RNA Quality: Before any microarray hybridization can be undertaken, it is necessary to confirm that the RNA to be labeled is of acceptable quality. We use the Agilent Bioanalyzer to accomplish this step.
Amplification and labeling: Small amounts of RNA are routinely amplified prior to labeling and hybridization. For this step we use the Agilent system for direct labeling of amplified cRNA.
Microarray hybridizations will be conducted using human or mouse Agilent whole genome microarrays as appropriate and standard hybridization and washing conditions.
Scanning: Microarrays are scanned using the Agilent DNA Microarray Scanner and its Feature Extraction Software, which is compatible with industry standard analysis applications.
Downstream Data Analysis: We continue to use previously developed tools for data analysis, while collaborating closely with our Informatics and Biostatistics Core in the development and application of more sophisticated and specific tools in the course of this project.