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Comparison of standard exponential and linear techniques to amplify small cDNA samples for microarrays.doc

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Comparison of standard exponential and linear techniques to amplify small cDNA samples for microarrays

BMC Genomics BioMedCentral Research article Open Access Comparison of standard exponential and linear techniques to amplify small cDNA samples for microarrays Johan Wadenb?ck*1, David H Clapham1, Deborah Craig2, Ronald Sederoff2, Gary F Peter3, Sara von Arnold1 and Ulrika Egertsdotter4 Address: 1Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, P.O. Box 7080, Uppsala, Sweden, 2Department of Forestry, North Carolina State University, Raleigh, NC 27695, USA, 3School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611, USA and 4Department of Forestry, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA Email: Johan Wadenb?ck* - johan.wadenback@vbsg.slu.se; David H Clapham - david.clapham@vbsg.slu.se; Deborah Craig - dlcraig@; Ronald Sederoff - ron_sederoff@; Gary F Peter - gfpeter@; Sara von Arnold - sara.von.arnold@vbsg.slu.se; Ulrika Egertsdotter - uegertsd@ * Corresponding author Published: 04 May 2005 Received: 29 October 2004 Accepted: 04 May 2005 BMC Genomics 2005, 6:61 doi:10.1186/1471-2164-6-61 This article is available from: /1471-2164/6/61 ? 2005 Wadenb?ck et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: The need to perform microarray experiments with small amounts of tissue has led to the development of several protocols for amplifying the target transcripts. The use of different amplification protocols could affect the comparability of microarray experiments. Results: Here we compare expression data from Pinus taeda cDNA microarrays using transcripts amplified either exponentially by PCR or linearly by T7 transcription. The amplified transcripts vary significantly in estimated le