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Related Experiment Video

Updated: May 27, 2025

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A versatile and efficient method to isolate nuclei from low-input cryopreserved tissues for single-nuclei

Cristopher Segovia1,2, Vincent Desrosiers3,4, Fatemeh Khadangi1,2

  • 1Centre de recherche du CHU de Québec - Université Laval, Axe Oncologie, 1401, 18e rue, Québec, Québec, G1J 1Z4, Canada.

Scientific Reports
|February 15, 2025
PubMed
Summary
This summary is machine-generated.

This study presents an optimized single-nuclei RNA sequencing protocol, enabling detailed analysis of rare human tissues. The method efficiently extracts nuclei from minimal tissue amounts, crucial for advancing disease research with limited biospecimens.

Keywords:
CancerNuclei isolationNuclei sortingTissue heterogeneityTissue homogenizationTranscriptomics

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Area of Science:

  • Genomics
  • Molecular Biology
  • Cancer Research

Background:

  • Clinical samples are essential for disease research but often scarce.
  • Single-cell technologies require well-characterized tissues, posing a challenge with limited sample availability.

Purpose of the Study:

  • To develop an optimized protocol for single-nuclei RNA sequencing (snRNA-seq) from minimal amounts of cryopreserved human tissue.
  • To demonstrate the protocol's efficacy in capturing tissue heterogeneity comparable to existing single-cell atlases.

Main Methods:

  • Developed and optimized a snRNA-seq protocol for nuclei extraction from 15 mg of cryopreserved human tissue.
  • Applied the protocol to four distinct cancer tissue types (brain, bladder, lung, prostate).
  • Analyzed the resulting single-nuclei transcriptomic data to assess tissue heterogeneity.

Main Results:

  • Successfully extracted and sequenced nuclei from small tissue samples (15 mg).
  • Profiled between 1550 and 7468 nuclei per tissue sample.
  • Revealed transcriptomic heterogeneity comparable to established single-cell atlases.

Conclusions:

  • The optimized snRNA-seq protocol effectively utilizes scarce, cryopreserved human tissues.
  • Enhances the potential for research requiring limited sample quantities and comprehensive tissue characterization.
  • Facilitates greater use and sharing of valuable, rare biospecimens for scientific discovery.