Faculty Publications
Comparison of RNA amplification methods and chip platforms for microarray analysis of samples processed by laser capture microdissection
Comparison of RNA amplification methods and chip platforms for microarray analysis of samples processed by laser capture microdissection
J Cell Biochem. 2008 Feb;103(2):556-63.
Abstract Laser capture microdissection (LCM) permits isolation of pure cell populations from which RNA can be extracted, amplified, and subjected to microarray analysis, allowing information to be obtained on the gene expression profile of defined cell types. To avoid amplification artifacts and detect genes expressed at different levels, it is important to optimize the choice of both RNA amplification step and microarray platform. We captured by LCM the same colon cancer biopsy and conducted a cross comparison of distinct RNA amplification methods and different chip platforms. We tested two RNA amplification methods with different chemistry: the one-cycle Ovation (TM) system (NuGEN) and the two-cycle Ribo OA (TM) method (Arcturus). We also compared two different whole genome platforms, based on Affymetrix technology: the U133 plus 2.0 and the X3P array, with probe sets closer to the 3' end of transcripts. After RNA amplification, microarray analysis, and data normalization, we in!