title: Gene expression analysis of RNA purified from embryonic stem cells and embryoid body-derived cells using a high-throughput microarray platform.
abstract: In this unit, starting with purified RNA, experimental protocols for performing microarray expression analysis of embryonic stem cell lines compared to their corresponding differentiated embryocidal 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, summarizes the critical parameters necessary for obtaining reproducible experimental results, and outlines quantitative PCR methods for validating microarray results.
authors.affiliation: National Cancer Institute, Bethesda, Maryland, USA.
authors.forename: Audrey
authors.initials: A
authors.lastname: Player
authors.forename: Yonghong
authors.initials: Y
authors.lastname: Wang
authors.forename: Mahendra
authors.initials: M
authors.lastname: Rao
authors.forename: Ernest
authors.initials: E
authors.lastname: Kawasaki
mesh_terms: D000818:Animals; D001483:Base Sequence; D017931:DNA Primers / Q000235:genetics; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism*; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D039904:Pluripotent Stem Cells / Q000166:cytology / Q000378:metabolism; D012313:RNA / Q000235:genetics / Q000378:metabolism
chemical_list: D017931:DNA Primers; D012313:RNA