Nucleic Acids Research Advance Access published online on May 12, 2008
Nucleic Acids Research, doi:10.1093/nar/gkn263
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Methods Online |
Assessment of gene expression in many samples using vertical arrays
Sidney Kimmel Cancer Center, 10905 Road to the Cure, San Diego, CA 92121, USA
*To whom correspondence should be addressed. Tel: +1 619 450 5990, ext. 282; Fax: +1 619 550 3998; Email: jwelsh{at}skcc.org
Received January 11, 2008. Revised April 1, 2008. Accepted April 21, 2008.
Microarrays and high-throughput sequencing methods can be used to measure the expression of thousands of genes in a biological sample in a few days, whereas PCR-based methods can be used to measure the expression of a few genes in thousands of samples in about the same amount of time. These methods become more costly as the number of biological samples increases or as the number of genes of interest increases, respectively, and these factors constrain experimental design. To address these issues, we introduced ‘vertical arrays’ in which RNA from each biological sample is converted into multiple, overlapping cDNA subsets and spotted on glass slides. These vertical arrays can be queried with single gene probes to assess the expression behavior in thousands of biological samples in a single hybridization reaction. The spotted subsets are less complex than the original RNA from which they derive, which improves signal-to-noise ratios. Here, we demonstrate the quantitative capabilities of vertical arrays, including the sensitivity and accuracy of the method and the number of subsets needed to achieve this accuracy for most expressed genes.
Present addresses: Rosa Ana Risques, Department of Pathology, University of Washington, Seattle, WA 98195, USA Martin Judex, Landrat-Wagner-Str. 43a, 84085 Langquaid, Germany
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.