Transcriptome profiling of NE-4C cells and NE-4C cells with knockdown of Setdb1 by RNA-sequencing

NE-4C is a mouse neural stem cell line used for study of neuronal differentiation. 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 NE-4C cells led to neuronal differentiation. Setdb1 was knocked down with specific short-hairpin RNA (shSetdb1) in NE-4C cells using lentiviral infection (NE4C_B), while cells infected with virus carrying only the empty vector was used as control (NE4C_A). Knockdown cells showed neuronal differentiation phenotype. Control cells and knockdown cells were cultured in MEM supplemented with 1% MEM non-essential amino acids, 1% Glutamax and 10% FBS, at 37°C plus 5% CO2 for 5 days, and then collected and subjected to RNA-sequencing.