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Spatial Transcriptomics of Early Tooth Morphogenesis in Formalin-fixed Paraffin-embedded Mouse Embryonic Tissue.

Resmi Raju1, Marianna Bei2

  • 1Section on Craniofacial Genetic Disorders, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institutes of Health (NIH); Department of Surgery, Massachusetts General Hospital; Department of Surgery, Harvard Medical School; Shriners Hospital for Children; rraju2@mgh.harvard.edu.

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Summary

This study presents a protocol for spatial transcriptomics of mouse embryonic craniofacial tissues. This method preserves tissue architecture and RNA integrity, enabling detailed analysis of tooth development.

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Area of Science:

  • Developmental Biology
  • Genomics
  • Histology

Background:

  • Tooth development involves complex cell interactions crucial for form and function.
  • Disruptions in tooth development can lead to congenital disorders like tooth agenesis.
  • Single-cell RNA sequencing (scRNA-seq) reveals cellular heterogeneity but lacks spatial context.

Purpose of the Study:

  • To develop a protocol for spatial transcriptomic analysis of early tooth morphogenesis.
  • To enable in situ localization of molecular signatures within craniofacial tissues.
  • To link gene expression patterns to tissue architecture during embryonic development.

Main Methods:

  • A step-by-step protocol for collecting, fixing, and paraffin-embedding mouse embryonic craniofacial tissue.
  • Optimized sectioning and handling of formalin-fixed, paraffin-embedded (FFPE) tissue.
  • Workflow designed to preserve RNA integrity and tissue morphology for spatial transcriptomics.

Main Results:

  • The protocol yields FFPE mouse embryonic craniofacial tissue suitable for spatial transcriptomics.
  • The method preserves both RNA integrity and tissue morphology for high-resolution analysis.
  • Demonstrated compatibility with both sequencing and image-based spatial transcriptomics platforms.

Conclusions:

  • This protocol facilitates reproducible spatial transcriptomic profiling of early tooth morphogenesis.
  • The approach provides insights into the spatial organization of craniofacial structures.
  • Enables linking molecular mechanisms to tissue morphology in developmental and pathological contexts.