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Nucleic Acids Research, 2002, Vol. 30, No. 7 e30
© 2002 Oxford University Press

An assessment of Motorola CodeLinkTM microarray performance for gene expression profiling applications

Ramesh Ramakrishnan*, David Dorris, Anna Lublinsky, Allen Nguyen, Marc Domanus, Anna Prokhorova, Linn Gieser, Edward Touma, Randall Lockner, Murthy Tata, Xiaomei Zhu, Marcus Patterson, Richard Shippy, Timothy J. Sendera and Abhijit Mazumder

Motorola Life Sciences, 4088 Commercial Avenue, Northbrook, IL 60062, USA

DNA microarrays enable users to obtain information on differences in transcript abundance on a massively parallel scale. Recently, however, data analyses have revealed potential pitfalls related to image acquisition, variability and misclassifications in replicate measurements, cross-hybridization and sensitivity limitations. We have generated a series of analytical tools to address the manufacturing, detection and data analysis components of a microarray experiment. Together, we have used these tools to optimize performance in an expression profiling study. We demonstrate three significant advantages of the Motorola CodeLinkTM platform: sensitivity of one copy per cell, coefficients of variation of 10% in the hybridization signals across slides and across target preparations, and specificity in distinguishing highly homologous sequences. Slides where oligonucleotide probes are spotted in 6-fold redundancy were used to demonstrate the effect of replication on data quality. Lastly, the differential expression ratios obtained with the CodeLinkTM expression platform were validated against those obtained with quantitative reverse transcription–PCR assays for 54 genes.

* To whom correspondence should be addressed. Tel: +1 847 714 7637; Fax: +1 847 714 7008; Email: ramesh.ramakrishnan{at}motorola.com A.M. would like to dedicate this paper to David S. Sigman, who passed away on 11/11/01


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