Optimized procedures for microarray analysis of histological specimens processed by laser capture microdissection

Journal of Cellular Physiology
John J UpsonAlfonso Bellacosa

Abstract

Analysis of cell-specific gene expression patterns using microarrays can reveal genes that are differentially expressed in diseased and normal tissue, as well as identify genes associated with specialized cellular functions. However, the cellular heterogeneity of the tissues precludes the resolution of expression profiles of specific cell types. While laser capture microdissection (LCM) can be used to obtain purified cell populations, the limited quantity of RNA isolated makes it necessary to perform an RNA amplification step prior to microarray analysis. The linearity and reproducibility of two RNA amplification protocols--the Baugh protocol (Baugh et al., 2001, Nucleic Acids Res 29:E29) and an in-house protocol have been assessed by conducting microarray analyses. Cy3-labeled total RNA from the colorectal cell line Colo-205 was compared to Cy5-labeled Colo-205 amplified RNA (aRNA) generated with each of the two protocols, using a human 10K cDNA array. The correlation of the gene intensities between amplified and total RNA measured in the two channels of each microarray was 0.72 and 0.61 for the Baugh protocol and the in-house protocol, respectively. The two protocols were further evaluated using aRNA obtained from normal colo...Continue Reading

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Citations

Aug 9, 2005·Journal of Immunological Methods·Kathryne Melissa KeaysMark P Burgoon
Apr 5, 2007·Nature Protocols·Virginia EspinaLance A Liotta
Oct 6, 2005·Nephrology, Dialysis, Transplantation : Official Publication of the European Dialysis and Transplant Association - European Renal Association·Michael EikmansJan A Bruijn
Aug 10, 2005·Eukaryotic Cell·Weihua FanJoseph Heitman
Feb 21, 2006·NeuroRx : the Journal of the American Society for Experimental NeuroTherapeutics·B Gomez-MancillaM E Schmidt
Feb 18, 2010·International Journal of Cancer. Journal International Du Cancer·Takatoshi MatsuyamaKenichi Sugihara
Sep 26, 2006·Journal of Biotechnology·Cecilia LaurellJoakim Lundeberg
Sep 1, 2005·Meat Science·Christian BendixenPer Horn
Oct 1, 2011·The Journal of Craniofacial Surgery·Shih-Hao HuangSiew-Ging Gong

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