MCMV infection causes substantial alterations in the microglia transcriptome. Newborn BALB/c mice were infected with MCMV. (A) Gating strategy used to define microglia (left). Kinetics of microglia in the brain was analyzed by flow cytometry at indicated time points p.i. (right). Mean values ± SEM are shown (n = 3–6). The data are representative of three independent experiments. (B) IBA-1⁺ microglia in hippocampus from MCMV-infected and naive mice (n = 5). Scale bars, 50 µm. The data are representative of two independent experiments. (C) Infected microglia were identified with dual staining for IBA-1 (brown) and the intranuclear viral IE1 protein (red). Counterstaining was performed with hematoxylin. Arrowheads point to infected microglia. Scale bar, 50 µm (n = 5). The data are representative of two independent experiments. (D) Volcano plot of DE genes in microglia from MCMV-infected versus microglia from naive mice (n = 3). (E) Gene Ontology overrepresentation analysis showing the top 10 perturbed biological pathways in microglia from infected mice, ranked by p_adj. p_adj < 0.01 (n = 3). (F) Heatmap of DE IFN-γ response genes, MHC-I and MHC-II genes, and markers of activated microglia from naive and MCMV-infected mice (n = 3).