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. 2024 Apr 1;9:70. doi: 10.1038/s41541-024-00860-w

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 6 — a Left, Volcano plots of scRNA-seq differential expression analysis of “durable” vs. “transient” expanded CD8 T cells. Right, Breakdown of the statistical significance of differential expression into the discrete component (expressed vs. non-expressed) and continuous component (changes in expression level given that the gene is expressed). Each dot summarizes the result for a gene. FDR: false discovery rate. FC: fold change. b Summary of gene set enrichment analyses for responsive “transient” vs. non-responsive, responsive “durable” vs. non-responsive, and responsive “durable” vs. “transient” expanded CD8 T cells. NES, normalized enrichment score. c Gene set enrichment plots for selected significant pathways in the differential expression of “durable” vs. “transient” expanded CD8 T cells. Dashed lines represent minimum and maximum cumulative enrichment scores. d Uniform manifold approximation (UMAP) plots of T cells from expression clusters enriched for “transient” or “durable” expanded V160-responsive clones identified in Fig. 4b. Cells are colored by V160 response type (top) or T cell type (bottom). e Left, Volcano plots of scRNA-seq differential expression analysis of V160 responsive “durable” CD8 T cells subcluster C vs. B in (d). Right, Breakdown down the statistical significance of differential expression into the discrete and continuous components. f Summary of gene set enrichment analyses for V160 responsive “durable” CD8 T cells subcluster C vs. all other CD8 T cells; subcluster B vs. all other CD8 T cells; or subcluster C vs. B. NES, normalized enrichment score. g Percentages of cells expressing selected genes within each V160 responsive T cell cluster. Significance was assessed by Fisher’s exact test. Error bars indicate the mean ± standard error of the mean. h Violin plots showing the distributions of log single-cell expression counts in each response group. Each filled dot represents the log expression of a cell expressing the gene. Open diamonds represent mean log expression. Significance was determined by the Kruskal–Wallis test.