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. 2023 Apr 3;6:363. doi: 10.1038/s42003-023-04747-9

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© The Author(s) 2023

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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — a Principal component (PC) analysis plot of DEG from RNA-sequencing data showing each sample separated by first two components. b Bar plot representing number of up and downregulated DEG for each memory subset compared to naïve T cells. c Three-way representation of DEG expression between CD8⁺ T_CM, T_EM, and T_EMRA. Each dot represents a single DEG; dots falling directly on an axis represent exclusive upregulation in each group, and concentric rings represent degree of log₂-fold-change differences between groups. d Overlay of C with genes belonging to two gene sets (NK cell and cytotoxicity) upregulated in CD8⁺ T_EM and T_EMRA cells, or genes representing WNT-Beta catenin and stem-like T-cell expression are upregulated in CD8⁺ T_CM cells. e, h Heatmaps showing DEGs in CD8 + or CD4 + naïve and memory subsets clustered by fuzzy c-means clustering. Highlighted examples for each module are listed. f, i Line plots showing mean expression of all genes in each cluster by subset (error bars represent ±1 SD). g, j Line plots showing expression of individual genes in cluster colored by membership score for respective cluster. Average across modules shown by black line. k Heatmap of selected genes representing differences in expression of migration-related genes. Data represents the mean expression of each cell subset. l Gene expression bar plots showing reads per kilobase million (rpkm) for the indicated genes. Data are plotted as mean ± SD; asterisks indicate DEG as detected by DESeq2 algorithm.