RNA-seq analysis to identify the genes regulated by p53-SET interplay

To identify the genes regulated by SET in a p53-dependent manner, the endogenous SET was depleted by siRNA in control or p53 knockout U2OS cells. Total RNA from each sample was extracted and the whole profile of gene expression was analyzed by RNA-seq analysis. U2OS cells were transfected with control CRISPR/Cas9 construct or SET-specific targeting CRISPR/Cas9 construct. After selection and clone identification, we got a pair of cell lines: 1) control cell line which expresses p53 as normal; 2) p53 knockout cell line which is completely loss of p53 expression. Next, control siRNA or SET-specific siRNA was transfected into these cell lines for 96 hours. Total RNA was extracted for further RNA-seq analysis.