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

  • 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
  • Åke Borg
  • Fredrik Pontén
  • Paul Igor Costea
  • Pelin Sahlén
  • Jan Mulder
  • Olaf Bergmann
  • Joakim Lundeberg
  • Jonas Frisén
Publishing year: 2016-07-01
Language: English
Pages: 78-82
Publication/Series: Science
Volume: 353
Issue: 6294
Document type: Journal article review
Publisher: The American Association for the Advancement of Science

Abstract english

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.


  • Medical Genetics


  • ISSN: 0036-8075
Åke Borg
Åke Borg
E-mail: ake [dot] borg [at] med [dot] lu [dot] se

Principal investigator

Oncology and Pathology, MV

+46 46 275 25 52

MV 404 C21B2


Project manager

Familial Breast Cancer



Oncology and Pathology, MV

MV 404 C21C2