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. 2021 Jan 19;34(3):108661. doi: 10.1016/j.celrep.2020.108661

Figure 3.

Figure 3

Single-cell RNA sequencing identifies a core gene set distinguishing two CD8+ TRM cell populations

(A) Hierarchical clustering and Uniform Manifold Approximation and Projection in R (UMAP) plot of 196 index-sorted CD103− and CD103+ CD8+ donor-derived T cells from two subjects in experiment 2 identified three transcriptionally distinct clusters of conventional CD8+ T cells. Cell labels below the dendrogram indicate the sorting plate, the subject, and CD103 expression determined by index sorting. For UMAP plot: circles, CD103− cells by index sorting; triangles, CD103+ cells by index sorting; square, unknown CD103 expression (n = 1 cell) by index sorting.

(B) Volcano plot of differential gene expression between cluster 1 and clusters 2 + 3 identified in experiment 2, with genes upregulated (right) or downregulated (left) in clusters 2 + 3 compared with cluster 1. Log2 fold change is plotted against the false discover rate (FDR)-adjusted p-value, with horizontal dotted line at FDR = 0.05. Differentially expressed genes are marked in blue, with those differentially expressed in both experiments 1 and 2 marked in red.

(C) Correlation of log2 fold change in CD8+ population 1 versus 2 in experiment 1 (10× Genomics, x axis) and clusters 2 + 3 versus cluster 1 in experiment 2 (Smart-Seq2, y axis). Blue, genes differentially expressed in both experiments; green, genes differentially expressed in experiment 1 only; yellow, genes differentially expressed in experiment 2 only; gray, genes not differentially expressed.

(D) Venn diagram showing differentially expressed genes upregulated in clusters 2 + 3 (experiment 2)/CD8+ population 1 (experiment 1) (red) versus genes upregulated in cluster 1 (experiment 2)/CD8+ population 2 (experiment 1) (green). A core gene set of 30 genes that differentiated the two populations in both experiments is listed.

(E) Violin plots showing expression of transcription factors ZNF683, JUN, and ZEB2, which showed differential expression between CD8+ TRM cell populations in experiment 1.