CORE--GENE EXPRESSION

Washington University, Saint Louis MO

Investigators

Linked publications & trials

Abstract

Core D Gene Expression Core The PI has approximately 1500 sf of lab and office space that is divided between the computation group and the biochemistry group. Available for this computational proposal we have a Sun Ultra-30 with 512 MB RAM and about 28 GM disk that functions as our lab served. All personnel have desk/cubicle space and workstations (either Sun or Intel-PCs). We have the necessary printers and Internet connections and the necessary databases. Description, performance site, personnel Washington University The Microarray facility (MAF) at Washington University School of Medicine (WUSM) was created in the fall of 1998, growing out of the Center for Genetics in Medicine, the original human physical mapping project. The MAF is a facility which enables investigators to carry out DNA microarray hybridization experiments, using technology pioneered by Patrick Browen's laboratory at Stanford University. The goals of the MAF are to: 1) provide a DNA microarray facility with sufficient capacity to accommodate the needs of the WUSM scientific community.. In addition, a portion of the MAF's activity serves as core lab function for various program project grants. 2) to make the cost as reasonable as possible to WUSM investigators. 3) to provide expertise, advice, and training the use and analysis of microarrays. 4) to extend and develop new microarray methodology. 5) to apply microarray technology creatively to many problems in current biology and medicine. 6) to develop new areas of research in gene expression and comparative genomics. 7) to help develop new technologies extending our tools for assessing global gene expression for any cell type. The MAF has successfully completed several pilot studies on a large enough scale to demonstrate that this technology is working and is accessible to the entire Washington University community. Arrays are now routinely constructed using DNA from several organisms with low complexity genomes as model systems (Leishmania , Toxoplasma, Plasmodium). In one set of studies, 1,154 genes could be reliably in quadruplicate (about 4616 total spots) on 42 slides in a "quasi- production' mode. Other studies have tested various methods for amplifying and preparing array quality DNAs in 96-well microtiter trays. Currently, the facility is using the Leishmania model system to screen a 10,000 clone library by microarray the results of this large scale project has paved the way for generating mouse and human arrays that are now produced. Robust protocols for the generation of fluor-dye labeled target cDNAs from RNA have also been successful hybridization, scanning, and image analysis are routinely performed, and improved methods for data handling and informatics are being developed with the input of faculty from the departments of genetics and medicine (see appendix 4). Finally, the facility has completely assessed several issues including quality of Array DNA preparation, hybridization consistency, slide to slide consistency, pin printing consistency, 'shelf-life' and probe performance.