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

Ståhl, Patrik L.; Salmén, Fredrik; Vickovic, Sanja; Lundmark, Anna; Navarro, José Fernández; Magnusson, Jens; Giacomello, Stefania; Asp, Michaela; Westholm, Jakub O. and Huss, Mikael, et al. (2016) In Science 353(6294). p.78-82
Abstract

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... (More)

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.

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publication status
published
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Science
volume
353
issue
6294
pages
5 pages
publisher
The American Association for the Advancement of Science
external identifiers
  • scopus:84976875145
  • wos:000378816200040
ISSN
0036-8075
DOI
10.1126/science.aaf2403
language
English
LU publication?
yes
id
af0be4d1-9fc7-4a87-b5f6-0307ec8103f5
date added to LUP
2017-01-24 13:42:21
date last changed
2017-11-19 04:37:01
@article{af0be4d1-9fc7-4a87-b5f6-0307ec8103f5,
  abstract     = {<p>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.</p>},
  author       = {Ståhl, Patrik L. and Salmén, Fredrik and Vickovic, Sanja and Lundmark, Anna and Navarro, José Fernández and Magnusson, Jens and Giacomello, Stefania and Asp, Michaela and Westholm, Jakub O. and Huss, Mikael and Mollbrink, Annelie and Linnarsson, Sten and Codeluppi, Simone and Borg, Åke and Pontén, Fredrik and Costea, Paul Igor and Sahlén, Pelin and Mulder, Jan and Bergmann, Olaf and Lundeberg, Joakim and Frisén, Jonas},
  issn         = {0036-8075},
  language     = {eng},
  month        = {07},
  number       = {6294},
  pages        = {78--82},
  publisher    = {The American Association for the Advancement of Science},
  series       = {Science},
  title        = {Visualization and analysis of gene expression in tissue sections by spatial transcriptomics},
  url          = {http://dx.doi.org/10.1126/science.aaf2403},
  volume       = {353},
  year         = {2016},
}