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

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


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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Chromatin Immunoprecipitation*
  • Epigenesis, Genetic*
  • Epigenomics* / methods
  • Gene Library
  • High-Throughput Nucleotide Sequencing*
  • Histones / metabolism*
  • Humans
  • Regulatory Sequences, Nucleic Acid*
  • Sequence Analysis, DNA


  • Histones