We obtained three independent sets of endothelial cells differentiated from iPSCs derived from a Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) patient as well as iPSCs that has been corrected for the mitochondrial mutation. Overall design: To determine transcriptomic differences between diseased endothelial cells when compared to normal controls. Please note that the processed data contains 9 sample data columns. The H9.EC.B* sample data was included in the initial analysis but removed from further analysis, and their raw data is unavailable. The H9 data was included in the processed data file to enable other users to reproduce the normalized data (e.g. Normalized Read Counts).