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An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing
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A cell-sorting-based protocol for cell cycle small-scale ChIP sequencing.

Johnathan R Whetstine1,2, Capucine Van Rechem3

  • 1Cancer Signaling and Epigenetics Program, Fox Chase Cancer Center, Philadelphia, PA 19111, USA.

STAR Protocols
|March 21, 2022
PubMed
Summary

This protocol enables cell cycle analysis and epigenome profiling using chromatin immunoprecipitation sequencing (ChIP-seq) without chemical interference. It allows for detailed analysis of histone modifications and protein recruitment across cell cycle phases.

Keywords:
Cell isolationChIPseqChromatin immunoprecipitation (ChIP)Flow Cytometry/Mass CytometryMolecular Biology

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Area of Science:

  • Cell Biology
  • Epigenetics
  • Molecular Biology

Background:

  • Traditional cell cycle characterization methods can alter cellular states.
  • Chemicals or altered nucleotide pools may impact chromatin structure and histone modifications.
  • Understanding cell cycle-dependent epigenomic changes is crucial.

Purpose of the Study:

  • To present a protocol for cell cycle analysis and epigenome profiling.
  • To enable chromatin immunoprecipitation sequencing (ChIP-seq) on small cell populations.
  • To avoid chemical artifacts in cell cycle and epigenome studies.

Main Methods:

  • Cell fixation and sorting based on DNA content.
  • Immunoprecipitation and library preparation for ChIP-seq.
  • Analysis of the epigenome in specific cell cycle phases.

Main Results:

  • Successful characterization of cell cycle phases via DNA content.
  • Enables epigenome analysis (ChIP-seq) from limited cell numbers.
  • Provides a method to study histone modifications and protein recruitment without chemical artifacts.

Conclusions:

  • This protocol offers a robust method for cell cycle-based epigenome analysis.
  • It facilitates the study of dynamic epigenomic changes across the cell cycle.
  • The method is suitable for researchers working with small cell samples.