Supplementary Figure 4: RNA and protein abundance exhibit low correlation.

a, Log₂ fold change in WCP protein abundance and RNA transcript abundance identified in WCP mass spectrometry and RNA-seq experiments, respectively, in CD4⁺ T cells rested or restimulated for 4 h with CD3+CD28 antibody coated beads (3:1 cell:bead ratio). WCP and RNA data is shown for all identified WCP proteins (gray) or significantly increased and decreased WCP proteins (red), along with the correlation coefficients for each group. Significantly increase and decreased proteins were classified by WCP log₂ fold change p-value < 0.01, as calculated by a two-tailed student’s t-test. b, WCP protein abundance (measured by z-score on average of rested and restimulated CD4⁺ T cells) compared to RNA transcript abundance (measured by log₁₀ transformed read count average of rested and restimulated CD4⁺ T cells) in CD4⁺ T cells rested or restimulated, as described in (a). WCP and RNA data is shown for all proteins (gray) or ubiquitylated proteins (cyan), identified in di-glycine remnant mass spectrometry experiments in CD4⁺ T cells rested or restimulated, as described in (a). a, b, Correlation coefficients were calculated using the Pearson’s method.