Guidelines to Analyze ChIP-Seq Data: Journey Through QC and Analysis Considerations

Bony De Kumar; Jaya Krishnan

doi:10.1007/978-1-0716-4322-8_14

Guidelines to Analyze ChIP-Seq Data: Journey Through QC and Analysis Considerations

Methods Mol Biol. 2025:2889:193-206. doi: 10.1007/978-1-0716-4322-8_14.

Authors

Bony De Kumar^{1

2}, Jaya Krishnan^{3

4}

Affiliations

¹ Yale Center for Genome Analysis, West Haven, CT, USA.
² Department of Genetics, Yale School of Medicine, New Haven, CT, USA.
³ Genes & Human Disease Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, USA. [email protected].
⁴ Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, USA. [email protected].

PMID: 39745614
DOI: 10.1007/978-1-0716-4322-8_14

Abstract

ChIP-Seq is used to study DNA-protein interactions, unraveling chromatin states and gene regulatory properties of transcription factors. ChIP-Seq involves immunoprecipitation followed by sequencing using Next-Generation sequencing approaches. The ENCODE consortium provides extensive guidelines for ChIP-Seq analysis. Meanwhile, appropriate QC metrics and knowledge to interpret outcomes are essential for a good ChIP-Seq experiment. This chapter outlines the various QC metrics and analytical tools for ChIP-Seq analysis to provide a better understanding of the results.

Keywords: ChIP-Seq; ENCODE; Fraction of reads in peak (FRiP); Inconsistency discovery rate (IDR); Non-redundant fraction (NRF); Strand cross-correlation (SCC).

MeSH terms

Chromatin / genetics
Chromatin / metabolism
Chromatin Immunoprecipitation / methods
Chromatin Immunoprecipitation Sequencing* / methods
Computational Biology / methods
DNA / genetics
Guidelines as Topic
High-Throughput Nucleotide Sequencing / methods
Humans
Quality Control
Sequence Analysis, DNA / methods
Software

Substances

Chromatin
DNA