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Updated: Apr 1, 2026
Tissue Preparation and Immunostaining of Mouse Craniofacial Tissues and Undecalcified Bone
Published on: May 10, 2019
Spatial Transcriptomics of Early Tooth Morphogenesis in Formalin-fixed Paraffin-embedded Mouse Embryonic Tissue
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.
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.
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.
