Beyond the Identification of Transcribed Sequences: Functional and Expression Analysis

9th Annual Workshop, October 28-31, 1999

Co-sponsored by the U.S. Department of Energy


Development of expression profiling technologies for the rat

Tom Freeman, David Vetrie, Clare East, Adam Butler, Liz Campbell and Peter Wooding

Gene Expression Group, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, United Kingdom

The rat is a widely used animal model for biological investigation including many pharmacological, neurobiological and physiological studies. Over the last few years there has been a significant increase in the amount of information available on the rat genome and genetics. We have therefore begun to develop the tools to allow us to exploit this new information resource in order to perform large-scale expression studies of rat systems. We have developed a cDNA sequence-based database named RATACE, based on the widely used platform of ACeDB.  It currently contains all the publicly available rat sequence, with the exception of ESTs.  Sequence comparison has allowed sequences originating from the same gene to be identified and clustered, and sequence alignments can be viewed graphically from within the database.  We are currently developing it as a tool for handling all the reagents and data required for, and generated by, large-scale expression studies.  Expression studies are being carried out using RT-PCR and high-density microarrays.  To date, we have over 1,000 working primer pairs for rat genes and have used these to profile the expression of each gene over a range of 22 rat tissues using RT-PCR.  We have also been optimising the conditions necessary for spotting these PCR products on glass slides to act as probes for microarrays, as well as determining how they perform during hybridisation.  We are currently scaling up the production of probes for the rat microarrays.  It is our intention to use these tools on rat pharmacological models to further our understanding of the mechanism of drug action, as well as to identify novel therapeutic targets.

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