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Tissue RNA Integrity in Visium Spatial Protocol (Fresh Frozen Samples).

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  • 1Molecular Biotechnology Center, University of Torino, Torino, Italy.

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Summary

Spatial transcriptomics (ST) preserves tissue architecture and fragile cells lost in single-cell RNA sequencing (scRNA-seq). This guide details the Visium protocol for fresh frozen tissues, ensuring high-quality spatial gene expression data.

Keywords:
RNA quality controlSpatial TranscriptomicsTissue preparationVisium

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Single-cell RNA sequencing (scRNA-seq) requires tissue dissociation, potentially losing spatial information and fragile cells.
  • Spatial transcriptomics (ST) methods detect single-cell transcripts within intact tissue sections, preserving cellular organization.
  • The Visium platform offers whole-transcriptome ST without specialized instruments, accessible to pathology labs.

Purpose of the Study:

  • To describe critical steps of the Visium protocol for fresh frozen tissues.
  • To provide guidance on interpreting quality control data for Visium spatial transcriptomics.
  • To highlight the importance of proper tissue handling in ST.

Main Methods:

  • Detailed protocol for Visium spatial transcriptomics on fresh frozen tissues.
  • Emphasis on tissue handling to maintain morphology and mRNA integrity.
  • Quality control analysis interpretation for downstream library preparation and sequencing.

Main Results:

  • Successful application of Visium protocol on fresh frozen tissues.
  • Demonstration of preserved tissue morphology and mRNA integrity.
  • Guidelines for interpreting quality control metrics.

Conclusions:

  • Spatial transcriptomics, particularly with the Visium platform, is a valuable tool for studying tissue cellular organization.
  • Proper tissue handling and adherence to protocol steps are crucial for reliable ST data.
  • The described workflow facilitates the acquisition and interpretation of spatial gene expression data.