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Summary A defined protocol for efficiently deriving endothelial cells from human pluripotent stem cells was established and vascular morphogenesis was used as a model system to understand how synthetic hydrogels influence global biological function compared with common 2D and 3D culture platforms. RNA sequencing demonstrated that gene expression profiles were similar for endothelial cells and pericytes cocultured in polyethylene glycol (PEG) hydrogels or Matrigel, while monoculture comparisons identified distinct vascular signatures for each cell type. Endothelial cells cultured on tissue-culture polystyrene adopted a proliferative phenotype compared with cells cultured on or encapsulated in PEG hydrogels. The proliferative phenotype correlated to increased FAK-ERK activity, and knockdown or inhibition of ERK signaling reduced proliferation and expression for cell-cycle genes while increasing expression for “3D-like” vasculature development genes. Our results provide insight into the influence of 2D and 3D culture formats on global biological processes that regulate cell function., Graphical Abstract, Highlights • Defined, high-efficiency differentiation of human PSCs to endothelial cell • Comprehensive genome-wide comparisons of 2D and 3D cell-culture formats • Gene expression profiles for endothelial cells and pericytes in 3D cell culture • Highly proliferative phenotypes on tissue-culture polystyrene surfaces, Murphy, Schwartz and colleagues report a genome-wide analysis of biological function for endothelial cells and pericytes cultured using 2D or 3D formats. Global gene expression patterns are comparable for vascular cells cultured in synthetic hydrogels or Matrigel during vascular network formation, while cells cultured on tissue-culture polystyrene surfaces adopt a proliferative phenotype that correlates to increased FAK-ERK activity.