CORE--DNA MICROARRAY

DESCRIPTION (provided by applicant): A DNA Microarray Shared Resource became operational at AECCC in 1998. The system utilizes a high speed, high precision robot to spot thousands of DNA samples onto glass slides. The slides are than simultaneously probed with fluorescent labeled cDNAs generated from mRNA isolated from cells or tissues in two different states that are compared. A different fluorescent dye is used to make the cDNAs for each state allowing direct comparisons on a single trip. The facility produces both human and mouse DNA chips for the quantitative measurement of mRNAs from a variety of model systems. Data from the hybridization reactions are collect using a two-color laser scanning microscope, custom designed for maximum sensitivity required to measure low abundance mRNAs, and analyzed with a variety of software. Ongoing upgrades to the assay (currently approximately 1 micro gm). A new custom chip has been implemented for investigators who have identified their target genes and wish to use smaller gene sets or genes fro other model organisms. Initially, human and mouse cDNAs were obtained from Genome Systems. Incyte provided 18,394 unique human cDNAs from the I.M.A.G.E. consortium and the GEM1 set of 8,900 mouse cDNA clones. More recently provided their 9,000 GEM2 clones. The current human array contain 9,216 of these clones and it is expected that at least 27,000 will be on a chip within the year. The National Institute of Aging has provided 7,5000 out of a total of 15,000 additional mouse clones and 5,000 mouse IMAGE clones were recently obtained from a collaborator. Hence, the facility currently has about 43,000 human, and will shortly have 38,000 mouse, clones available to AECCC users. The facility is also a regional center for the Affymetrix technology providing hardware, software and technical expertise for use of oligonucleotide arrays by AECCC members. Affymetrix chips are purchased by a consortium of area institutions at reduced cost.