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Nucleic Acids Research, 2002, Vol. 30, No. 2 e4
© 2002 Oxford University Press

An evaluation of tyramide signal amplification and archived fixed and frozen tissue in microarray gene expression analysis

Stanislav L. Karsten, Vivianna M. D. Van Deerlin1, Chiara Sabatti2, Lisa H. Gill1 and Daniel H. Geschwind*

Department of Neurology, Program in Neurogenetics, UCLA School of Medicine, 710 Westwood Plaza, Los Angeles, CA 90095-1769, USA, 1Department of Pathology and Laboratory Medicine, University of Pennsylvania Health System, 7.098 Founders Pavilion, 3400 Spruce Street, Philadelphia, PA 19104, USA and 2Department of Human Genetics and Statistics, UCLA School of Medicine, 695 Charles Young Drive South, Los Angeles, CA 90095-7088, USA

Archival formalin-fixed, paraffin-embedded and ethanol-fixed tissues represent a potentially invaluable resource for gene expression analysis, as they are the most widely available material for studies of human disease. Little data are available evaluating whether RNA obtained from fixed (archival) tissues could produce reliable and reproducible microarray expression data. Here we compare the use of RNA isolated from human archival tissues fixed in ethanol and formalin to frozen tissue in cDNA microarray experiments. Since an additional factor that can limit the utility of archival tissue is the often small quantities available, we also evaluate the use of the tyramide signal amplification method (TSA), which allows the use of small amounts of RNA. Detailed analysis indicates that TSA provides a consistent and reproducible signal amplification method for cDNA microarray analysis, across both arrays and the genes tested. Analysis of this method also highlights the importance of performing non-linear channel normalization and dye switching. Furthermore, archived, fixed specimens can perform well, but not surprisingly, produce more variable results than frozen tissues. Consistent results are more easily obtainable using ethanol-fixed tissues, whereas formalin-fixed tissue does not typically provide a useful substrate for cDNA synthesis and labeling.

* To whom correspondence should be addressed. Tel: +1 310 794 6570; Fax: +1 310 267 2401; Email: dhg{at}ucla.edu


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