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Related Experiment Video

Updated: May 2, 2026

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Protocol for preparing formalin-fixed paraffin-embedded musculoskeletal tissue samples from mice for spatial

Esther Wehrle1, Denise Günther2, Neashan Mathavan2

  • 1Institute for Biomechanics, ETH Zurich, Zurich, Switzerland; AO Research Institute Davos, Davos Platz, Switzerland.

STAR Protocols
|March 31, 2024
PubMed
Summary
This summary is machine-generated.

This study details a new protocol for spatial transcriptomics on mouse bone and musculoskeletal tissues. The method enables detailed molecular analysis of formalin-fixed paraffin-embedded samples.

Keywords:
GenomicsHealth SciencesMicroscopyMolecular BiologyMolecular/Chemical Probes

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biotechnology

Background:

  • Spatial transcriptomics offers unprecedented insights into tissue architecture and cellular function.
  • Analyzing bone and musculoskeletal tissues presents unique challenges due to their complex composition and mineralization.
  • Formalin-fixed paraffin-embedded (FFPE) samples are valuable for retrospective studies but require specific processing for transcriptomic analysis.

Purpose of the Study:

  • To establish and present a comprehensive protocol for applying spatial transcriptomics to mouse bone and multi-tissue musculoskeletal FFPE samples.
  • To provide detailed procedural steps from tissue harvesting to data analysis.
  • To address the specific technical hurdles associated with FFPE musculoskeletal tissues.

Main Methods:

  • Tissue harvesting, processing, and paraffin embedding of mouse musculoskeletal samples.
  • Sectioning of FFPE blocks and placement onto specialized slides for spatial transcriptomics.
  • Decrosslinking, RNA library preparation, and subsequent high-throughput sequencing.
  • Bioinformatic analysis pipelines for spatial transcriptomic data interpretation.

Main Results:

  • A complete 18-day protocol is described for mouse femora and adjacent muscle FFPE samples.
  • Over 50% of the protocol time is dedicated to decalcification of mineralized bone tissue.
  • The protocol yields high-quality spatial transcriptomic data from challenging FFPE musculoskeletal samples.

Conclusions:

  • This protocol facilitates high-resolution spatial transcriptomic analysis of mouse bone and musculoskeletal tissues.
  • The method is crucial for understanding tissue heterogeneity and cellular interactions in complex anatomical structures.
  • It expands the utility of archived FFPE samples for advanced molecular research in musculoskeletal biology.