In vitro transcription amplification and labeling methods contribute to the variability of gene expression profiling with DNA microarrays.

ABSTRACT: The effect of different amplification and labeling methods on DNA microarray expression results has not been previously delineated. To analyze the variation associated with widely accepted T7-based RNA amplificationand labeling methods, aliquots of the Stratagene Human Universal Reference RNA were labeled using three eukaryotic target preparation methods followed by uniform replicate array hybridization (Affymetrix U95Av2). Method-dependent variability was observed in the yield and size distribution of labeled products, as well as in the gene expression results. A significant increase in short transcripts, when compared to unamplified mRNA, was observed in methods with long in vitro transcription reactions. Intramethod reproducibility showed correlation coefficients >0.99, whereas intermet

SUBMITTER: Ma C 

PROVIDER: S-EPMC1867595 | biostudies-literature | 2006 May

REPOSITORIES: biostudies-literature