Gene expression analysis of RNA purified from embryonic stem cells and embryoid body-derived cells using a high-throughput microarray platform.

In this unit, starting with purified RNA, experimental protocols for performing microarrray expression analysis of embryonic stem cell lines compared to their corresponding differentiated embryoidal bodies are described. Methods for data analysis are suggested, with the goal of determining which genes are differentially expressed between the preparations. As an example, the use of the Affymetrix microarray expression platform is described, but alternative experimental options for analysis of RNA transcript levels are also summarized. This unit suggests quality control metrics, summazrizes the critical parameters necessary for obtaining reproducible experimental results, and outlines quantitative PCR methods for validating microarray results. Curr. Protoc. Stem Cell Biol. 2:1B.2.1-1B.2.36. © 2007 by John Wiley & Sons, Inc. Keywords: embryonic stem cells; embryoid bodies; RNA expression analysis; microarray platform