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Chromatin Immunoprecipitation Followed by Next-Generation Sequencing (ChIP-Seq) Analysis in Ewing Sarcoma

Part of the Methods in Molecular Biology book series (MIMB,volume 2226)

Abstract

ChIP-seq is the method of choice for profiling protein–DNA interactions, and notably for characterizing the landscape of transcription factor binding and histone modifications. This technique has been widely used to study numerous aspects of tumor biology and led to the development of several promising cancer therapies. In Ewing sarcoma research, ChIP-seq provided important insights into the mechanism of action of the major oncogenic fusion protein EWSR1-FLI1 and related epigenetic and transcriptional changes. In this chapter, we provide a detailed pipeline to analyze ChIP-seq experiments from the preprocessing of raw data to tertiary analysis of detected binding sites. We also advise on best practice to prepare tumor samples prior to sequencing.

Key words

  • ChIP-seq
  • Binding sites
  • Transcription factors
  • Histone modifications
  • Motif analysis
  • Ewing sarcoma

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Acknowledgments

This work was funded through institutional support from Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, ATIP-Avenir, the ARC Foundation (ARC-RAC16002KSA-R15093KS), the SIRIC CARPEM (No. INCA-DGOS-INSERM_12561), and the “Who Am I?” Laboratory of Excellence ANR-11-LABX-0071, funded by the French Government through its Investissement d′Avenir program, operated by the French National Research Agency (ANR-11-IDEX-0005-02).

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Kerdivel, G., Boeva, V. (2021). Chromatin Immunoprecipitation Followed by Next-Generation Sequencing (ChIP-Seq) Analysis in Ewing Sarcoma. In: Cidre-Aranaz, F., G. P. Grünewald, T. (eds) Ewing Sarcoma . Methods in Molecular Biology, vol 2226. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1020-6_21

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  • DOI: https://doi.org/10.1007/978-1-0716-1020-6_21

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