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    Optimization of transcription factor binding map accuracy utilizing knockout-mouse models

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    Author
    Krebs, W; Schmidt, SV; Goren, A; De Nardo, D; Labzin, L; Bovier, A; Ulas, T; Theis, H; Kraut, M; Latz, E; ...
    Date
    2014-12-01
    Source Title
    Nucleic Acids Research
    Publisher
    OXFORD UNIV PRESS
    University of Melbourne Author/s
    de Nardo, Dominic
    Affiliation
    Medical Biology (W.E.H.I.)
    Metadata
    Show full item record
    Document Type
    Journal Article
    Citations
    Krebs, W., Schmidt, S. V., Goren, A., De Nardo, D., Labzin, L., Bovier, A., Ulas, T., Theis, H., Kraut, M., Latz, E., Beyer, M. & Schultze, J. L. (2014). Optimization of transcription factor binding map accuracy utilizing knockout-mouse models. NUCLEIC ACIDS RESEARCH, 42 (21), pp.13051-13060. https://doi.org/10.1093/nar/gku1078.
    Access Status
    Open Access
    URI
    http://hdl.handle.net/11343/256242
    DOI
    10.1093/nar/gku1078
    Abstract
    Genome-wide assessment of protein-DNA interaction by chromatin immunoprecipitation followed by massive parallel sequencing (ChIP-seq) is a key technology for studying transcription factor (TF) localization and regulation of gene expression. Signal-to-noise-ratio and signal specificity in ChIP-seq studies depend on many variables, including antibody affinity and specificity. Thus far, efforts to improve antibody reagents for ChIP-seq experiments have focused mainly on generating higher quality antibodies. Here we introduce KOIN (knockout implemented normalization) as a novel strategy to increase signal specificity and reduce noise by using TF knockout mice as a critical control for ChIP-seq data experiments. Additionally, KOIN can identify 'hyper ChIPable regions' as another source of false-positive signals. As the use of the KOIN algorithm reduces false-positive results and thereby prevents misinterpretation of ChIP-seq data, it should be considered as the gold standard for future ChIP-seq analyses, particularly when developing ChIP-assays with novel antibody reagents.

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