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The UniTrap resource: tools for the biologist enabling optimized use of gene trap clones.

Roma G, Sardiello M, Cobellis G, Cruz P, Lago G, Sanges R, Stupka E - Nucleic Acids Res. (2007)

Bottom Line: We have developed a comprehensive resource devoted to biologists wanting to optimize the use of gene trap clones in their experiments.The UniTrap resource contains data relative to 9583 trapped genes, which represent 42.3% of the mouse gene content.Among the trapped genes, 7,728 have a counterpart in humans, and 677 are known to be involved in the pathogenesis of human diseases.

View Article: PubMed Central - PubMed

Affiliation: Telethon Institute of Genetics and Medicine (TIGEM), Via P. Castellino, 111, 80131, Napoli, Italy.

ABSTRACT
We have developed a comprehensive resource devoted to biologists wanting to optimize the use of gene trap clones in their experiments. We have processed 300 602 such clones from both public and private projects to generate 28,199 'UniTraps', i.e. distinct collections of unambiguous insertions at the same subgenic region of annotated genes. The UniTrap resource contains data relative to 9583 trapped genes, which represent 42.3% of the mouse gene content. Among the trapped genes, 7,728 have a counterpart in humans, and 677 are known to be involved in the pathogenesis of human diseases. The aim of this analysis is to provide the wet lab researchers with a comprehensive database and curated tools for (i) identifying and comparing the clones carrying a trap into the genes of interest, (ii) evaluating the severity of the mutation to the protein function in each independent trapping event and (iii) supplying complete information to perform PCR, RT-PCR and restriction experiments to verify the clone and identify the exact point of vector insertion. To share this unique resource with the scientific community, we have designed and implemented a web interface that is freely accessible at http://unitrap.cbm.fvg.it/.

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Related in: MedlinePlus

The UniTrap resource: data display. The image provides information regarding a trapped gene, i.e. eya1. Researchers can compare each distinct gene-trap insertion along with other genomic features, such as protein domains, restriction sites, etc., through a dynamic graphical representation of the genomic region of interest. A physical map of the trapped locus can be visualized to retrieve the sequences of restriction fragments or PCR primers to be used for the amplification of gene-specific probes. For each UniTrap, the page shows (i) the predicted vector insertion site, (ii) the list of public and private ES cell clones available, (iii) the severity of the mutation on the protein function and (iv) a link to retrieve the proposed experimental design for vector insertion validation.
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Figure 2: The UniTrap resource: data display. The image provides information regarding a trapped gene, i.e. eya1. Researchers can compare each distinct gene-trap insertion along with other genomic features, such as protein domains, restriction sites, etc., through a dynamic graphical representation of the genomic region of interest. A physical map of the trapped locus can be visualized to retrieve the sequences of restriction fragments or PCR primers to be used for the amplification of gene-specific probes. For each UniTrap, the page shows (i) the predicted vector insertion site, (ii) the list of public and private ES cell clones available, (iii) the severity of the mutation on the protein function and (iv) a link to retrieve the proposed experimental design for vector insertion validation.

Mentions: Each of these queries generates a list of trapped genes that meet the search criteria. Information regarding the gene of interest is visualized in a specific page where a clickable graphical representation allows a close look of all the features present in the same genomic region (Figure 2). A physical map of the trapped locus is visualized to retrieve the sequences of restriction fragments or PCR primers to be used for the amplification of gene-specific probes. Moreover, a list of all the UniTraps for the gene of interest, with information regarding public and private gene trap clones, is provided. For each UniTrap, the putative impact of the gene trap vector insertion on the protein function is shown and comprehensive information is provided to perform PCR and RT-PCR experiments in order to verify the clone and identify the exact site of vector insertion.Figure 2.


The UniTrap resource: tools for the biologist enabling optimized use of gene trap clones.

Roma G, Sardiello M, Cobellis G, Cruz P, Lago G, Sanges R, Stupka E - Nucleic Acids Res. (2007)

The UniTrap resource: data display. The image provides information regarding a trapped gene, i.e. eya1. Researchers can compare each distinct gene-trap insertion along with other genomic features, such as protein domains, restriction sites, etc., through a dynamic graphical representation of the genomic region of interest. A physical map of the trapped locus can be visualized to retrieve the sequences of restriction fragments or PCR primers to be used for the amplification of gene-specific probes. For each UniTrap, the page shows (i) the predicted vector insertion site, (ii) the list of public and private ES cell clones available, (iii) the severity of the mutation on the protein function and (iv) a link to retrieve the proposed experimental design for vector insertion validation.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238955&req=5

Figure 2: The UniTrap resource: data display. The image provides information regarding a trapped gene, i.e. eya1. Researchers can compare each distinct gene-trap insertion along with other genomic features, such as protein domains, restriction sites, etc., through a dynamic graphical representation of the genomic region of interest. A physical map of the trapped locus can be visualized to retrieve the sequences of restriction fragments or PCR primers to be used for the amplification of gene-specific probes. For each UniTrap, the page shows (i) the predicted vector insertion site, (ii) the list of public and private ES cell clones available, (iii) the severity of the mutation on the protein function and (iv) a link to retrieve the proposed experimental design for vector insertion validation.
Mentions: Each of these queries generates a list of trapped genes that meet the search criteria. Information regarding the gene of interest is visualized in a specific page where a clickable graphical representation allows a close look of all the features present in the same genomic region (Figure 2). A physical map of the trapped locus is visualized to retrieve the sequences of restriction fragments or PCR primers to be used for the amplification of gene-specific probes. Moreover, a list of all the UniTraps for the gene of interest, with information regarding public and private gene trap clones, is provided. For each UniTrap, the putative impact of the gene trap vector insertion on the protein function is shown and comprehensive information is provided to perform PCR and RT-PCR experiments in order to verify the clone and identify the exact site of vector insertion.Figure 2.

Bottom Line: We have developed a comprehensive resource devoted to biologists wanting to optimize the use of gene trap clones in their experiments.The UniTrap resource contains data relative to 9583 trapped genes, which represent 42.3% of the mouse gene content.Among the trapped genes, 7,728 have a counterpart in humans, and 677 are known to be involved in the pathogenesis of human diseases.

View Article: PubMed Central - PubMed

Affiliation: Telethon Institute of Genetics and Medicine (TIGEM), Via P. Castellino, 111, 80131, Napoli, Italy.

ABSTRACT
We have developed a comprehensive resource devoted to biologists wanting to optimize the use of gene trap clones in their experiments. We have processed 300 602 such clones from both public and private projects to generate 28,199 'UniTraps', i.e. distinct collections of unambiguous insertions at the same subgenic region of annotated genes. The UniTrap resource contains data relative to 9583 trapped genes, which represent 42.3% of the mouse gene content. Among the trapped genes, 7,728 have a counterpart in humans, and 677 are known to be involved in the pathogenesis of human diseases. The aim of this analysis is to provide the wet lab researchers with a comprehensive database and curated tools for (i) identifying and comparing the clones carrying a trap into the genes of interest, (ii) evaluating the severity of the mutation to the protein function in each independent trapping event and (iii) supplying complete information to perform PCR, RT-PCR and restriction experiments to verify the clone and identify the exact point of vector insertion. To share this unique resource with the scientific community, we have designed and implemented a web interface that is freely accessible at http://unitrap.cbm.fvg.it/.

Show MeSH
Related in: MedlinePlus