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Provided herein are methods of reducing or eliminating undifferentiated pluripotent stem cells, where the methods comprise contacting an effective amount of a compound to a heterogeneous cell population or sample comprising or suspected of comprising differentiated cell types and undifferentiated pluripotent stem cells, whereby the contacting selectively reduces or eliminates undifferentiated pluripotent stem cells from the cell population or sample. Also provided are methods for obtaining a population of stem cell-derived cell types substantially free of undifferentiated pluripotent stem cells as well as isolated populations of such of stem cell-derived cell types.

Disclosed are methods and systems for testing the effects of various morphogens and/or feeder cells on the differentiation of pluripotent cells. The assays described herein can be used for determining the optimum conditions that lead to differentiation of stem cells. Once the optimum conditions for stem cell differentiation are determined, such cells may be used in a variety of therapies.