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Comprehensive Spatial Profiling of Species-agnostic Transcriptomes via Stereo-seq
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A Protocol for Spatial Transcriptomics Using the 10× Genomics Visium Platform.

Jing Yi Lee1,2, Bavani Kannan1, Zhen Wei Neo3

  • 1Cancer Discovery Hub, National Cancer Centre Singapore, Singapore, Singapore.

Methods in Molecular Biology (Clifton, N.J.)
|April 30, 2026
PubMed
Summary
This summary is machine-generated.

This study optimizes the 10× Visium spatial transcriptomics protocol to analyze tissue samples. This method retains spatial information, aiding in understanding complex biological systems like the tumor microenvironment.

Keywords:
ImmunotherapyNext generation sequencingProtocolSpatial transcriptomicsTumor microenvironment

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biotechnology

Background:

  • Conventional transcriptomics loses spatial information crucial for understanding tissue heterogeneity.
  • Single-cell profiling identifies cell types but lacks spatial context.
  • Understanding the spatial attributes of cells is vital for biological research.

Purpose of the Study:

  • To describe an optimized 10× Visium spatial transcriptomics protocol.
  • To enable deconvolution of heterogeneous tissues while preserving spatial information.
  • To highlight the protocol's utility in studying the tumor microenvironment and cellular interactions.

Main Methods:

  • Optimization of the 10× Visium spatial transcriptomics protocol.
  • Application to both fresh frozen and formalin-fixed paraffin-embedded (FFPE) tissues.
  • Transcriptomic profiling while retaining native spatial information.

Main Results:

  • The optimized protocol successfully retains spatial information in transcriptomic data.
  • It allows for the deconvolution of heterogeneous tissues.
  • The protocol is applicable to various tissue types in human and mouse samples.

Conclusions:

  • The 10× Visium spatial transcriptomics protocol is a powerful tool for analyzing tissue architecture.
  • It facilitates the study of complex biological questions, including tumor microenvironment dynamics.
  • This method aids in elucidating cellular interactions and their role in disease progression.