Fig. 3

Cerebellar microglia regulate distinct subsets of genes in response to the cytokine environments induced by chronic IL-6 versus IFN-α signaling. a Microglia were isolated from the cerebellum of 1-month-old MacGreen-WT, -GFAP-IL6 and -GFAP-IFN mice and purified by FACS of live eGFP⁺ 4D4⁺ cells. RNA was isolated and reverse transcribed into cDNA, which was then amplified by PCR and sequenced. b Fragments per kilobase of transcript per million mapped reads (FPKM) of cell type-specific genes for microglia, other CNS-resident cells and peripheral leukocytes. c PCA of RNA-seq datasets of cerebellar microglia from WT, GFAP-IL6 and GFAP-IFN mice. d MA plot (representing log-ratio (M) on the y-axis and mean average (A) on the x-axis) showing transcripts differentially expressed by GFAP-IL6 cerebellar microglia compared with WT microglia. e Enrichment map of enriched GO biological processes by WebGestalt generated from the IL-6-regulated DEGs. f MA plot showing transcripts differentially expressed by GFAP-IFN cerebellar microglia compared with WT microglia. g Enrichment map of enriched GO biological processes by WebGestalt generated from the IFN-α-regulated DEGs. For d, f, the number of significantly (FDR < 0.05) upregulated and downregulated genes are indicated. For e, g, nodes in enrichment maps are significantly enriched in GO lists (FDR < 0.05) and were used to name clusters. n = 3 mice/group