Fig. 3

a Schematic of region-specific bulk-sequencing approach using Tg(mpeg1.1:EGFP). b Principal component analysis (PCA) plot of top 500 most variable genes for OT, MB, HB regions (dots = independent replicates from 10 pooled fish/replicate). c Heatmap of differentially expressed genes (DEGs) from mpeg1.1-EGFP positive cells across brain regions (adjusted p value < 0.05). Selected top differentially expressed genes from each cluster highlighted. Color-coding, decreased expression; blue, no expression; white, high expression; red. d?e Representative images and quantification of cd74a expression across brain regions by in situ hybridization (ISH), colocalized with mpeg1.1-GFP+. Quantification shows a percentage of cd74+ mpeg1.1-GFP+ microglia within each brain region. Dots represent three individual fish, data are mean ± SD. One-way ANOVA with Tukey?s post hoc test. **p < 0.0079, ****p < 0.0001, **p < 0.0021. Scale: 50 µm. All images are representative of the n = 3 replicates. f?g Representative images and quantification of ctsba expression by ISH colocalized with mpeg1.1-GFP. Quantification shows percentage ctsba+ mpeg1.1-GFP+ microglia within each brain region. Dots represent three individual fish, data are mean ± SD. One-way ANOVA with Tukey?s post hoc test. ***p < 0.0003, ****p < 0.0001. Scale: 50 µm. All images are representative of the n = 3 replicates. See also Fig. S4, Supplementary Data S4.