Microarray Core Facility

In 1997 the HCI invested in microarray technology by entering a strategic collaboration with Molecular Dynamics. This collaboration gave HCI access to microarray technology early in its dissemination to the academic community. HCI offers microarray technology to Institute members through the Microarray Core Facility. The facility is directed by Dr. Brian Dalley, Ph.D., and is staffed by three expert research associates. Facility oversight is provide by Drs. David Jones and Brad Cairns. The instrumentation used at HCI to print and scan microarray slides has been developed by Molecular Dynamics following principles originally described by Dr. Patrick Brown’s laboratory.

Analysis of array images is currently accomplished in two ways: by visual inspection or by a quantitative electronic assessment of the fluorescent intensities of individual spots (i.e. genes). Visual inspection of microarray images is done using the ImageQuant NT software. Using this computer program, the fluorescent intensities of each channel (red and green) can be adjusted and low intensity background eliminated. This package will also allow simple cut and paste functions between applications and allow hardcopy color prints to be produced. Electronic spot quantification is currently accomplished using ArrayVision 4 from Imaging Research. This product is still under development, but does provide a fairly easy and reliable way to numerically determine hybridization intensities of individual spots. Once captured, the data can be exported to programs like MicroSoft Excel for further analysis.

The HCI Microarray Facility offers three basic services to interested investigators. These include cDNA synthesis and labeling of investigator supplied mRNAs, array generation and hybridization, and scanning and quantification of fluorescence intensities. Data, including array images, are stored on a networked file server for direct access by end users. Design, interpretation and follow-up analyses for microarray experiments are the responsibility of individual investigators. The HCI Microarray Facility has performed numerous experiments to address the quality, reproducibility and robustness of the microarray system. These studies have lead to high quality data that is distributed to investigators and is beginning to result in substantial scientific progress in a number of areas.

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