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Related Experiment Video

Updated: Oct 11, 2025

Mapping Genome-wide Accessible Chromatin in Primary Human T Lymphocytes by ATAC-Seq
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Mapping Chromatin Accessibility in Human Naïve Pluripotent Stem Cells Using ATAC-Seq.

Jessica K Cinkornpumin1, Ishtiaque Hossain1, William A Pastor2,3

  • 1Department of Biochemistry, McGill University, Montreal, QC, Canada.

Methods in Molecular Biology (Clifton, N.J.)
|December 6, 2021
PubMed
Summary

This chapter details producing and assessing Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) libraries from human pluripotent stem cells to map open chromatin sites and regulatory elements.

Keywords:
ATAC-seqChromatinEnhancersNaïve hESCsPluripotencyRegulatory elementsTransposase

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Area of Science:

  • Genomics
  • Molecular Biology
  • Epigenetics

Background:

  • Regulatory elements like promoters and enhancers exhibit reduced nucleosome occupancy, a state known as open chromatin.
  • Open chromatin distribution offers insights into transcription factors and regulatory networks governing gene expression.
  • Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is a powerful technique for mapping these open chromatin regions.

Purpose of the Study:

  • To provide a comprehensive guide on generating ATAC-seq libraries.
  • To outline methods for assessing the quality of ATAC-seq libraries.
  • To focus on applications in naïve human pluripotent stem cells.

Main Methods:

  • Detailed protocol for ATAC-seq library preparation.
  • Quality control metrics for assessing ATAC-seq library integrity and complexity.
  • Application of ATAC-seq in human pluripotent stem cell models.

Main Results:

  • Successful generation of high-quality ATAC-seq libraries.
  • Characterization of open chromatin landscapes in human pluripotent stem cells.
  • Demonstration of ATAC-seq's capability to identify nucleosome and transcription factor binding sites.

Conclusions:

  • ATAC-seq is a robust method for mapping open chromatin and regulatory elements.
  • The described methods enable reliable ATAC-seq library production and quality assessment.
  • This work facilitates the study of gene regulation in human pluripotent stem cells.