Gene Expression Profi ling and Validation Using Agilent SurePrint G3 Gene Expression Arrays

Gene expression analysis is currently carried out using three methods that provide complementary data: microarrays, RNA-Seq, and RT-qPCR. Microarrays provide comprehensive whole-genome coverage in single experiments, with rapid data acquisition and results at a low price per sample. RNA-Seq provides the most comprehensive data across all RNA transcripts present in a sample. However, RNA-Seq also requires the largest sample amounts, the most time, and the highest investment. RT-qPCR provides the fastest and the most cost effective solution for reliable expression analysis, but it is most suitable for experiments involving a small number of genes across a large number of samples. In this study, we compare Agilent SurePrint G3 gene expression microarray data with the results achieved using RT-qPCR and RNA-Seq. The data demonstrates excellent correlation between G3 microarray data and these two complementary techniques. A key factor in achieving strong correlation between microarrays and RT-qPCR data is the design of the primers and probes to the same target sequence on the microarray. This study also demonstrates the coverage of Agilent’s gene expression workfl ow from discovery through biological validation. Authors Bahram Arezi, Nilanjan Guha and Anne Bergstrom Lucas Agilent Technologies Inc. Santa Clara, CA USA