Gene Microarray and Pharmacogenomics Core

Location: University of California, San Francisco

Overview | Investigators | Background | Resources

Overview
The ITN has established a microarray core designed to evaluate global patterns of gene expression using the Affymetrix GeneChip array technology. The newly released Affymetrix HG-U133 GeneChip arrays will be used for hybridization of RNA obtained from ITN-supported studies. The HG-U133 GeneChip arrays (U133A and U133B) contains approximately 39,000 human transcripts from more than 33,000 well-characterized human genes. Multiple gene arrays will be run for each specimen collected in ITN trials to adequately address the biologic variability.

Because of the requirements for significant amounts of high quality total RNA obtained as quickly as possible from the clinical source, the ITN has developed a protocol for rapid, easy collection of peripheral blood using RNA-extraction-based vacutainer tubes. These tubes directly lyse and stabilize RNA at the time of collection. Tubes are simply incubated at room temperature (at the site) for 2 hours, frozen and then shipped to the ITN sample repository located at McKesson Bioservices, Rockville MD. High quality RNA is produced at McKesson using the peripheral blood from the collection tubes. This RNA is then sent on to the Gene Chip Core and Real Time PCR Core for analysis.

The ITN Gene Microarray and Pharmacogenomics Core Facility is located at the University of California San Francisco. The facility is outfitted with 3 microfluidics stations, one Affymetrix scanner, the latest Affymetrix software tools, several technicians and onsite data analysis personnel. The ITN Core has the capacity to run 2000-3000 gene chips per year.

Participating Investigators

	Jeffrey A. Bluestone, The Diabetes Center at UCSF
	Shirley Zhu, The Diabetes Center at UCSF

Background Articles

	High-Throughput Gene Expression Profiling Using Gene Chips - Genome Research [go]
	Flexible Use of High-Density Oligonucleotide Arrays for Single-Nucleotide Polymorphism Discovery and Validation - Genome Research [go]

Resources & Interesting Links

Affymetrix, Inc. [go]