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Related Experiment Video

Updated: Jul 9, 2025

An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues
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High-capacity sample multiplexing for single cell chromatin accessibility profiling.

Gregory T Booth1, Riza M Daza1, Sanjay R Srivatsan1

  • 1Department of Genome Sciences, University of Washington, Seattle, WA, USA.

BMC Genomics
|December 4, 2023
PubMed
Summary
This summary is machine-generated.

Introducing sciPlex-ATAC-seq, a new method for single-cell chromatin accessibility profiling across many samples. This technique enables large-scale epigenomic studies and identifies drug-altered regulatory sites and immune responses.

Keywords:
ChromatinGenomicsPerturbationScreeningSequencingSingle-cell

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Area of Science:

  • Epigenetics
  • Genomics
  • Molecular Biology

Background:

  • Single-cell chromatin accessibility is crucial for understanding cellular epigenetic states.
  • Current methods face challenges in scalability and cost for multi-specimen analysis.

Purpose of the Study:

  • To introduce sciPlex-ATAC-seq, a novel method for high-throughput, multiplexed single-cell chromatin accessibility profiling.
  • To demonstrate the utility of sciPlex-ATAC-seq in chemical epigenomics and immune response studies.

Main Methods:

  • sciPlex-ATAC-seq utilizes sample-specific DNA oligos for nuclear labeling.
  • Enables concurrent profiling of chromatin accessibility from numerous single nuclei.
  • Applied to chemical epigenomics screening and analysis of immune cell responses.

Main Results:

  • Identified drug-altered distal regulatory sites linked to compound- and dose-dependent transcriptional effects.
  • Quantified cell type-specific chromatin changes in PBMCs upon immune stimulation.
  • Isolated unique effects of allogeneic stimulation on T-lymphocyte chromatin accessibility.
  • Observed correlation between impaired chromatin decondensation and chemical inhibition of T-cell activation.

Conclusions:

  • sciPlex-ATAC-seq offers a scalable solution for single-cell epigenomic profiling across diverse experimental conditions.
  • The method facilitates discovery in chemical biology and immunology by linking chromatin changes to cellular responses.