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Administration Basic Sciences Clinical Sciences Centers of Excellence

 Microarray and Genome Bioinformatics Core

Doan Nguyen, PhD, Core Director

The Microarray Core provides researchers with the expertise and instrumentation necessary for RNA transcript profiling using Affymetrix's GeneChip technology. Consultation on RNA extraction, experimental design, data analysis, and data mining options are available. Since December 2000, the Core has helped researchers from around the world process over 3000 samples, resulting in numerous peer-reviewed scientific publications.

Available equipment includes the Nanodrop Spectrophotometer, Agilent Bioanalyzer 2100, Affymetrix GeneArray 7G scanner, two GeneChip fluidics stations, a GeneChip Hybridization Oven 640, and a GeneChip bioinformatics system. The system includes a complete laboratory information management system (LIMS), which gives users direct access to their raw data, as well as the ability to use Affymetrix GeneChip Operating Software (GCOS v 1.4) and GeneChip RNA Expression Analysis Software (GREX) or other third party data analysis packages on their own computers to analyze and query gene expression data. In the near future, we will offer users the ability to use the new Exon and Tiling GeneChip arrays.

The Bioinformatics Core allows researchers to use the Rosetta Biosoftware Resolver software to analyze their own data. Other available data analysis packages include GCOS and Data Mining Tools (DMT), GeneSpring, and BioConductor/R. The Bioinformatics Center also is developing a web service ( that users can use to mine their gene- and protein-related data, and the ability to add additional public as well as user's databases. Gene2function will also enable users to search and extract annotated PubMed literatures through the GeneRif database.