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Chromatin Immunoprecipitation pp 9–28Cite as

Considerations on Experimental Design and Data Analysis of Chromatin Immunoprecipitation Experiments

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1689))

Abstract

Arguably one of the most valuable techniques to study chromatin organization, ChIP is the method of choice to map the contacts established between proteins and genomic DNA. Ever since its inception, more than 30 years ago, ChIP has been constantly evolving, improving, and expanding its capabilities and reach. Despite its widespread use by many laboratories across a wide variety of disciplines, ChIP assays can be sometimes challenging to design, and are often sensitive to variations in practical implementation.

In this chapter, we provide a general overview of the ChIP method and its most common variations, with a special focus on ChIP-seq. We try to address some of the most important aspects that need to be taken into account in order to design and perform experiments that generate the most reproducible, high-quality data. Some of the main topics covered include the use of properly characterized antibodies, alternatives to chromatin preparation, the need for proper controls, and some recommendations about ChIP-seq data analysis.

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Acknowledgments

Our work is supported by grants from The Swedish Research Council and The Swedish Cancer Society to N.V. A.J.P. was supported by the Department of Molecular Biosciences, The Wenner-Gren Institute at the Stockholm University.

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  1. Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20c, 10691, Stockholm, Sweden

    Antonio Jordán-Pla & Neus Visa

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  1. Antonio Jordán-Pla
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Correspondence to Antonio Jordán-Pla .

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  1. Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden

    Neus Visa

  2. Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden

    Antonio Jordán-Pla

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Jordán-Pla, A., Visa, N. (2018). Considerations on Experimental Design and Data Analysis of Chromatin Immunoprecipitation Experiments. In: Visa, N., Jordán-Pla, A. (eds) Chromatin Immunoprecipitation. Methods in Molecular Biology, vol 1689. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7380-4_2

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