Differential Analysis of Protein-DNA Binding Using ChIP-Seq Data.

Autor:	Boeckel C; Core Facility Genomics, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany., Pastor X; Core Facility Genomics, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany., Heinig M; Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.; Department of Computer Science, TUM School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.; DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany., Walzthoeni T; Core Facility Genomics, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany. thomas.walzthoeni@helmholtz-munich.de.
Jazyk:	angličtina
Zdroj:	Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2024; Vol. 2846, pp. 63-89.
DOI:	10.1007/978-1-0716-4071-5_5
Abstrakt:	Chromatin immunoprecipitation in combination with next-generation sequencing (ChIP-Seq) allows probing of protein-DNA binding in a rapid and genome-wide fashion. Herein we describe the required steps to preprocess ChIP-Seq data and to analyze the differential binding of proteins to DNA for perturbation experiments. In these experiments, different conditions are compared to find the underlying biological mechanisms caused by the stimulus or treatment. In addition, we provide a sample analysis using the steps outlined in the chapter. (© 2024. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)
Databáze:	MEDLINE
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