The Microarray portion of this Core B will manufacture spotted DNA microarrays for the genomes of Yersinia pestis, Francisella tularensis, and E. coli. In addition, the facility will make custom human microarrays of up to 5,000 genes as needed. The facility will also provide equipment for the initial analysis of the arrays with fluorescent scanners and computers and will deposit the data in a database maintained by the Bioinformatics facility. The Microarray facility will have access to Affymetrix gene chips and an Affymetrix gene chip scanner already present at Stony Brook. Affymetrix chips will be used to analyze the response of mammalian cells to infection with the three Category A agents that are represented in this Project. Analysis of Affymetrix data will be essentially the same as for spotted DNA microarrays. The microarray and bioinformatics facilities of this Core will work closely together on microarray experiments. The Bioinformatics portion of the Core will maintain a cluster of computers for the use of this Project. Software suites for analysis of various kinds of genomic data will be maintained for sequence comparisons, and microarray analysis. The Facility will maintain databases for storage of microarray results, and for gene annotation of the organisms of interest. The Core will be able to provide advice and assist with the design of both spotted DNA and Affymetrix microarray experiments; it will assist in the interpretation of microarray experiments; and it will provide training, programming support, and guidance in the use of various software packages.
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