Fig. 1: Minor changes to T cell proteome during early stages of activation.

a Schematic of CD4 and CD8 T cells isolation, TCR stimulation, and parallel transcriptomic and proteomic analysis at 6-time points using RNA sequencing (RNA-seq) and data-dependent acquisition proteomic analysis (DDA-proteomics), respectively. The number of transcripts/proteins pre- and post-quality control is indicated, along with criteria for differential expression (DE) analysis. b Characterization of stages of T cell activation using the T cell activation markers, CD69 and CD226, and proliferative T cells (CTV^-) by flow cytometry; early activation (CD69^highCD226^lowCTV⁺) and late activation (CD69^highCD226^lowCTV^-). c Bar graphs show the mean percentage and the standard error of the mean (SEM) error bars of CD69⁺ and CTV^- T cells at 7d. Significance was determined using Mann-Whitney rank analysis to compare between CD4 and CD8 T cells. *p < 0.05. d Principal component analysis shows the relationship of mRNA and protein data from three biological replicates across different time points. e The ratio of mRNA and protein differentially expressed at different time points in relation to their corresponding unstimulated controls (0 h = 1). f Bar charts indicate DE genes and proteins in CD4 T cells and CD8 T cells as a percentage of total mRNA/ proteins detected at each time point in relation to unstimulated cells (0 h). yellow: upregulated, blue: downregulated mRNA/ proteins.