An assessment of Motorola CodeLink microarray performance for gene expression profiling applications.
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.
Ramakrishnan
Ramesh
R
Motorola Life Sciences, 4088 Commercial Avenue, Northbrook, IL 60062, USA. ramesh.ramakrishnan@motorola.com
Dorris
David
D
Lublinsky
Anna
A
Nguyen
Allen
A
Domanus
Marc
M
Prokhorova
Anna
A
Gieser
Linn
L
Touma
Edward
E
Lockner
Randall
R
Tata
Murthy
M
Zhu
Xiaomei
X
Patterson
Marcus
M
Shippy
Richard
R
Sendera
Timothy J
TJ
Mazumder
Abhijit
A
D020869:Gene Expression Profiling; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012313:RNA / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012680:Sensitivity and Specificity
D012313:RNA