The purpose of this Core is to provide cDNA microarrays, computational and experimental support required by the projects of this program to carry out gene expression studies in a highly parallel fashion. The Functional Genomics Center will provide a series of services to investigators at the Salk Institute to establish and develop their research studies using microarrays The core has gel/sequence-verified, mapped to NCBI's UniGene database, unique IMAGE Consortium clones from Genome Systems, Inc. including 8,700 mouse genes and 7,000 human genes. Amplification of templates is done using PCR and preparation of templates for spotting is performed using a High-Throughput Liquid Hander BioRobot 9604 liquid handler system from QUAGEN Molecular Biology for automated duplicating and rearraying of clones, DNA plasmid purification, PCR product purification. For arraying of clones we use the microarray generation III spotter from Molecular Dynamics. The Spotter holds twelve 384-well DNA source plates, and up to 36 slides can be spotted in a single run in approximately four hours. Users will be instructed in the preparation of labeled cDNA for hybridization to the array. Labeled probe will be hybridized by the core using an Automated Slide Processor, Molecular Dynamics. Data acquisition and communication with the database to retrieve pre-set scanning parameters is performed using Array Vision Software. The analysis software runs under Windows NT, on standard, on standard PCs. Following data acquisition the investigators will receive data in excel data in excel format. This data can then be used in a variety of analysis programs that are available through the core and include Spotfire Pro v4.0.1, GeneSpring and freeware available on the web. Expertise and training in the use of these programs is available through the core. The core also uses the Gen 3DB Database Manager for microarray data management. Gen3DB allows you to interface in the database by entering and querying all experimental data and information generated by the system. It is based on the Microsoft access relational database environment and can be up- scape to the large-scale database software such as Microsoft Sql Server and Oracle. The core also provides software for analysis of data using commercially available array, including those from Clonetech (Atlas Array Analysis Software) and Incyte.
