What you will learn
In this chapter the theoretical background, the experimental requirements, and some ways to evaluate Chromatin Immunoprecipitation followed by NGS (ChIP-Seq) are represented and explained using practical examples. You will learn about the main differences between sequencing DNA regions with certain histone modifications or transcription factor binding sites. Moreover, we will introduce a software tool HOMER, which offers a variety of (epigenetic) sequencing data analysis options. Herefore, the most important scripts, commands, and options and their purpose are illustrated in this chapter. After you have worked through this chapter you will understand the impact of epigenetic sequencing approaches and you will be able to perform the ChIP-Seq data analysis workflow—from receiving your raw data after sequencing to motif discovery in your identified ChIP-Seq peaks/regions.
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Acknowledgements
We thank Prof. Dr. Anja Bosserhoff (Institute of Biochemistry (Emil-Fischer Center), Friedrich-Alexander University Erlangen-Nürnberg) for reviewing this chapter and suggesting extremely relevant enhancements to the original manuscript.
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Kappelmann-Fenzl, M. (2021). Design and Analysis of Epigenetics and ChIP-Sequencing Data. In: Kappelmann-Fenzl, M. (eds) Next Generation Sequencing and Data Analysis. Learning Materials in Biosciences. Springer, Cham. https://doi.org/10.1007/978-3-030-62490-3_12
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DOI: https://doi.org/10.1007/978-3-030-62490-3_12
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