基于 ChIP-Seq 数据的蛋白质与 DNA 结合的差异分析。

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

机构信息

Core Facility Genomics, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.

Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.

出版信息

Methods Mol Biol. 2024;2846:63-89. doi: 10.1007/978-1-0716-4071-5_5.

DOI:10.1007/978-1-0716-4071-5_5

PMID:39141230

Abstract

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.

摘要

染色质免疫沉淀结合下一代测序（ChIP-Seq）允许快速和全基因组方式探测蛋白质-DNA 结合。本文描述了预处理 ChIP-Seq 数据和分析扰动实验中蛋白质与 DNA 差异结合所需的步骤。在这些实验中，通过比较不同条件来寻找刺激或处理引起的潜在生物学机制。此外，我们还提供了使用本章中概述的步骤进行的示例分析。