Fig. 6: Inflammatory microglia (IAMs) derive from resident microglia and co-express MSR1 and CD206.

a Heatmap of mean expression of indicated genes between IAMs and non-IAMs. b Example flow cytometry of IAMs gating. c Total number of MSR1⁺CD206⁺ microglia in uninfected or infected (day 6 post-infection) brains. Data pooled from 2 independent experiments, n = 9 mice per time point. Data analysed by unpaired t-test, *P = 0.0166. Whiskers refer to the maximum/minimum values, the box refers to interquartile ranges, the centre line refers to the mean. d Quantification of Tmem119 expression by qRT-PCR on CD206⁺MSR1⁺ and CD206^-MSR1^- microglia (defined as CD45^intCX3CR1^hi), compared to macrophages (defined as CD45^hiCX3CR1⁺) at day 6 post-infection. Each point represents an independent sort experiment pulled from a batch of mice (10 mice per batch, n = 3 sorts in total), presented as mean +/- SEM. e Normalised counts of microglia signature genes in IAMs (red violin) and non-IAMs (grey violin), calculated from the sequencing dataset. Data analysed by Mann Whitney U-tests. *P < 0.0001. f Example histogram of Sall1-dTomato expression by microglia (CD45^intCX3CR1^hi) and macrophages (CD45^hiCX3CR1⁺) in Sall1^CreERRosa26^Ai14 mice. Graph shows quantification for 8 different animals, from 2 independent experiments. g Expression of IAMs markers CD206 and MSR1 within the Sall1-dTomato⁺ population and Sall1-dTomato^- population^. The graph shows quantification from 2 independent experiments, where each point represents an individual animal (n = 8 mice total). Data in (f, g) analysed by paired t-tests. **P = 0.0055, ***P = 0.0004.