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Protocol for Xenium spatial transcriptomics studies using fixed frozen mouse brain sections.

Xiaokuang Ma1, Peng Chen1, Jing Wei1

  • 1Basic Medical Sciences, University of Arizona College of Medicine-Phoenix, Phoenix, AZ, USA.

STAR Protocols
|November 13, 2024
PubMed
Summary
This summary is machine-generated.

This study introduces a new protocol for Xenium spatial transcriptomics on fixed frozen mouse brain sections. The method ensures compatibility with the Xenium platform, yielding high-quality gene expression data.

Keywords:
RNA-seqgene expressionmolecular biologyneurosciencesystems biology

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Area of Science:

  • Neuroscience
  • Molecular Biology
  • Genomics

Background:

  • Spatial transcriptomics enables the study of gene expression within the cellular context of tissues.
  • The Xenium platform offers high-resolution spatial gene expression analysis.
  • Standard protocols often utilize formalin-fixed paraffin-embedded (FFPE) or fresh frozen tissues.

Purpose of the Study:

  • To present a protocol for Xenium spatial transcriptomics using fixed frozen mouse brain sections.
  • To demonstrate the compatibility of fixed frozen sections with the Xenium platform.
  • To validate the quality of gene expression data obtained from this method.

Main Methods:

  • Intracardiac perfusion of mouse brains.
  • Cryosectioning of fixed frozen brain tissue.
  • Floating section mounting for Xenium analyzer compatibility.

Main Results:

  • Fixed frozen mouse brain sections are compatible with the Xenium spatial transcriptomics platform.
  • The protocol yields excellent imaging results.
  • Accurate quantification of spatially resolved gene expression is achieved.

Conclusions:

  • The developed protocol expands the utility of the Xenium platform for spatial transcriptomics.
  • Fixed frozen sections offer a viable alternative for Xenium studies, providing high-quality data.
  • This method facilitates detailed analysis of gene expression patterns in the mouse brain.