This subproject is one of many research subprojects utilizing theresources provided by a Center grant funded by NIH/NCRR. The subproject andinvestigator (PI) may have received primary funding from another NIH source,and thus could be represented in other CRISP entries. The institution listed isfor the Center, which is not necessarily the institution for the investigator.The major goal of BayGenomics (also known as the NHLBI-Bay Area Functional Genomics Consortium) is to use gene-trap vectors to inactivate thousands of genes in mouse embryonic stem (ES) cells for the purpose of generating knockout mice. This will allow us to study a variety of phenotypes relevant to cardiovascular and pulmonary disease. Our insertional mutants have already been transmitted through the germline and the characterization of these mice has uncovered completely novel gene products with important roles in cardiopulmonary development and disease. As they are generated, all of these cell lines are made freely available to the scientific research community. A key objective of BayGenomics is to use gene-trap vectors to inactivate 2,500 genes per year in ES cells. All of our 'trapped' ES cells are posted on our website and will be distributed freely for the purpose of producing knockout mice. Our second objective is to assess which of the ES cell clones are involved in cardiopulmonary development and common cardiopulmonary diseases, thereby increasing the value of our resource to investigators. Computational approaches are used to gain insights into expression patterns and to assess functions of novel genes. In addition, we obtain probes for our 'trapped' genes for use in in situ hybridization experiments to define expression patterns in development and in specific cardiopulmonary diseases. We also use cDNA microarray studies to define which of the trapped genes might be important for cardiopulmonary diseases. A third objective of this project is to select a subset of ES cell clones determined to be most important to understanding cardiopulmonary development and disease and produce knockout mice for the purpose of further analysis. Selection of genes for the production of knockout mice are based on our group's long-standing biological interests and on the anticipated level of interest in those mice by the broader research community.Key to this project is the development of a relational database and associated 'middleware' software tools to allow access via a standard web browser to the wealth of data we have produced. We have developed computational protocols for calling DNA sequences from ABI sequence trace files using Phred, locating the part of sequences that correspond to trapped genes, and identified the trapped genes from the sequence fragments. The data is stored in a MySql database and made available to the broader scientific community via the International Gene Trap Consortium: www.genetrap.org The entire web site has been developed and are maintained by the RBVI. Other public resources such as MGI, Entrez, Ensembl, and the UCSC genome map have been incorporated into the annotation protocol. Additional details for this project, including access to scientific data, are available from the web site.
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