Endothelial cell (EC) dysfunction plays a key role in the pathogenesis of pulmonary arterial hypertension (PAH). To avoid cell cultures and whole lung tissue samples, we have, for the first time, used CD31 antibody coated magnetic beads in conjunction with genome scale RNA expression microarrays to profile ECs in vivo at any stage of PAH. We hypothesized that targeting early stages of the disease would identify novel mediators of PAH and genes linked to bone morphogenetic protein receptor 2 (BMPR2) signaling. Overall design: Rats were treated with either monocrotaline (60mg/kg) or saline as control with 4 animals in each experimental group. Gene expression profiling was performed on primary pulmonary endothelial cells directly after isolation from whole lung tissue 5 days after treatment.