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Nucleic Acids Research 2004 32(15):e123; doi:10.1093/nar/gnh118
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Published online 27 August 2004

Nucleic Acids Research, Vol. 32 No. 15 © Oxford University Press 2004; all rights reserved

Quantitative assessment of a novel flow-through porous microarray for the rapid analysis of gene expression profiles

Ying Wu*, Peggy de Kievit, Lars Vahlkamp, Dirk Pijnenburg, Maarten Smit, Martijn Dankers, Diana Melchers, Martijn Stax1, Piet J. Boender, Colin Ingham, Niek Bastiaensen, Rik de Wijn, Dirk van Alewijk, Henk van Damme, Anton K. Raap1, Alan B. Chan and Rinie van Beuningen

PamGene International BV, Nieuwstraat 30, PO Box 1345, 5200 BJ 's-Hertogenbosch, The Netherlands and 1 Department of Molecular Cell Biology, Leiden University Medical Center, Leiden, The Netherlands

* To whom correspondence should be addressed. Tel: +31 73 615 8092; Fax: +31 73 615 8081; Email: ywu{at}pamgene.com

Received June 1, 2004; Revised July 23, 2004; Accepted August 6, 2004

A novel microarray system that utilizes a porous aluminum-oxide substrate and flow-through incubation has been developed for rapid molecular biological testing. To assess its utility in gene expression analysis, we determined hybridization kinetics, variability, sensitivity and dynamic range of the system using amplified RNA. To show the feasibility with complex biological RNA, we subjected Jurkat cells to heat-shock treatment and analyzed the transcriptional regulation of 23 genes. We found that trends (regulation or no change) acquired on this platform are in good agreement with data obtained from real-time quantitative PCR and Affymetrix GeneChips. Additionally, the system demonstrates a linear dynamic range of 3 orders of magnitude and at least 10-fold decreased hybridization time compared to conventional microarrays. The minimum amount of transcript that could be detected in 20 µl volume is 2–5 amol, which enables the detection of 1 in 300 000 copies of a transcript in 1 µg of amplified RNA. Hybridization and subsequent analysis are completed within 2 h. Replicate hybridizations on 24 identical arrays with two complex biological samples revealed a mean coefficient of variation of 11.6%. This study shows the potential of flow-through porous microarrays for the rapid analysis of gene expression profiles in clinical applications.


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