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

Abstract

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.

Analysis of gene expression in carbon tetrachloride-treated rat livers using a novel bioarray technology

“…59 Overall, reproducibility test results were consistent with other acceptable published results. 55,60 Furthermore, array quality and specification for these studies were consistent with those described by Ramakrishnan et al 54 for this particular platform.…”

“…This paper describes the use of this new oligonucleotide array in a biological validation study involving the treatment of rats with carbon tetrachloride (CCl 4 ), a well-established model of chemically induced hepatotoxicity. 9,11,12,52,53 The goal of this study was to show that this novel bioarray, which has already been demonstrated to meet or exceed current industry standards and specifications, 54 could be successfully employed to measure expected gene expression changes. It was hypothesized that the results of histopathological and gene expression analysis of hepatic tissue from CCl 4 -treated animals would confirm and/or reject previously published gene expression findings, as well as identify other target genes of interest, either not tested or missed by previously published studies that used other microarray platforms or more traditional methods of gene expression analysis.…”

Role of Oxygen Availability in CFTR Expression and Function

“…Briefly, the RNA was processed as previously described (16,17). A reaction mix containing 5 mg of total RNA, bacterial RNA controls, 0.5 pmol/ml T7-(dT)24 oligonucleotide primers, and SuperscriptTM II reverse transcriptase (200 U/ml; Invitrogen, Carlsbad, CA) was incubated at 428C for 1 hour.…”

Candesartan-Induced Gene Expression in Five Organs of Stroke-Prone Spontaneously Hypertensive Rats

“…The present study utilized the CodeLink Bioarray Perfect system (GE Healthcare UK Ltd., Buckinghamshire, UK), which uses the UniSet Rat I Expression Bioarray that contains 9,028 gene probes, abbreviated hereafter as the 10K CodeLink array (11)(12)(13)(14). The 10K CodeLink array accommodates a broad range of genes derived from publicly available, well-annotated mRNA sequences.…”