Fig. 4
scRNA-seq reveals novel HSE-associated microglia/microglia-like cell transcriptome expressing neutrophil-related genes in highly infected thalamus. Chromium 10X coupled with Illumina sequencing was used to analyze the transcriptome of 2000 CD11b+ immune cells isolated with magnetic beads from the thalamus of the intranasally infected mouse on day 6 p.i. a td-UMAP visualization of aggregated scRNA-seq data, labeled by sample (three infected and two uninfected mice on day 6 p.i.), showing different cell clusters for each sample. b td-UMAP visualization of all sub-clusters labeled with different colors on aggregated scRNA-seq data. c Heatmap showing the top 150 genes whose levels of expression are highest and most differentiating in each of the 17 cell sub-clusters, revealing similar transcriptomic signatures between “in transition” microglia/microglia-like cell and Mono2 subsets. d Violin plots demonstrating differential expression (in log2 fold-change) of 4 neutrophils (Retnlg, Asprv1, Cxcr2, Il1f9) and 4 microglia (Tmem119, Fclrs, Csf1r, P2ry12)-related genes in “in transition” microglia/microglia-like cells, surveillant microglia, reactive microglia, reactive proliferating microglia, Mono1, and Mono2. Statistical analyses were performed on Loupe Browser v5. Statistically, significant results are indicated as follows: ****P < 0.001. e Stacked bar plot showing the mean relative proportion of each cell type in the thalamus of three HSV-1-infected mice (day 6 p.i.) and two uninfected control group (day 0). f Heatmap showing the number of surveillant, reactive, reactive proliferating microglia, “in transition” microglia/microglia-like cells, Mono 1 and Mono2 in three infected samples with different viral titers on day 6 p.i. The minimum and the maximum number of cells (0 and 800 cells, respectively) correspond to red and green colors, respectively