Illumina HiSeq 4000 sequencing; mRNA-seq of HCT116 RNF40 knockdown cells upon TNF-alpha stimulation
mRNA-seq of HCT116 RNF40 knockdown cells upon TNF-alpha stimulation
HCT116 were grown in McCoy's medium supplemented with 10% fetal bovine serum, 100 units/ml penicillin and 100 μg/ml streptomycin at 37°C and 5% CO2.  siRNA transfections were performed using Lipofectamine® RNAiMAX (Invitrogen) according to the manufacturer's instructions. 48 hours post-transfection, cells were treated with 10 ng/mL of human recombinant TNFα for 30 min. RNA was extracted usiung QIAzol® Lysis Reagent (Qiagen) according to the manufacturer's protocol. Libraries were prepared using TruSeq RNA Library Preparation Kit v2 (Illumina®) after verifying the RNA integrity on an agarose gel. Library quality was assessed using an Agilent Bioanalyzer 2100
Experimental Factor: stimulus
none
Experimental Factor: RNA interference
scrambled siRNA