Bulk RNAseq analysis of Regnase-1 and/or Roquin-1 knockout primary human T cells

This repo describes analysis performed in the publication titled "Combined disruption of T cell inflammatory regulators Regnase-1 and Roquin-1 enhances antitumor activity of engineered human T cells".

Bulk RNAseq data

Sample type: primary human T cells

Number of bio samples: 3

• sample 1: mesothelin-targeting CAR-T cells, donor ID # 539, 1 technical replicate
• sample 2: mesothelin-targeting CAR-T cells, donor ID # 561, 2 technical replicates
• sample 3: NY-ESO-1-targeting TCR-T cells, donor ID # 579, 2 technical replicates

Number of experimental groups per sample: 4

• Regnase-1 knockout (Reg1-KO)
• Roquin-1 knockout (Roq1-KO)
• Regnase-1 and Roquin-1 double knockout (DKO)
• No knockout (Mock)

Total samples = 20 (sample 1 * 4 groups * 1 rep + sample 2 * 4 groups * 2 reps + sample 3 * 4 groups * 2 reps)

See Reg1_Roq1_knockout_analysis.Rmd for main analysis code and generation of data files and plots.

See XXX for processing code from raw data to input data into main analysis.