EHS Center - Microarray and Bioinformatics Facility Core




			Microarray and Bioinformatics Facility Core Resources: The MBFC occupies approximately 780 square feet of dedicated space that includes laboratory bench areas and a computational facility. MBFC facilities are centrally located in rooms 4305 and 4115 of the Institute of Environmental Health Sciences. MBFC instrumentation and computational resources include: 1. Instrumentation: Agilent G2565AA dual-laser microarray scanner with auto-load carousel (simultaneous capacity of 96 arrays) Axon dual-laser microarray scanner ABI Prism 7000 RT-PCR The microarray instrumentation available through the MBFC offers Center members outstanding microarray quality and true high-throughput capacity. These scanners provide “two color” microarray analysis where two samples, each labeled with a distinctive fluorophore, are co-hybridized to a glass microarray slide which is subsequently scanned to obtain the fluorescence image. The Agilent scanner is complemented by extremely accurate image analysis software that uses microarray slide design information to assist in quantification of fluorescent intensity values. Additionally, the Agilent scanner can be simultaneously loaded with 96 arrays which can be processed in an automated manner. Validation of microarray results can be accomplished using the ABI Prism RT-PCR. Link to Agilent Microarray Web Site 2. Computer Hardware: Sun V880 dual processor server with 8 Gigabyte of memory and 438 Gigabyte of disk storage Sun L25 tape backup library with up to 2.5 Terabyte of storage SGI Onyx multiprocessor Sun Ultra 10 workstations with additional Windows compatible Intel processors High speed ethernet network Color graphics laser printing The MBFC provides access to quality computational equipment that would otherwise be out of reach to most investigators due to hardware costs and the expertise required for implementing and sustaining a bioinformatics data center. Microarray data are moved seamlessly from the Agilent scanner to the Rosetta Resolver® system, resident on the MBFC server. The server provides investigators with remote access to microarray data managed through an Oracle database, an integral component of the Resolver® system. 3. Computer Software: Rosetta Resolver® microarray data analysis system Agilent microarray image and data analysis software GeneSpring microarray clustering, statistical analysis, and visualization (Silicon Genetics) SPSS statistical analysis SAM microarray data analysis (Stanford) GenMapp analysis of microarray data in the context of biological pathways (UCSF) MBFC software resources and associated expertise allow investigators to translate raw microarray data into biologically relevant results. The MBFC has implemented leading software for data management, analysis, and visualization of microarray data. Rosetta Resolver® is an enterprise package that provides high-capacity data management and analysis, including biological pathway analysis, statistical analysis, and clustering. Resolver® also includes a development tool that enables the incorporation of custom programs and data resources. The MBFC provides a number of other microarray analysis applications, including GeneSpring.