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Brief Bioinform. 2017 Mar 1;18(2):279-290. doi: 10.1093/bib/bbw023.

Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation.

Author information

1
Research Center for Epigenetic Disease, Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, Japan.
2
Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Kawaguchi, Japan.

Abstract

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis can detect protein/DNA-binding and histone-modification sites across an entire genome. Recent advances in sequencing technologies and analyses enable us to compare hundreds of samples simultaneously; such large-scale analysis has potential to reveal the high-dimensional interrelationship level for regulatory elements and annotate novel functional genomic regions de novo. Because many experimental considerations are relevant to the choice of a method in a ChIP-seq analysis, the overall design and quality management of the experiment are of critical importance. This review offers guiding principles of computation and sample preparation for ChIP-seq analyses, highlighting the validity and limitations of the state-of-the-art procedures at each step. We also discuss the latest challenges of single-cell analysis that will encourage a new era in this field.

KEYWORDS:

chromatin immunoprecipitation; differential analysis; experimental design; large-scale analysis; quality management; single-cell analysis

PMID:
26979602
PMCID:
PMC5444249
DOI:
10.1093/bib/bbw023
[Indexed for MEDLINE]
Free PMC Article

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