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Related Experiment Video

Updated: Jul 25, 2025

Reusable Single Cell for Iterative Epigenomic Analyses
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Characterization and Optimization of Multiomic Single-Cell Epigenomic Profiling.

Leticia Sandoval1,2, Wazim Mohammed Ismail1,2, Amelia Mazzone1,2

  • 1Division of Experimental Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA.

Genes
|June 28, 2023
PubMed
Summary

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This summary is machine-generated.

Optimizing nuclei isolation is crucial for single-cell multiomic assays. NP-40 detergent-based isolation improves sequencing results for ovarian cancer, enhancing cell type identification in both fresh and frozen samples.

Area of Science:

  • Single-cell multiomics
  • Epigenomics and transcriptomics
  • Human tissue analysis

Background:

  • Single-cell assays like snATAC + snRNA require high-quality nuclei for accurate epigenomic and gene expression profiling.
  • Optimized nuclei isolation methods are essential for human tissue samples in multiomic studies.
  • Current methods need evaluation for reliability and efficiency, especially for challenging sample types.

Purpose of the Study:

  • To compare different nuclei isolation techniques for peripheral blood mononuclear cells (PBMC) and ovarian cancer (OC) tissues.
  • To assess the impact of isolation methods on sequencing output and cell type identification.
  • To validate the effectiveness of nuclei isolation for both fresh and frozen human samples.

Main Methods:

  • Comparison of NP-40 detergent-based versus collagenase-based nuclei isolation for PBMC and OC.
Keywords:
epigenomic profilingnuclei preparationsingle-cell sequencingsnATAC-seqsnRNA-seq

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  • Evaluation of nuclei morphology and sequencing data quality.
  • Assessment of frozen versus fresh sample preparation for nuclei isolation.
  • Reproducibility testing of single-cell RNA (scRNA) and snATAC + snRNA platforms.

    • Main Results:

    • NP-40 detergent-based isolation provided superior sequencing results for ovarian cancer compared to collagenase digestion.
    • Nuclei isolation method significantly impacted cell type identification and downstream analysis.
    • Frozen and fresh samples yielded comparable quality after appropriate preparation.
    • Gene expression profiling from scRNA and snRNA measurements proved comparable and effective for cell identification.

    Conclusions:

    • The choice of nuclei isolation method is critical for successful single-cell multiomic profiling.
    • NP-40 based isolation is recommended for ovarian cancer tissues to improve data quality.
    • The snATAC + snRNA platform demonstrates reproducibility and effectiveness for analyzing both fresh and frozen human samples.