A High Throughput Chip Analysis System for the U of Wisc

Blattner, Frederick

Abstract

This proposal requests funding to acquire three pieces of equipment that will work in concert as part of a high through put system. The equipment will be used for hybridization and analysis of high-density oligonucleotide arrays produced using a maskless array synthesizer developed by NimbleGen Systems, Inc. The Ventana Discovery hybridization station is capable of reproducibly hybridizing 20 microarray chips at a time. It can be used for both our spotted arrays as well as the Nimblechips. The automated hybridization station will allow us to increase our hybridization capacity and at the same time reduce the human induced variation in the hybridizations. The 0.9 um resolution Applied Precision scanner is required to obtain high quality data from the small features on the NimbleGen chips. Because of the large number of features and the small pixel size required to obtain useful data, the image files are very large. To handle and analyze these large images, we are requesting an Omni Tech Fortris 4100: Quad Processor Xeon Server with 8 GB of RAM and 730 GB of hard disk storage. The arrays will be used in a wide range of projects, including projects designed to determine RNA expression levels, detect and map single nucleotide polymorphisms and identify regulatory regions of genes. Currently six NIH funded users are actively involved in using this technology, with an additional 10 users with planned experiments who are in line to receive chips within the next several months. This equipment will complement the current capabilities of the Gene Expression Center located within the Biotechnology Center at the University of Wisconsin-Madison, and will enable researchers to utilize the newest array technology in their research.