Efficacy of RNA amplification is dependent on sequence characteristics: implications for gene expression profiling using a cDNA microarray.

摘要: Minute tissue samples or single cells increasingly provide the starting material for gene expression profiling, which often requires RNA amplification. Although much effort has been put into optimizing amplification protocols, relative abundance of templates in amplified product is frequently biased. We applied a T7 polymerase-based technique to amplify from two tissues cichlid fish and compared levels unamplified on cDNA microarray. Amplification bias was generally minor comprised features that were lost (1.3%) gained (2.5%) through scored as regulated before but unregulated after (4.2%) vice versa (19.5%). examined 10 sequence-specific properties found GC content, folding energy, hairpin length number, lengths poly(A) poly(T) stretches significantly affected conclude that, if used studies, preceding experiments controlling should be performed.