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Methods Mol Biol. 2012;802:275-91. doi: 10.1007/978-1-61779-400-1_18.

Analyzing ChIP-seq data: preprocessing, normalization, differential identification, and binding pattern characterization.

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  • 1Department of Molecular Virology, Immunology & Medical Genetics, The Ohio State University, Columbus, OH, USA.

Abstract

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a high-throughput antibody-based method to study genome-wide protein-DNA binding interactions. ChIP-seq technology allows scientist to obtain more accurate data providing genome-wide coverage with less starting material and in shorter time compared to older ChIP-chip experiments. Herein we describe a step-by-step guideline in analyzing ChIP-seq data including data preprocessing, nonlinear normalization to enable comparison between different samples and experiments, statistical-based method to identify differential binding sites using mixture modeling and local false discovery rates (fdrs), and binding pattern characterization. In addition, we provide a sample analysis of ChIP-seq data using the steps provided in the guideline.

PMID:
22130887
[PubMed - indexed for MEDLINE]
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