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    Randomized ligation control for chromosome conformation capture

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    Authors
    Belton, Jon-Matthew
    Dekker, Job
    UMass Chan Affiliations
    Department of Biochemistry and Molecular Pharmacology
    Program in Systems Biology
    Document Type
    Journal Article
    Publication Date
    2015-06-01
    Keywords
    Biochemistry, Biophysics, and Structural Biology
    Genetics and Genomics
    Laboratory and Basic Science Research
    Systems Biology
    
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    Link to Full Text
    http://dx.doi.org/10.1101/pdb.prot085183
    Abstract
    In experiments using chromosome conformation capture followed by PCR (3C-PCR) or chromosome conformation capture carbon copy (5C), it is critical to control for intrinsic biases in the restriction fragments of interest and the probes or primers used for detection. Characteristics such as GC%, annealing temperature, efficiency of 3C primers or 5C probes, and length of restriction fragment can cause variations in primer or probe performance and fragment ligation efficiency. Bias can be measured empirically by production of a random control library, as described here, to be used with the 3C library of interest.
    Source
    Cold Spring Harb Protoc. 2015 Jun 1;2015(6):587-92. doi: 10.1101/pdb.prot085183. Link to article on publisher's site
    DOI
    10.1101/pdb.prot085183
    Permanent Link to this Item
    http://hdl.handle.net/20.500.14038/49951
    PubMed ID
    26034305
    Related Resources
    Link to Article in PubMed
    ae974a485f413a2113503eed53cd6c53
    10.1101/pdb.prot085183
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