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

Research output: Contribution to journalReview article


Analysis of the pattern of proteins or messenger RNAs (mRNAs) in histological tissue sections is a cornerstone in biomedical research and diagnostics.This typically involves the visualization of a few proteins or expressed genes at a time. We have devised a strategy, which we call "spatial transcriptomics," that allows visualization and quantitative analysis of the transcriptome with spatial resolution in individual tissue sections. By positioning histological sections on arrayed reverse transcription primers with unique positional barcodes, we demonstrate high-quality RNA-sequencing data with maintained two-dimensional positional information from the mouse brain and human breast cancer. Spatial transcriptomics provides quantitative gene expression data and visualization of the distribution of mRNAs within tissue sections and enables novel types of bioinformatics analyses, valuable in research and diagnostics.


  • Patrik L. Ståhl
  • Fredrik Salmén
  • Sanja Vickovic
  • Anna Lundmark
  • José Fernández Navarro
  • Jens Magnusson
  • Stefania Giacomello
  • Michaela Asp
  • Jakub O. Westholm
  • Mikael Huss
  • Annelie Mollbrink
  • Sten Linnarsson
  • Simone Codeluppi
  • Fredrik Pontén
  • Paul Igor Costea
  • Pelin Sahlén
  • Jan Mulder
  • Olaf Bergmann
  • Joakim Lundeberg
  • Jonas Frisén
External organisations
  • KTH Royal Institute of Technology
  • Karolinska Institutet
  • Stockholm University
  • Uppsala University
Research areas and keywords

Subject classification (UKÄ) – MANDATORY

  • Medical Genetics
Original languageEnglish
Pages (from-to)78-82
Number of pages5
Issue number6294
Publication statusPublished - 2016 Jul 1
Publication categoryResearch

Related research output

Fredrik Salmén, Sanja Vickovic, Ludvig Larsson, Linnea Stenbeck, Johan Vallon-Christersson, Anna Ehinger, Jari Häkkinen, Åke Borg, Jonas Frisén, Patrik Stahl & Joakim Lundeberg, 2018 Jun 29

Research output: Other contributionMiscellaneous

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