An assessment of Motorola CodeLink™ microarray performance for gene expression profiling applications

• Published in: Nucleic acids research 2002-04, Vol.30 (7), p.e30-e30
• Main Authors: Ramakrishnan, Ramesh, Dorris, David, Lublinsky, Anna, Nguyen, Allen, Domanus, Marc, Prokhorova, Anna, Gieser, Linn, Touma, Edward, Lockner, Randall, Tata, Murthy, Zhu, Xiaomei, Patterson, Marcus, Shippy, Richard, Sendera, Timothy J., Mazumder, Abhijit
• Format: Article
• Language: English
• Subjects: DNA microarrays; Gene Expression Profiling; NAR Methods Online; Oligonucleotide Array Sequence Analysis - methods; Reproducibility of Results; Reverse Transcriptase Polymerase Chain Reaction; RNA - genetics; RNA - metabolism; Sensitivity and Specificity
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/30.7.e30

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 CodeLink™ 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 CodeLink™ expression platform were validated against those obtained with quantitative reverse transcription–PCR assays for 54 genes.