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Updated: Feb 3, 2026

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
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Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections.

Fredrik Salmén1,2, Patrik L Ståhl3, Annelie Mollbrink1

  • 1Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.

Nature Protocols
|October 25, 2018
PubMed
Summary
This summary is machine-generated.

Spatial Transcriptomics integrates high-throughput RNA sequencing with tissue location data. This method allows precise mapping of gene expression within tissues, advancing biological research.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biotechnology

Background:

  • Traditional methods like immunohistochemistry (IHC) and in situ hybridization (ISH) offer spatial gene expression insights but are limited to analyzing few genes.
  • Advances in RNA sequencing (RNA-seq) provide high-throughput gene expression data but lack spatial resolution.
  • Spatial Transcriptomics bridges this gap by combining spatial information with large-scale gene expression analysis.

Purpose of the Study:

  • To present a protocol for applying Spatial Transcriptomics technology to mammalian tissue sections.
  • To enable spatially resolved, high-throughput gene expression analysis in biological tissues.

Main Methods:

  • The protocol integrates histological staining with spatially resolved RNA sequencing of intact tissue sections.
  • It involves library construction and next-generation sequencing.
  • Data processing is efficient, with library construction and sequencing completed in approximately 5-6 days.

Main Results:

  • The study details a protocol for Spatial Transcriptomics in mammalian tissues.
  • The method combines histological staining and spatially resolved RNA-seq.
  • It offers a high-throughput approach to gene expression analysis with spatial resolution.

Conclusions:

  • Spatial Transcriptomics provides a powerful method for mapping gene expression within tissues.
  • This protocol enables researchers to gain spatially resolved, high-throughput gene expression data.
  • The technique is accessible to laboratories with standard equipment like cryostats and microscopes.