Figure 3

Single-cell RNA sequencing of trigeminal ganglia-resident CD45⁺ leukocytes from HSV-1 infected symptomatic vs. asymptomatic HLA Tg rabbits. (a) Illustration of the experimental design and validation of differentially expressed genes in CD45⁺ leukocytes sorted on day 15 p.i. from the trigeminal ganglia (TG) of SYMP and ASYMP HLA Tg rabbits. (b) Heatmap expression of the most significant 140 differentially expressed genes among eight different clusters detected in TG-resident CD45⁺ leukocytes from HSV-1 infected SYMP and ASYMP HLA Tg rabbits (top two heatmap panels). Each cluster represents an individual immune cell population, determined on the basis of specific molecular markers: CD8⁺ T cells (CD8A), CD4⁺ T cells (CD4), NK cells (NKG7), B cells (CD19), macrophages (CD68), monocytes (CD14), granulocytes (FUT4) and dendritic cells (CD1c). The t-SNE dimensionality reduction, applied to single-cell RNA sequencing data revealed eight distinct clusters of immune cell populations among CD45⁺ leukocytes for the TG of HSV-1 infected ASYMP HLA Tg rabbits (middle panels). The total number of differentially expressed genes within each immune cell clusters (nCount) (lower panels). (c) Average frequencies of different immune cell populations detected within TG-resident CD45⁺ leukocytes of SYMP and ASYMP HLA Tg rabbits. (d) Volcano plot illustrates the total copy number reads observed for all the genes within one single cell (nFeature).