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Nucleic Acids Research, 2001, Vol. 29, No. 5 e29
© 2001 Oxford University Press

Quantitative analysis of mRNA amplification by in vitro transcription

L. R. Baugh, A. A. Hill1, E. L. Brown1 and Craig P. Hunter*

Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA and 1Department of Genomics, Genetics Institute, Wyeth-Ayerst Research, Cambridge, MA, USA

Effective transcript profiling in animal systems requires isolation of homogenous tissue or cells followed by faithful mRNA amplification. Linear amplification based on cDNA synthesis and in vitro transcription is reported to maintain representation of mRNA levels, however, quantitative data demonstrating this as well as a description of inherent limitations is lacking. We show that published protocols produce a template-independent product in addition to amplifying real target mRNA thus reducing the specific activity of the final product. We describe a modified amplification protocol that minimizes the generation of template-independent product and can therefore generate the desired microgram quantities of message-derived material from 100 ng of total RNA. Application of a second, nested round of cDNA synthesis and in vitro transcription reduces the required starting material to 2 ng of total RNA. Quantitative analysis of these products on Caenorhabditis elegans Affymetrix GeneChips shows that this amplification does not reduce overall sensitivity and has only minor effects on fidelity.

* To whom correspondence should be addressed. Tel: +1 617 495 8309; Fax: +1 617 495 9300; Email: hunter{at}mcb.harvard.edu


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