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Related Experiment Video

Updated: Jan 7, 2026

Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
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Protocol to evaluate mouse brain spatial cell type-resolved transcriptomic discoveries using 10× Visium spatial

Mara S Burns1, Ricardo Miramontes2, John C Reidling2

  • 1Department of Neurobiology & Behavior, University of California, Irvine, Irvine, CA 92617, USA.

STAR Protocols
|December 28, 2025
PubMed
Summary
This summary is machine-generated.

This study details a protocol for spatial transcriptomics and single-cell RNA sequencing in mouse tissues. It enables investigation of gene expression and cell signaling in diseased tissue microenvironments.

Keywords:
RNA-seqcell biologygene expressionmolecular biologyneurosciencesequencingsingle cell

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Area of Science:

  • Molecular Biology
  • Genomics
  • Neuroscience

Background:

  • Understanding spatial gene expression and cell-cell signaling in diseased tissues is crucial for elucidating disease mechanisms.
  • Current methods may not fully capture the intricate molecular landscape within intact tissue structures.

Purpose of the Study:

  • To present a comprehensive protocol for investigating molecular transcriptional drivers within intact murine tissue.
  • To integrate spatial transcriptomics and single-cell RNA sequencing for high-resolution tissue analysis.

Main Methods:

  • The protocol involves collecting and processing mouse brain tissue across various ages.
  • It details tissue mounting, staining, FLEX tissue section collection, fixation, dissociation, and cell storage.
  • Utilizes 10× Genomics Visium spatial transcriptomics and 10× Genomics FLEX single-cell RNA sequencing (scRNA-seq).

Main Results:

  • The protocol provides a framework for detailed analysis of gene expression patterns within specific spatial regions of the tissue.
  • Enables the identification of molecular drivers and cell-cell communication networks in situ.
  • Facilitates the study of transcriptional changes associated with disease states in complex tissues.

Conclusions:

  • This protocol offers a robust method for high-resolution molecular profiling of intact tissues.
  • It enhances the understanding of spatial heterogeneity in gene expression and cellular interactions.
  • The presented methodology is valuable for research in developmental biology, neuroscience, and disease pathology.