Figure 1. T_MEM, T_INT, and T_EFF cells express distinct transcriptional profiles.

(A) Gating strategy for cell sorting prior to RNA-seq.

(B) The first two principal components of the sorted GRA6-specific populations.

(C) Heatmap displaying the normalized expression for all genes differentially expressed in pairwise comparison (T_MEM versus T_INT, T_INT versus T_EFF, and T_MEM versus T_EFF cells). Genes were ordered and grouped based on the results of differential expression tests. Each column represents independent biological replicates (n = 3 mice for T_MEM and T_INT cells, n = 4 mice for T_EFF cells).

(D) Selected results of GSEA with Hallmark gene sets using one-versus-all comparisons (T_MEM versus T_INT and T_EFF cells, T_INT versus T_MEM and T_EFF cells, T_MEM versus T_EFF and T_INT cells). The full set of enriched Hallmark gene sets is displayed in Figure S1. Plots show normalized enrichment score (NES).

(E) Heatmap displaying the normalized expression of selected differentially expressed genes related to the indicated function.

(F) Representative flow cytometry histograms showing protein staining on T_MEM, T_INT, and T_EFF cells.

(G) Heatmap displaying the expression of selected genes from group 7, arranged by the indicated functional categories.

Values are from sorted GRA6-specific subsets (current study) or published transcriptional data on stem, transitory, and exhausted cells during LCMV infection (Hudson et al., 2019).