Systemic determination of PRDM16 regulatory genes in the aorta
We determined the differentially expressed genes in the thoracic aorta (TA) from vascular smooth muscle cell (VSMC)-specific Prdm16 knockout (Prdm16SMKO) and control mice by RNA-sequencing (RNA-seq) analysis. We also performed chromatin immunoprecipitation (ChIP)-sequencing (ChIP-seq) analysis to identify potential target genes of PRDM16. By overlapping the RNA-seq and ChIP-seq dataset, we are able to identify the target genes of PRDM16 in the aorta and investigate the roles of PRDM16 in the vascular biology. Overall design: The thoracic aorta from Prdm16SMKO and control mice were harvested and subjected to RNA-seq analysis. The differentially expressed genes between Prdm16SMKO and control mice were analyzed. For ChIP-seq analysis, mouse fibroblast cells were infected with lentivirus carrying flag-tagged PRDM16 or vector (as control) for 48 hours and were selected with 2 ug/mL puromycin for 1 week, followed by ChIP using anti-flag antibody. The purified DNA was subjected to ChIP-seq.