Calcification of the aortic valve is a common disease affecting many people, and requires invasive valve replacement surgery to prevent irreparable damage to the heart. Understanding the molecular mechanisms that contribute to this disease will allow us to hopefully development non-invasive treatments that can slow or reverse this disease process and could potentially help treat the similar and related process of atherosclerosis. Shear stress and NOTCH1 have both been linked to aortic valve calcification and are important regulators of endothelial cell biology. We showed using RNA-seq in primary endothelial cells from human aortic valve, that shear stress controled a genetic program normally responsible for maintaining epiphyseal plates in a proliferative, non-calcified state. In addition, using siRNA knockdown of the NOTCH1 receptor and ChIP-seq, we showed activation of many of these genes including the potent inhibitor of soft tissue calcification, MGP, are directly regulated by NOTCH1 in the endothelium. Furthermore, we developed an efficient method to direct the differentiation of embryonic stem (ES) or induced pluripotent stem (iPS) cells into endothelial cells and determined that this highly pure somatic cell population has limited gene expression variation between cell lines. This method will be used to test human iPS cells derived from patients with valve calcification and NOTCH1 mutations in order to more fully define the mechanism of their disease, and hopefully allow us to directly target important signaling cascades responsible for this ectopic calcification.