Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

Patrik L. Ståhl, Fredrik Salmén, Joakim Lundeberg, Jonas Frisén · 21 authors total; first authors Ståhl and Salmén, senior/corresponding authors Lundeberg and Frisén. Full list: Ståhl, Salmén, Vickovic, Lundmark, Fernández Navarro, Magnusson, Giacomello, Asp, Westholm, Huss, Mollbrink, Linnarsson, Codeluppi, Borg, Pontén, Costea, Sahlén, Mulder, Bergmann, Lundeberg, Frisén.

Published 1 July 2016 · Science · Journal article

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Summary

The authors introduce 'spatial transcriptomics,' a method that places thin histological tissue sections onto a glass surface arrayed with barcoded reverse-transcription primers, so that mRNA captured at each position retains its two-dimensional spatial coordinates. Sequencing the barcoded cDNA reconstructs genome-wide expression maps directly on the tissue image. They demonstrate the approach on mouse brain and human breast cancer sections, recovering spatially resolved transcriptomes that align with tissue morphology.

Key findings

Spatially barcoded RT primer arrays let researchers obtain quantitative, genome-wide transcriptome data while preserving the 2D position of each transcript within a tissue section.
Applied to mouse olfactory bulb/brain and human breast cancer tissue, the method generated high-quality RNA-seq data mapped onto histology.
The approach enables unsupervised identification of spatial expression patterns and tissue regions, establishing a foundation for the spatial transcriptomics field.

Subjects & keywords

Biology & Genetics spatial transcriptomics gene expression rna-seq tissue sections genomics

Cite this paper

APA

Patrik L. Ståhl, Fredrik Salmén, Joakim Lundeberg, & Jonas Frisén [21 authors total; first authors Ståhl and Salmén, senior/corresponding authors Lundeberg and Frisén. Full list: Ståhl, Salmén, Vickovic, Lundmark, Fernández Navarro, Magnusson, Giacomello, Asp, Westholm, Huss, Mollbrink, Linnarsson, Codeluppi, Borg, Pontén, Costea, Sahlén, Mulder, Bergmann, Lundeberg, Frisén.] (2016). Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science. https://doi.org/10.1126/science.aaf2403

BibTeX

@article{sthl2016visualization,
  author    = {Patrik L. Ståhl and Fredrik Salmén and Joakim Lundeberg and Jonas Frisén and {21 authors total; first authors Ståhl and Salmén, senior/corresponding authors Lundeberg and Frisén. Full list: Ståhl, Salmén, Vickovic, Lundmark, Fernández Navarro, Magnusson, Giacomello, Asp, Westholm, Huss, Mollbrink, Linnarsson, Codeluppi, Borg, Pontén, Costea, Sahlén, Mulder, Bergmann, Lundeberg, Frisén.}},
  title     = {Visualization and analysis of gene expression in tissue sections by spatial transcriptomics},
  journal   = {Science},
  year      = {2016},
  doi       = {10.1126/science.aaf2403},
  url       = {https://doi.org/10.1126/science.aaf2403}
}

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