Figure 5 Single-cell RNA sequencing (scRNA-seq) cross-validation and characterization of the newly identified CD8+CD45RA+CD27+CD161+T cell population
A. Uniform manifold approximation and projection (UMAP) plot visualizing the clustering results from re-analysis of the scRNA-seq data for naïve CD8+ T cells from GEO: GSE158493.
B. Violin plot visualizing the expression of KLRB1(encoding CD161) across clusters identified by Seurat from scRNA-seq analysis. Red dots indicate the average expression of the corresponding group.
C. Volcano plot showing the differentially expressed genes comparing CD8+CD45RA+CD27+CD161+and CD8+CD45RA+CD27+CD161-T cell subsets. The red dots indicate genes up-regulated in CD8+CD45RA+CD27+CD161+T cells, the blue dots indicate genes down-regulated in CD8+CD45RA+CD27+CD161+T cells, and the black ones are genes without significant changes.KLRB1 , the gene that we used as the population-defining gene for cluster3 was specified.
D. Dot plot for the activated (left) and suppressed (right) pathways in CD8+CD45RA+CD27+CD161+T cell subset compared to CD8+CD45RA+CD27+CD161-T cell subset analyzed by ClusterProfiler. The size of the dot corresponds to the number of genes within the corresponding pathway, the GeneRatio is calculated by the ratio between the number of genes that are significantly differentially expressed comparing CD8+CD45RA+CD27+CD161+and CD8+CD45RA+CD27+CD161-T cell subsets and the number of total genes involved in the corresponding pathway, and the color gradient reflects the adjusted p-value for the comparison.
E. The top enriched gene sets of gene set enrichment analysis (GSEA) comparing CD8+CD45RA+CD27+CD161+and CD8+CD45RA+CD27+CD161-T cell subsets based on the Hallmark gene sets and the representative GSEA plot of the top enriched gene set “TNFA SIGNALING VIA NFKB”.
(F-G ). Visualization of differentially expressed genes comparing CD8+CD45RA+CD27+CD161+T cell subsets relative to CD8+CD45RA+CD27+CD161-T cell subsets that are involved in T cell receptor (TCR) signaling pathway (F ) and mitogen-activated protein kinase (MAPK) signaling pathway (G ).