Systemic determination of PRDM16 regulatory genes in the aorta. 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.