We are requesting funds to acquire a Roche NimbleGen MS200 25m Microarray Scanner. The instrument will be placed in the University of Wisconsin Biotechnology Center's Gene Expression Center (GEC). The GEC was established over ten years ago as a central fee-for-service core service facility at UW-Madison for global gene expression analysis using state-of-the-art DNA microarray technologies. This scanner is needed to capture data from high-density arrays such as Roche NimbleGen High Density arrays (HD2). Roche NimbleGen's MAS (Maskless Array Synthesis) technology offers a unique ability to make high-density arrays for advanced genomic analysis methods such as CGH, ChIP-chip, microbial resequencing, DNA methylation and gene expression. With 2.1 million probes, NimbleGen HD2 arrays offer the opportunity to fully interrogate copy number variation, transcription factor binding, and chromatin structure. The UW-Madison also has a preferred pricing agreement for Roche NimbleGen array purchases that makes the use of this particular HD array technology very cost effective to federally funded researchers. The GEC also currently offers subsidized comprehensive services that allow investigators not only to fully utilize Nimblegen MAS arrays but also to explore and improve upon their standard capabilities. In addition some investigators are developing exciting novel high-density platforms such as DNA and small molecule arrays and local access to a HD scanner is essential for this work. The currently available Axon 4000B scanner at the GEC does not have the required resolution needed for data capture from the new generation of recently introduced HD2 arrays and to our knowledge there is not a scanner that offers this resolution available to researchers on campus. In this proposal we will highlight seven laboratories out of many funded by NIH at the UW-Madison whose research would benefit from using high-density arrays and/or access to the high-resolution scanner. Our goal however, is to provide access to this relatively new technological platform to all NIH funded researchers at UW-Madison. This facilitated access will accelerate both the pace and scope of basic medical research at the UW. Placing this instrumentation in a central core service facility will provide equitable cost-effective access to this technological platform and also ensure that the instrument is heavily used and well maintained. Local access also facilitates adoption of this new genomics platform by investigators currently unfamiliar with the capabilities of this instrument.
