Fig. 3

VISTA KO microglia in PBS-treated mice are transcriptionally distinct but not after LPS. a Number of differentially expressed genes (DEGs; logFC > 1; adjusted p-value < 0.05) comparing VISTA KO vs WT microglia from whole brain after PBS and LPS injection. b Gene ontology biological processes (red bars), molecular signatures database hallmark (blue bars), and ENCODE/CHEA transcription factors (green bars) associated with genes enriched (left) and depleted (right) in VISTA KO microglia compared to WT in PBS-treated mice. c Four-way plot illustrating logFC of DEGs after LPS compared to PBS in VISTA WT and KO mice. Color of dots indicates whether genes are differentially expressed (adjusted p-value < 0.05) in WT (blue), KO (orange), or both (grey). d Average expression of genes uniquely up- (left) or downregulated (right) in VISTA KO microglia after LPS across all samples. e Expression of Eigengenes of gene modules significantly correlating with genotype identified by WGCNA illustrated as row z-score. f Average expression of published gene sets associated with distinct microglia functions across all samples [24, 28, 29, 31, 42]. Additional information on gene sets can be found in Additional file 1: Table S3. logFC = log2 fold change, ARM = activated response microglia, DAM = disease-associated microglia, MgND = microglia neurodegenerative phenotype