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

Patrik L. StåhlKTH Royal Institute of TechnologyFredrik SalménKTH Royal Institute of TechnologySanja VickovićKTH Royal Institute of TechnologyAnna LundmarkScience for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, SE-106 91 Stockholm, SwedenJosé Fernández NavarroKTH Royal Institute of TechnologyJens P. MagnussonDepartment of Cell and Molecular Biology, Karolinska Institute, SE-171 77 Stockholm, SwedenStefania GiacomelloKTH Royal Institute of TechnologyMichaela AspKTH Royal Institute of TechnologyJakub Orzechowski WestholmScience for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, SE-171 21 Solna, SwedenMikael HussScience for Life LaboratoryAnnelie MollbrinkKTH Royal Institute of TechnologySten LinnarssonDivision of Molecular Neuroscience, Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE-17177 Stockholm, SwedenSimone CodeluppiDepartment of Physiology and Pharmacology, Karolinska Institute, SE-17177 Stockholm, SwedenÅke BorgDivision of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, SE-223 81 Lund, SwedenFredrik PonténDepartment of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, SwedenPaul Igor CosteaScience for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, SE-106 91 Stockholm, SwedenPelin SahlénScience for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, SE-106 91 Stockholm, SwedenJan MulderScience for Life Laboratory, Department of Neuroscience, Karolinska Institute, SE-171 77 Stockholm, SwedenOlaf BergmannDepartment of Cell and Molecular Biology, Karolinska Institute, SE-171 77 Stockholm, SwedenJoakim LundebergKTH Royal Institute of TechnologyJonas FrisénDepartment of Cell and Molecular Biology, Karolinska Institute, SE-171 77 Stockholm, Sweden

2016en

ABI

Annotatsiya

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.

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DOI: 10.1126/science.aaf2403

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