Fig. 3

CD4⁺ T cell help primarily alters the steady-state transcriptome of T_EM CD8⁺ T cells. a, b Volcano plots depicting results of comparative transcriptome analysis of steady-state E7-specific CD8⁺ T_CM cells (a) and T_EM cells (b) isolated from spleen at day 100 after primary vaccination with Help or No Help vaccine (n = 3 mice per group). Blue and yellow dots indicate transcripts with significant differential expression (p < 0.01). See also Supplementary Data 1 and 2. c Hierarchical clustering and heat map of the differentially expressed genes in steady-state T_EM and T_CM cells taken from the Help versus No Help vaccination settings. d Molecules differentially expressed in steady-state T_EM cells after Help versus No Help vaccination, as assigned to the indicated functional categories and annotated for subcellular localization by IPA. e Gene Set Enrichment Analysis (GSEA) of published gene sets listing the top 200 up- or downregulated genes in effector CD8 T cells (day 8 after LCMV-Armstrong infection)³⁰ within the gene expression profile of helped versus helpless T_EM cells in steady-state. ES, enrichment score; NES, normalized enrichment score. f Hierarchical clustering and heat map of genes differentially expressed in steady-state T_EM cells taken at day 100 after primary vaccination with Help or No Help vaccine, as determined here and genes differentially expressed in primary CTLs taken at day 10 from the same settings, as determined previously²⁰. Numbers and adjacent boxes (right panels) indicate Cluster 1, denoting molecules differentially expressed in both helped versus helpless T_EM cells and primary CTLs and Cluster 2, denoting molecules only differentially expressed in helped versus helpless T_EM cells, as assigned to the indicated functional categories and annotated for subcellular localization by IPA.