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    Matrix and Steiner-triple-system smart pooling assays for high-performance transcription regulatory network mapping

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    Authors
    Vermeirssen, Vanessa
    Deplancke, Bart
    Barrasa, M. Inmaculada
    Reece-Hoyes, John S.
    Arda, H. Efsun
    Grove, Christian A.
    Martinez, Natalia Julia
    Sequerra, Reynaldo
    Doucette-Stamm, Lynn
    Brent, Michael R.
    Walhout, Albertha J. M.
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    Student Authors
    H. Efsun Arda; Christian A. Grove
    UMass Chan Affiliations
    Program in Molecular Medicine
    Program in Gene Function and Expression
    Document Type
    Journal Article
    Publication Date
    2007-06-26
    Keywords
    Animals; Caenorhabditis elegans; *Transcription, Genetic; Two-Hybrid System Techniques
    Genetics and Genomics
    Life Sciences
    Medicine and Health Sciences
    
    Metadata
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    Link to Full Text
    http://dx.doi.org/10.1038/nmeth1063
    Abstract
    Yeast one-hybrid (Y1H) assays provide a gene-centered method for the identification of interactions between gene promoters and regulatory transcription factors (TFs). To date, Y1H assays have involved library screens that are relatively expensive and laborious. We present two Y1H strategies that allow immediate prey identification: matrix assays that use an array of 755 individual Caenorhabditis elegans TFs, and smart-pool assays that use TF multiplexing. Both strategies simplify the Y1H pipeline and reduce the cost of protein-DNA interaction identification. We used a Steiner triple system (STS) to create smart pools of 4-25 TFs. Notably, we uniplexed a small number of highly connected TFs to allow efficient assay deconvolution. Both strategies outperform library screens in terms of coverage, confidence and throughput. These versatile strategies can be adapted both to TFs in other systems and, likely, to other biomolecules and assays as well.
    Source
    Nat Methods. 2007 Aug;4(8):659-64. Epub 2007 Jun 24. Link to article on publisher's site
    DOI
    10.1038/nmeth1063
    Permanent Link to this Item
    http://hdl.handle.net/20.500.14038/33778
    PubMed ID
    17589517
    Related Resources
    Link to Article in PubMed
    ae974a485f413a2113503eed53cd6c53
    10.1038/nmeth1063
    Scopus Count
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    Morningside Graduate School of Biomedical Sciences Scholarly Publications

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