The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse

Gene trapping is a method of generating murine embryonic stem (ES) cell lines containing insertional mutations in known and novel genes. A number of international groups have used this approach to create sizeable public cell line repositories available to the scientific community for the generation...

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Bibliographic Details
Published in:Nucleic acids research 2006-01, Vol.34 (suppl-1), p.D642-D648
Main Authors: Nord, Alex S., Chang, Patricia J., Conklin, Bruce R., Cox, Antony V., Harper, Courtney A., Hicks, Geoffrey G., Huang, Conrad C., Johns, Susan J., Kawamoto, Michiko, Liu, Songyan, Meng, Elaine C., Morris, John H., Rossant, Janet, Ruiz, Patricia, Skarnes, William C., Soriano, Philippe, Stanford, William L., Stryke, Doug, von Melchner, Harald, Wurst, Wolfgang, Yamamura, Ken-ichi, Young, Stephen G., Babbitt, Patricia C., Ferrin, Thomas E.
Format: Article
Language:English
Subjects:
Animals
Cell Line
Chromosome Mapping
Databases, Nucleic Acid
Embryo, Mammalian - cytology
International Cooperation
Internet
Mice - embryology
Mice - genetics
Mice, Knockout
Mutagenesis, Insertional - methods
RNA, Messenger - analysis
Systems Integration
User-Computer Interface
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Summary:Gene trapping is a method of generating murine embryonic stem (ES) cell lines containing insertional mutations in known and novel genes. A number of international groups have used this approach to create sizeable public cell line repositories available to the scientific community for the generation of mutant mouse strains. The major gene trapping groups worldwide have recently joined together to centralize access to all publicly available gene trap lines by developing a user-oriented Website for the International Gene Trap Consortium (IGTC). This collaboration provides an impressive public informatics resource comprising ∼45 000 well-characterized ES cell lines which currently represent ∼40% of known mouse genes, all freely available for the creation of knockout mice on a non-collaborative basis. To standardize annotation and provide high confidence data for gene trap lines, a rigorous identification and annotation pipeline has been developed combining genomic localization and transcript alignment of gene trap sequence tags to identify trapped loci. This information is stored in a new bioinformatics database accessible through the IGTC Website interface. The IGTC Website (www.genetrap.org) allows users to browse and search the database for trapped genes, BLAST sequences against gene trap sequence tags, and view trapped genes within biological pathways. In addition, IGTC data have been integrated into major genome browsers and bioinformatics sites to provide users with outside portals for viewing this data. The development of the IGTC Website marks a major advance by providing the research community with the data and tools necessary to effectively use public gene trap resources for the large-scale characterization of mammalian gene function.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkj097