Target Preparation for GeneChip* Expression Analysis Using the Biomek® 3000 Laboratory Automation Workstation and ArrayPlex Application

Poster: Zhu Zhu, Dan Allison, Yu Suen, Handy Yowanto, Tim Lancaster, Jeremy Smith and Keith Roby:
Microarray technology has become a standard tool for gene expression researchers, enabling the simultaneous assessment of changes in gene expression across the whole genome. However, the process of target preparation for the GeneChip expression analysis is time consuming, labor intensive and prone to human errors.

We have developed a solution, the ArrayPlex application, to automate the target preparation process on the Biomek 3000 Laboratory Automation Workstation (Beckman Coulter).

The ArrayPlex application is part of the GeneomeLab™ family of applications (Beckman Coulter). The highly automated process is comprised of three methods: cDNA Synthesis, in vitro Transcription (IVT), and Normalization and Fragmentation. It allows for processing a partial or a full 96-well plate of samples from 1 – 2 µg of total RNA to the biotin-labeled complementary RNA (cRNA) using Affymetrix’ GeneChip Expression 3’-Amplification reagents and the Agencourt® RNAClean™ kit.
The yield, of the target cRNA generated using these methods, was measured by OD260 with a DTX 880 Multimode Detector (Beckman Coulter).

The quality of the cRNA was analyzed on the Agilent 2100 Bioanalyzer*. The cRNA samples were normalized to a target concentration of 0.625 µg/µl, fragmented, and hybridized to Affymetrix’ Human Genome U133 Plus 2.0 Arrays*. The information provided here includes the description of the automated workstation, methods and
subsequent results.

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Additional Information:

• Biomek 3000
• Biomek 3000 ArrayPlex Workstation 
• More Information on eCatalog