Fig. 5: Single nuclei RNA sequencing (snRNAseq) analysis of LGTV infection shows strong IFN response in the cortex of WT mice.

a Schematic overview of the workflow. For each condition one male and one female mouse were pooled. Illustration was created using BioRender.com. b Uniform Manifold Approximation and Projection (UMAP) of 30,403 nuclei captured by droplet based snRNAseq (10x) colored by assigned identities; excitatory neurons; neuron.ex, inhibitory neurons; neuron.in, microglia/macrophages; micro/MØ, astrocytes; astro, oligodendrocytes; oligo, oligodendrocyte progenitor cells; OPC, vascular leptomeningeal cells; VLMCs, pericytes; peri, endothelial cells; endo, natural killer and CD8+ T-cells; CD8 + NK, choroid plexus epithelial cells; ChP. c Relative proportion of each cell type in uninfected and LGTV infected samples. d Dotplot showing expression of canonical marker genes used to identify major cell types. e Dotplot showing LGTV read counts for each cell type. f Number of DEGs (log₂FC > 1, p_adj < 0.05) induced by LGTV infection in WT or Ifnar^–/– mice. g Overlap in upregulated DEGs between five most reactive cell types, shown as a modified UpSet plot for WT and Ifnar^–/– separately. h Number of significant Reactome pathways following LGTV infection. i DotPlot showing examples of Reactome pathways altered by infection, color corresponding to Normalized Enrichment Score and size corresponding to -log₁₀ adjusted p-value. DotPlot showing expression of IFN-I and IFN-II (j) and ISGs (k) in infected data sets. Source data are provided as a Source Data file.