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Science. 2016 Jul 1;353(6294):78-82. doi: 10.1126/science.aaf2403.

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

Author information

1
Department of Cell and Molecular Biology, Karolinska Institute, SE-171 77 Stockholm, Sweden. Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden.
2
Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden.
3
Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden. Department of Dental Medicine, Division of Periodontology, Karolinska Institute, SE-141 04 Huddinge, Sweden.
4
Department of Cell and Molecular Biology, Karolinska Institute, SE-171 77 Stockholm, Sweden.
5
Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, SE-171 21 Solna, Sweden.
6
Division of Molecular Neuroscience, Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE-17177 Stockholm, Sweden.
7
Division of Molecular Neuroscience, Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE-17177 Stockholm, Sweden. Department of Physiology and Pharmacology, Karolinska Institute, SE-17177 Stockholm, Sweden.
8
Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, SE-223 81 Lund, Sweden.
9
Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden.
10
Science for Life Laboratory, Department of Neuroscience, Karolinska Institute, SE-171 77 Stockholm, Sweden.
11
Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden. joakim.lundeberg@scilifelab.se.

Abstract

Analysis of the pattern of proteins or messengerRNAs (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.

PMID:
27365449
DOI:
10.1126/science.aaf2403
[Indexed for MEDLINE]
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