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[Preprint]. 2023 Jan 24:2023.01.24.525203. [Version 1] doi: 10.1101/2023.01.24.525203

Figure 3: Antigen-specific clonal expansion of vaccine-induced CD8+ T cells.

Figure 3:

(A) Schematic of ECCITE-seq experimental design. (B) UMAP visualizations of 31,396 single cells profiled with ECCITE-seq and clustered based on weighted combination of RNA, protein and T-cell receptor information. (C) Violin plots for CD38, HLA-DR and KLRG1 protein levels, and the expression of identified vaccine-induced gene module. (D) Left: UMAP visualization from (B), dextramer-positive (Dex+) cells are highlighted in red. Right: The fraction of cells harboring spike-specific TCR in each cluster. A TCR clone is considered spike-specific when at least one cell of the clone is Dex+. Boxplot shows variation across n=10 samples. (E) UMAP visualization from (B), cells are colored by the expansion index of their associated clonotype based on TCR sequence information. (F) UMAP visualization from (B), cells representing the six most abundant spike-specific clones are highlighted.(G) Boxplots showing the fraction of cells harboring TCR matching SARS-CoV-2 spike antigens in public databases. (H) Boxplots showing the single-cell expression of the vaccine-induced gene module in antigen-specific cells. Cells are grouped by labels in (E).