) Monitoring gene expression patterns using microarrayed grids of eDNA fragments is a powerful new tool for analyzing tumors. An in-house capacity to design and prepare microarrays will give us the opportunity to tailor the design of low-cost gene chips to the needs of the melanoma program project. Expensive commercial chips (which presently contain >15,000 eDNAs per grid and are expected to soon include cDNAs representing most or all expressed human genes) can be purchased and used sparingly for very selected experiments, and interesting cDNA clones identified from the results of these """"""""global"""""""" experiments can he selected for inclusion on the smaller, cheaper, and more readily available core-generated microarrays. These novel microarray design strategies will avoid the huge expense likely to be incurred by the routine use of commercial gene chips, and will facilitate data interpretation by simplifying the quantitative gene expression readout to a limited (but still very large) set of eDNAs known to or expected to fluctuate in interesting ways in melanoma. Microarrays will be used extensively for 3 of the 4 projects. Core E will interact closely with the proteome analysis component of Core D in order to facilitate the design of custom microarrays for some of the projects.
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