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Related Experiment Video

Updated: Jan 11, 2026

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Protocol for isolating nuclei from human stem cell-derived grafts for single-nucleus RNA sequencing.

Edoardo Sozzi1, Petter Storm1, Alessandro Fiorenzano2

  • 1Developmental and Regenerative Neurobiology, Department of Experimental Medical Science, Wallenberg Neuroscience Center, Lund Stem Cell Center, Lund University, Lund, Sweden.

STAR Protocols
|November 9, 2025
PubMed
Summary

This study details a new protocol for isolating nuclei from human stem cell grafts in rat brains. This method aids in analyzing graft integration and neuronal identity in neurodegeneration research.

Keywords:
Cell BiologyGene ExpressionGenomicsMolecular BiologyNeuroscienceSequencingStem Cells

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Area of Science:

  • Neuroscience
  • Stem Cell Biology
  • Molecular Biology

Background:

  • Single-nucleus RNA sequencing (snRNA-seq) offers high-resolution transcriptomic analysis of brain tissue.
  • Understanding cell identity is crucial for studying neurodegeneration and neural repair.
  • Human stem cell grafts are promising for brain repair but require methods to assess their integration and function.

Purpose of the Study:

  • To present a detailed protocol for isolating nuclei from human stem cell-derived grafts within the rat brain.
  • To enable high-resolution transcriptomic analysis of these grafts in vivo.
  • To facilitate the assessment of graft composition, integration, and neuronal identity.

Main Methods:

  • Protocol involves vibratome sectioning of the rat brain.
  • Graft dissection and subsequent nuclear extraction are key steps.
  • Fluorescence-activated sorting is employed for nuclear isolation.

Main Results:

  • The presented workflow successfully isolates nuclei from human stem cell grafts in the rat brain.
  • This method is suitable for analyzing human neurons within host tissue.
  • It supports the assessment of neurons sensitive to dissociation procedures.

Conclusions:

  • This protocol provides a robust method for analyzing human stem cell grafts in vivo using snRNA-seq.
  • It enhances the study of neurodegeneration and repair by enabling detailed analysis of graft components.
  • The workflow supports comprehensive evaluation of graft integration and neuronal function in the living brain.