Gpnmb⁺mice. Microglia were FAC sorted from freshly isolated optic nerve heads and identified by being CD45^lo/CD11b⁺ (a, see also Methods). Following RNA-sequencing of microglia from D2 and D2-Gpnmb⁺ optic nerve heads, samples were grouped by unsupervised hierarchical clustering (b; blue = strong correlation, red = weak correlation), creating D2 and D2-Gpnmb⁺ clusters (* denotes outlier excluded from subsequent analysis). c 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 c. d Scatter plot of all genes by mean log₂ counts per million (CPM) for D2 (y) against D2-Gpnmb⁺ (x) showing DE genes (pink, q < 0.05; red, q < 0.001; non DE genes in grey) with top 20 DE genes annotated. Pathway analysis of DE genes revealed dysregulation of pathways involved in the microglial sensome and metabolism (e and f. Wikipathway analysis (e) showed significant dysregulation of 2 inflammatory pathways (q < 0.05). The number of DE genes within each pathway is shown . Ingenuity pathway analysis (f) also showed dysregulation of a number of sensome and inflammatory pathways, and metabolism pathways. Top 20 pathways sorted by z-score are shown, with the threshold for significant activation or inhibition marked. We queried metabolism dysregulation (g) demonstrating a trend towards an increased ratio of mt-RNA:nu-RNA in D2 microglia (P = 0.23) and DE gene expression (red, q < 0.05) in mitochondrial transcripts from nu-RNA and mt-RNA. DE of genes involved in OXPHOS and glycolysis/gluconeogenesis (GNG). In f^†PPRs = pattern recognition receptors