Microarray Center for Research on the Nervous System

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DESCRIPTION (provided by applicant): The Microarray Center of the Research Center of Genetic Medicine, Children?s National Medical Center, Washington DC offers the attached proposal, wherein an outline of a NINDS/NIMH Microarray Center (MC) for expression profiling is described. Assistance with experimental design, data generation, and data interpretation will be provided. It is important to recognize that the Children?s Microarray Center already fulfills such functions for NHLBI, NEI, and many other investigators, and, indeed, has well-established experimental protocols, web sites, and innovative bioinformatics methods which permit a high degree of throughput at relatively low cost (due to cost sharing with other grants and programs). Briefly, the MC is unique because we have built an expression profiling Center and amassed significant expertise through 1) an NHLBI PGA award for large-scale expression profiling (one of only 11 nationally) and an NEI intramural contract for cDNA construction, 2) becoming a "Center of Excellence" for Affymetrix technology, 3) development of a highly integrated array web site (microarray.cnmcresearch.org) for tutorials and data dissemination, 4) development of the first web-based query algorithm of our Oracle data repository, 5) being well-versed in both cDNA and Affymetrix technology, 6) having performed over 975 Affymetrix array experiments, 7) operation of the MC as a business with resident infrastructure, 8) assisting over 50 visiting investigators with array experiments to date, and 9) having resident scientific expertise for experimental design assistance. In this offering, we propose to establish a NINDS/NIMH Microarray Center for expression profiling within the existing Children?s Microarray Center. Much of the proposed structure and function of the MC is based upon our previous experience with a similar NHLBI-funded grant. The goals for the MC include: 1) web-based protocol tutorials and submission, 2) review and revisions by an experimental protocol committee (EPC) which has extensive neuroscience experience, 3) investigator-driven charge-back mechanisms (3 levels of subsidization), 4) data generation, 5) Oracle warehousing with automated timed release to the public via web-access at our site and NCBI, 6) web queries of our data repository, 5) data analysis tutorials and assistance, and 6) development of custom Affymetrix NeuroChips using our downstream large data structure and our "Center of Excellence" status as mechanisms to develop a unique, low-cost reagent for the community. While we are adept at both spotted cDNA arrays and Affymetrix arrays, we plan to offer Affymetrix stock chips as the primary data generation platform for NINDS/NIMH investigators. This is because of the inherent transportability and the ability to database results, allowing all investigators to use the results of all other investigators. Also, the databasing and web access to kernal database structures in the Oracle/LIMS Affymetrix platform is becoming quite mature, while such databasing and web access is considerably less mature with spotted cDNA arrays. We have printed and conducted large experiments with cDNA arrays (particularly the murine BMAP set), and this platform will be available to NINDS/NIMH-funded investigators as an optional service at limited, availability, even though the majority of genes in the BMAP collection are also on the MG_U74 array (more than 74%).