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    Polymerase Chain Reaction (PCR) Detection of 3C Ligation Products Present in 3C, ChIP-Loop, and Control Libraries: Library Titration and Interaction Frequency Analysis

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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
    Genetic Phenomena
    Genetics and Genomics
    Investigative Techniques
    Laboratory and Basic Science Research
    Molecular Biology
    Systems Biology
    
    Metadata
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    Link to Full Text
    https://doi.org/10.1101/pdb.prot097873
    Abstract
    In all 3C-based assays, the aim is to measure the frequency with which two loci interact within cells. This is achieved by determining the relative abundance of ligation products formed during the 3C protocol that carry sequences from both loci. Individual 3C ligation products that are present in a 3C library, the ChIP-loop library, or the control library can be detected by polymerase chain reaction (PCR) using locus-specific primers. The following protocol outlines the procedure to measure relative abundances of ligation products in these libraries using PCR. The first part of the protocol-library titration-is required only once to determine the linear range of PCR detection. Once the linear range of PCR detection is known for a given ligation product library, follow the second part-interaction analysis-to measure the abundance of ligation products of interest in that library. Specific issues regarding determining the relative abundance of ligation products, designing PCR primers, and quantifying interaction frequencies are also described.
    Source

    Cold Spring Harb Protoc. 2018 Sep 4;2018(9):pdb.prot097873. doi: 10.1101/pdb.prot097873. Link to article on publisher's site

    DOI
    10.1101/pdb.prot097873
    Permanent Link to this Item
    http://hdl.handle.net/20.500.14038/49874
    PubMed ID
    30181221
    Related Resources

    Link to Article in PubMed

    ae974a485f413a2113503eed53cd6c53
    10.1101/pdb.prot097873
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