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Methods Mol Biol. 2018;1799:303-326. doi: 10.1007/978-1-4939-7896-0_22.

An Integrated and Semiautomated Microscaled Approach to Profile Cis-Regulatory Elements by Histone Modification ChIP-Seq for Large-Scale Epigenetic Studies.

Author information

1
La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA, USA.
2
Clinical and Experimental Sciences, Faculty of Medicine, National Institute for Health Research, Southampton Respiratory Biomedical Research Unit, University of Southampton, Southampton, UK.
3
La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA, USA. gregory@lji.org.

Abstract

Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) is the preferred approach to map histone modifications and identify cis-regulatory DNA elements throughout the genome. Multiple methods have been described to increase the efficiency of library preparation and to reduce hands-on time as well as costs. This review describes detailed steps to perform cell fixation, chromatin shearing, immunoprecipitation, and sequencing library preparation for a batch of 48-96 samples with small cell numbers. The protocol implements a semiautomated platform to reduce technical variability and improve signal-to-noise ratio as well as reduce hands-on time, thus allowing large-scale epigenetic studies of clinical samples with limited cell numbers.

KEYWORDS:

ChIP-Seq; H3K27ac; IP-Star; Tagmentation

PMID:
29956160
PMCID:
PMC6844362
DOI:
10.1007/978-1-4939-7896-0_22
[Indexed for MEDLINE]
Free PMC Article

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