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    4C Analysis of 3C, ChIP-Loop, and Control Libraries

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    Authors
    Kim, Tae Hoon
    Dekker, Job
    UMass Chan Affiliations
    Program in Systems Biology
    Department of Biochemistry and Molecular Pharmacology
    Document Type
    Journal Article
    Publication Date
    2018-09-04
    Keywords
    Biochemistry
    Enzymes and Coenzymes
    Genetic Phenomena
    Genetics and Genomics
    Investigative Techniques
    Molecular Biology
    Systems Biology
    
    Metadata
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    Link to Full Text
    https://doi.org/10.1101/pdb.prot097881
    Abstract
    The 4C detection method starts with a 3C, ChIP-loop, or control library and then uses inverse polymerase chain reaction (PCR) to amplify all restriction fragments that are ligated to a single restriction fragment of interest. As a result, a genome-wide interaction profile of the restriction fragment of interest is obtained. Before starting a 4C experiment, first assess the quality of the 3C, ChIP-loop, or control library that will be studied by performing semiquantitative PCR with the library as template. This procedure ascertains that ligation products can be readily detected and that nearby restriction fragments become ligated more frequently than more distant fragments. Choice of a restriction enzyme for 4C analysis and determination of interaction frequencies using 4C are described in detail.
    Source

    Cold Spring Harb Protoc. 2018 Sep 4;2018(9):pdb.prot097881. doi: 10.1101/pdb.prot097881. Link to article on publisher's site

    DOI
    10.1101/pdb.prot097881
    Permanent Link to this Item
    http://hdl.handle.net/20.500.14038/49875
    PubMed ID
    30181222
    Related Resources

    Link to Article in PubMed

    ae974a485f413a2113503eed53cd6c53
    10.1101/pdb.prot097881
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