Single-cell transcript analysis of human embryonic stem cells.

We demonstrate the qualitative and quantitative power of single-cell transcript analysis to characterize transcriptome dynamics in human embryonic stem cells (hESC's). Single-cell analysis can systematically determine unique cellular profiles for use in cell sorting and identification, show the potential to augment standing models of cellular differentiation, and elucidate the behavior of stem cells exiting pluripotency. Using single-cell analysis of H9 hESC's differentiating under three culture conditions, we revealed transient expression of mesendodermal markers in all three protocols, followed by increasingly stable expression of embryonic endoderm and extra-embryonic endoderm markers.