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Related Concept Videos

Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

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Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
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Immunoprecipitation, or IP, is a widely used technique that employs protein-antibody interactions to isolate proteins or protein complexes in their native state for studying protein-protein interactions, quaternary structures, or supramolecular complexes. Various modifications of the technique, including chromatin IP, cross-linking IP, and fluorescence IP, are commonly used.
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Related Experiment Video

Updated: Nov 14, 2025

Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells
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A plug and play microfluidic platform for standardized sensitive low-input chromatin immunoprecipitation.

René A M Dirks1, Peter C Thomas2, Haoyu Wu1

  • 1Department of Molecular Biology, Faculty of Science, Radboud University, Radboud Institute for Molecular Life Sciences (RIMLS), 6525GA Nijmegen, the Netherlands.

Genome Research
|March 12, 2021
PubMed
Summary

We developed a new microfluidic Plug and Play ChIP-seq (PnP-ChIP-seq) method for sensitive epigenetic profiling. This automated workflow enables robust chromatin immunoprecipitation followed by sequencing on low-input samples, improving reproducibility and throughput for researchers worldwide.

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Area of Science:

  • Epigenetics
  • Molecular Biology
  • Bioengineering

Background:

  • Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is crucial for genome-wide analysis of regulatory elements and gene networks.
  • Current low-input ChIP-seq protocols are laborious, time-consuming, and suffer from poor reproducibility and low throughput.
  • Existing microfluidic ChIP-seq platforms require specialized equipment and expertise, limiting their broad applicability.

Purpose of the Study:

  • To develop a standardized, automated, and user-friendly ChIP-seq method for low-input samples.
  • To overcome the limitations of existing ChIP-seq protocols in terms of hands-on time, experimental variation, and throughput.
  • To enable sensitive epigenetic profiling of rare cell populations and precious samples.

Main Methods:

  • Construction of microfluidic polydimethylsiloxane (PDMS)-based plates for performing 24 sensitive ChIP reactions.
  • Development of a Plug and Play (PnP) workflow integrating disposable plates with a widely available controller for automation.
  • Application of the PnP-ChIP-seq method for profiling histone modifications in mouse embryonic stem cells (mESCs).

Main Results:

  • High-quality ChIP-seq data obtained from hundreds to a few thousand cells for six key histone modifications.
  • Robust detection of epigenetic differences in promoters and enhancers between naive and primed mESCs.
  • Successful generation of epigenetic profiles for rare mESC subpopulations resembling the two-cell stage.

Conclusions:

  • PnP-ChIP-seq provides a robust, standardized, and sensitive method for epigenetic profiling of low-input samples.
  • The platform's ease of use, high throughput, and consistency empower nonexpert laboratories globally.
  • This technology facilitates large-scale epigenomic studies on precious and rare biological samples.