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Related Experiment Video

Updated: Jul 12, 2025

Author Spotlight: Enhancing Nuclei Isolation for Multiome Sequencing in Challenging Tumor Microenvironments
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Optimized Nuclei Isolation from Fresh and Frozen Solid Tumor Specimens for Multiome Sequencing.

Deshka S Foster1, Michelle Griffin1, Michael Januszyk1

  • 1Hagey Laboratory for Pediatric Regenerative Medicine, Department of Surgery, Stanford University.

Journal of Visualized Experiments : Jove
|October 30, 2023
PubMed
Summary

Optimizing nuclear isolation for multiomic single-cell sequencing from solid tumors is crucial. This study provides key recommendations for tissue digestion and nuclear isolation to ensure high-quality data for cancer research.

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Area of Science:

  • Genomics
  • Cancer Research
  • Molecular Biology

Background:

  • Multiome sequencing (single-cell RNA and ATAC-sequencing) advances tumor heterogeneity research.
  • High-quality sequencing data relies heavily on optimal input material preparation.
  • Solid tumors present unique challenges due to dense matrices and fragile cells.

Purpose of the Study:

  • To describe best practices for nuclear isolation from solid tumor specimens for multiome sequencing.
  • To provide recommendations for optimizing tissue digestion and nuclear isolation protocols.
  • To ensure high-quality single-cell data for translational cancer research.

Main Methods:

  • Detailed protocols for tissue digestion of solid tumors.
  • Methods for single-cell suspension preparation and storage.
  • Nuclear isolation and assessment techniques tailored for multiome sequencing.

Main Results:

  • Established optimized digestion conditions to maximize cell yield from dense tumor tissues.
  • Developed robust nuclear isolation procedures compatible with 10x Genomics multiome platform.
  • Demonstrated the importance of specific lysis times and reagent ratios for nuclear integrity.

Conclusions:

  • Successful nuclear isolation is critical for high-quality multiome sequencing data from solid tumors.
  • The provided recommendations facilitate improved cell and nuclear recovery from challenging specimens.
  • This work supports advancements in understanding tumor cell heterogeneity through multiomic analyses.