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Related Experiment Video

Updated: Jul 28, 2025

Author Spotlight: Nuclei Isolation from Mouse Cardiac Progenitor Cells for Epigenome and Gene Expression Profiling at Single-Cell Resolution
10:03

Author Spotlight: Nuclei Isolation from Mouse Cardiac Progenitor Cells for Epigenome and Gene Expression Profiling at Single-Cell Resolution

Published on: May 12, 2023

3.1K

Nuclei Isolation from Mouse Cardiac Progenitor Cells for Epigenome and Gene Expression Profiling at Single-Cell

Stephanie Ibrahim1, Catherine Robert2, Camille Humbert2

  • 1Center for Cardiovascular Disease & Nutrition, U1263, Aix-Marseille University.

Journal of Visualized Experiments : Jove
|May 29, 2023
PubMed
Summary

Researchers developed a new protocol for isolating nuclei from frozen cardiac progenitor cells. This enables flexible single-nucleus dual-omics (combined snRNA-seq and snATAC-seq) analysis, overcoming limitations of fresh tissue processing.

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Last Updated: Jul 28, 2025

Author Spotlight: Nuclei Isolation from Mouse Cardiac Progenitor Cells for Epigenome and Gene Expression Profiling at Single-Cell Resolution
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Area of Science:

  • Cardiovascular biology
  • Genomics
  • Epigenomics

Background:

  • The developing heart comprises diverse progenitor cells regulated by intricate mechanisms.
  • Single-cell sequencing reveals cardiac progenitor cell heterogeneity but is limited to fresh tissues.
  • Current methods necessitate immediate processing of fresh tissue, restricting experimental flexibility and increasing variability.

Purpose of the Study:

  • To develop a flexible and accessible protocol for analyzing cardiac progenitor cells.
  • To enable dual-omics (snRNA-seq and snATAC-seq) analysis from frozen samples.
  • To overcome the limitations associated with processing fresh cardiac tissue.

Main Methods:

  • A novel protocol for rapid nuclei isolation from frozen cardiac progenitor cells.
  • Integration with single-nucleus RNA sequencing (snRNA-seq) and single-nucleus assay for transposase-accessible chromatin with high-throughput sequencing (snATAC-seq).
  • Compatibility with microfluidic chamber platforms for streamlined analysis.

Main Results:

  • Successful isolation of nuclei from frozen cardiac progenitor cell samples.
  • Demonstration of the protocol's utility for combined snRNA-seq and snATAC-seq.
  • Facilitation of flexible experimental designs and reduced technical variability.

Conclusions:

  • The presented protocol offers a significant advancement for cardiac progenitor cell research.
  • Enables robust dual-omics analysis from frozen samples, enhancing study flexibility.
  • Provides a valuable tool for investigating cardiac development and disease mechanisms.