Transcriptome profiling of HCT116 cells and HCT116 cells with knockdown of SETDB1 by RNA-sequencing

HCT116 is a colorectal cancer cell line. SETDB1 is an epigenetic modification factor responsible for catalyzing the histone modification H3K9me3. Transcription of SETDB1 gene is enriched in embryonic neural cells during vertebrate embryogenesis. SETDB1 is upregulated in cancer cells and promotes cancers. We found that knockdown of SETDB1 in HCT116 cells led to a neuronal-like differentiation phenotype. Overall design: SETDB1 was knocked down with specific short-hairpin RNA (shSETDB1) in HCT116 cells using lentiviral infection (HCT116_B), while cells infected with virus carrying only the empty vector was used as control (HCT116_A). Knockdown and control cells were cultured in DMEM supplemented with 10% FBS at 37°C in 5% CO2 for 5 days. Control cells and knockdown cells were then collected and subjected to RNA-sequencing.