Fig. 3.

Expression of microglia-associated transcripts in wild-type and Csf1rko rats.

RNA was extracted from brain regions of 3 male and 3 female rats of each genotype at 3 weeks of age and subjected to RNA-seq analysis. A) Expression of individual genes of interest in brain regions. Bars on the X-axis indicate the region (upper bar), sex (central bar) and genotype (lower bar). Upper bar - region: cerebellum (orange), cortex (blue), hippocampus (green), hypothalamus (yellow), olfactory bulb (grey), striatum (pink), pituitary (red). For each brain region, lighter colours show Csf1rko. Central bar – sex: female (purple), male (blue). Lower bar – genotype: Csf1rko – red; wild type – black. Y axis shows the expression level in transcripts per million (TPM). B) Average expression of the set of 105 genes in Cluster 20, across the brain regions. Colour code is the same as in Panel A. C) List of genes in Cluster 20. The cluster includes Csf1r (blue). Selected macrophage-specific marker genes and known microglia-enriched transcripts identified in Summers et al., 2020 are highlighted in red. Transcripts encoding transcription factors are in green. Note that DEG analysis for each of these genes in each brain region is available in Table S2.