Fig. 1. Microglia lack an NF-κB signature in the infected brain.

a–d Chronically infected CX₃CR₁^Cre-ERT2 × ZsGreen^fl/stop/fl mice were sacrificed and brains were harvested and processed for flow cytometry (n = 4 mice). Samples were run on a BD Aria, gated on live/singlets/CD45⁺/CD11b⁺ from which ZsGreen⁺ and ZsGreen⁻ populations were gated and sorted. Sorted cell populations were subjected to RNA sequencing. a Experimental setup. b Differential abundance testing was performed and results were plotted in R to produce a volcano plot showing differentially expressed genes between microglia and macrophage populations. Example genes are labeled in red corresponding to green dots. c GO terms statistically over-represented in macrophages compared to microglia were generated and a selection of significantly enriched pathways of interest were plotted using R. d Significantly differentially expressed genes between the two cell populations were selected based on interest and plotted in a heatmap using complete-linkage clustering of a euclidean distance matrix of all samples. e–l Representative images of brain sections from chronically infected CX₃CR₁^Cre-ERT2 × ZsGreen^fl/stop/fl mice. Experiment was performed twice. ZsGreen is shown in green (e, f, j, l) and sections were stained for Iba1 (green, g, h; gray, i, k), RelA (e, g red), Rel (f, h red), IL-1β (i, j red), and IL-1α (k, l red). Scale bars indicate 30 μm.