Fig. 2.

CD4⁺ T_IA cells have a distinct transcriptional profile. (A) IFN-g response in NKG2D⁺ and NKG2D⁺ CD44⁺CD4⁺ T cells (Top) and representative FACS plot gated on CD44⁺CD4⁺ T cells (Bottom) obtained from lungs of LCMV memory mice challenged with Lpn (2 dpi; n = 9, Wilcoxon matched-pairs signed-rank test). (B–E) RNA-seq analysis of CD4⁺ T cells isolated from spleens of control (Ctrl) and LCMV memory (Mem) mice. (B) Sorting strategy and principal component analysis (PCA) of the resulting populations. (C) Heatmap of genes in CD44⁻NKG2D⁻ (DN), CD44^hiNKG2D⁻ (SP), and CD44^hiNKG2D⁺ (DP) CD4⁺ T cells from LCMV memory and control mice (averaged normalized count from any population ≥10). (D and E) Differentially expressed genes (DEGs) relating to T cell migration (D) or activation (E) are highlighted. Balloon plots depicting average counts of the indicated genes for each cell population. DEGs are color-coded according to their GO classification. A curated list of migration- or cytokine receptor- and stimulatory/inhibitory receptor-related genes is shown.