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Related Experiment Video

Updated: Jul 7, 2026

Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells
08:34

Automating ChIP-seq Experiments to Generate Epigenetic Profiles on 10,000 HeLa Cells

Published on: December 10, 2014

Genome-scale ChIP-chip analysis using 10,000 human cells.

Luis G Acevedo1, A Leonardo Iniguez, Heather L Holster

  • 1Cell and Molecular Biology Program, University of Wisconsin-Madison, WI 95616, USA.

Biotechniques
|February 7, 2008
PubMed
Summary

This study presents a miniaturized chromatin immunoprecipitation (ChIP) technique, enabling genome-wide analysis from just 10,000 cells. This MicroChIP method overcomes cell number limitations for transcription factor and chromatin modification studies.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Epigenetics

Background:

  • Chromatin immunoprecipitation (ChIP) identifies DNA-protein interactions and chromatin states.
  • Standard ChIP requires large cell numbers, limiting studies on rare or primary cells.
  • Existing low-cell ChIP methods are unsuitable for genome-wide assays like ChIP-sequencing.

Purpose of the Study:

  • To develop a miniaturized ChIP protocol (MicroChIP) for genome-wide analysis using minimal cell input.
  • To enable ChIP-based studies on biologically significant cell populations with limited cell numbers.

Main Methods:

  • Miniaturization of the standard ChIP protocol.
  • Utilized as few as 10,000 cells without carrier chromatin.
  • Validated MicroChIP using high-density oligonucleotide arrays and specific antibodies.

Main Results:

  • Successfully obtained sufficient sample material for whole-genome analysis from 10,000 cells.
  • Demonstrated reproducibility of the MicroChIP technique.
  • Confirmed reliable detection of RNA polymerase II and specific histone modifications.

Conclusions:

  • The MicroChIP technique significantly reduces the cell input requirement for genome-wide ChIP analysis.
  • This method expands the scope of ChIP applications to include low-cell-number samples.
  • MicroChIP provides a robust platform for studying transcription factor binding and chromatin modifications in diverse cell types.