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Related Experiment Video

Updated: Jul 19, 2025

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Protocol for bulk and single-nuclei chromatin accessibility quantification in mouse liver tissue.

Noga Korenfeld1, Nicolaj I Toft2, Trine V Dam2

  • 1Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, POB 12, Rehovot 7610001, Israel.

STAR Protocols
|August 17, 2023
PubMed
Summary

This study presents a modified transposase-accessible chromatin sequencing (ATAC-seq) protocol for genome-wide chromatin accessibility measurement. The optimized method includes detailed steps for liver tissue and offers both bulk and single-nuclei ATAC-seq approaches.

Keywords:
GenomicsMetabolismMolecular BiologySingle Cell

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Area of Science:

  • Genomics
  • Molecular Biology
  • Epigenetics

Background:

  • Chromatin accessibility is crucial for cell function, regulating DNA-binding protein access.
  • Transposase-accessible chromatin sequencing (ATAC-seq) is a key technique for genome-wide accessibility studies.

Purpose of the Study:

  • To detail a modified ATAC-seq protocol for measuring genome-wide chromatin accessibility.
  • To optimize the protocol for liver tissue, which presents unique nuclei isolation challenges.
  • To provide comprehensive guidance for both bulk and single-nuclei ATAC-seq applications.

Main Methods:

  • Modified transposase-accessible chromatin sequencing (ATAC-seq) assay.
  • Detailed protocol for nuclei isolation, tagmentation, and PCR amplification.
  • Inclusion of pre- and post-sequencing quality control steps.

Main Results:

  • A refined ATAC-seq protocol enabling genome-wide chromatin accessibility measurement.
  • Specific optimizations for nuclei isolation from liver tissue.
  • Two distinct experimental vignettes: bulk ATAC-seq and single-nuclei ATAC-seq.

Conclusions:

  • The presented modified ATAC-seq protocol is effective for assessing chromatin accessibility.
  • The protocol is robust and adaptable, particularly for liver tissue analysis.
  • Provides valuable resources for researchers utilizing bulk and single-nuclei ATAC-seq.