Figure S4. IL-2 and TCR signaling induce... | Rockefeller University Press

Figure S4.

$IL-2 and TCR signaling induce dynamic proteins near Foxp3. (A) Overlap of the proteins identified by Foxp3 PSI MS and whole-cell lysate MS. (B) Cross-comparison of differentially represented proteins after IL-2 stimulation identified by Foxp3 PSI MS versus whole-cell lysate MS. Data were derived from two or three replicates per condition. (C) Protein and mRNA levels measured by TMT MS or RNA-seq after IL-2 stimulation. iTreg cells induced from WT CD4 Tn cells in the presence of supplemented ASC were stimulated by IL-2 for 0.5 h before being harvested for RNA-seq (n = 2 biological replicates) or whole-cell lysate TMT MS (n = 3 biological replicates). (D) Top 30 factors depleted after IL-2 signaling in Foxp3 PSI MS (Foxp3 PSI FC < 1, P < 0.01, ranked by Foxp3 PSI FC). (E and F) Protein levels measured by TMT proteomics (E) or RNA-seq (F) in iTreg cells with or without TCR stimulation. iTreg cells induced from WT CD4 Tn cells in the presence of supplemented ASC were stimulated by TCR agonists for 3 h before being harvested for whole-cell lysate TMT MS (n = 3 biological replicates) or RNA-seq (n = 2 biological replicates). (G) Western blotting of indicated proteins in the following cellular fractions: cytoplasm (Cyto.), membrane (Mem.), nuclear (Nuc.), and chromatin (Chr.). iTreg cells induced from WT CD4 Tn cells in the presence of supplemented ASC were stimulated by TCR agonists for 3 h before being harvested for western blotting. Data represent two experiments. (H) Proteins enriched and depleted in Foxp3 PSI (p for PSI < 0.01) with significant changes of their total quantities after TCR stimulation (p for total proteins < 0.05). Source data are available for this figure: SourceData FS4.$

IL-2 and TCR signaling induce dynamic proteins near Foxp3. (A) Overlap of the proteins identified by Foxp3 PSI MS and whole-cell lysate MS. (B) Cross-comparison of differentially represented proteins after IL-2 stimulation identified by Foxp3 PSI MS versus whole-cell lysate MS. Data were derived from two or three replicates per condition. (C) Protein and mRNA levels measured by TMT MS or RNA-seq after IL-2 stimulation. iTreg cells induced from WT CD4 Tn cells in the presence of supplemented ASC were stimulated by IL-2 for 0.5 h before being harvested for RNA-seq (n = 2 biological replicates) or whole-cell lysate TMT MS (n = 3 biological replicates). (D) Top 30 factors depleted after IL-2 signaling in Foxp3 PSI MS (Foxp3 PSI FC < 1, P < 0.01, ranked by Foxp3 PSI FC). (E and F) Protein levels measured by TMT proteomics (E) or RNA-seq (F) in iTreg cells with or without TCR stimulation. iTreg cells induced from WT CD4 Tn cells in the presence of supplemented ASC were stimulated by TCR agonists for 3 h before being harvested for whole-cell lysate TMT MS (n = 3 biological replicates) or RNA-seq (n = 2 biological replicates). (G) Western blotting of indicated proteins in the following cellular fractions: cytoplasm (Cyto.), membrane (Mem.), nuclear (Nuc.), and chromatin (Chr.). iTreg cells induced from WT CD4 Tn cells in the presence of supplemented ASC were stimulated by TCR agonists for 3 h before being harvested for western blotting. Data represent two experiments. (H) Proteins enriched and depleted in Foxp3 PSI (p for PSI < 0.01) with significant changes of their total quantities after TCR stimulation (p for total proteins < 0.05). Source data are available for this figure: SourceData FS4.