title: Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.
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.
authors.affiliation: 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.
authors.forename: Patrik L
authors.initials: PL
authors.lastname: Ståhl
authors.affiliation: Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden.
authors.forename: Fredrik
authors.initials: F
authors.lastname: Salmén
authors.affiliation: Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden.
authors.forename: Sanja
authors.initials: S
authors.lastname: Vickovic
authors.affiliation: 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.
authors.forename: Anna
authors.initials: A
authors.lastname: Lundmark
authors.affiliation: 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.
authors.forename: José Fernández
authors.initials: JF
authors.lastname: Navarro
authors.affiliation: Department of Cell and Molecular Biology, Karolinska Institute, SE-171 77 Stockholm, Sweden.
authors.forename: Jens
authors.initials: J
authors.lastname: Magnusson
authors.affiliation: Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden.
authors.forename: Stefania
authors.initials: S
authors.lastname: Giacomello
authors.affiliation: Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden.
authors.forename: Michaela
authors.initials: M
authors.lastname: Asp
authors.affiliation: Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, SE-171 21 Solna, Sweden.
authors.forename: Jakub O
authors.initials: JO
authors.lastname: Westholm
authors.affiliation: Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Box 1031, SE-171 21 Solna, Sweden.
authors.forename: Mikael
authors.initials: M
authors.lastname: Huss
authors.affiliation: Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden.
authors.forename: Annelie
authors.initials: A
authors.lastname: Mollbrink
authors.affiliation: Division of Molecular Neuroscience, Department of Medical Biochemistry and Biophysics, Karolinska Institute, SE-17177 Stockholm, Sweden.
authors.forename: Sten
authors.initials: S
authors.lastname: Linnarsson
authors.affiliation: 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.
authors.forename: Simone
authors.initials: S
authors.lastname: Codeluppi
authors.affiliation: Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, SE-223 81 Lund, Sweden.
authors.forename: Åke
authors.initials: Å
authors.lastname: Borg
authors.affiliation: Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85 Uppsala, Sweden.
authors.forename: Fredrik
authors.initials: F
authors.lastname: Pontén
authors.affiliation: Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden.
authors.forename: Paul Igor
authors.initials: PI
authors.lastname: Costea
authors.affiliation: Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden.
authors.forename: Pelin
authors.initials: P
authors.lastname: Sahlén
authors.affiliation: Science for Life Laboratory, Department of Neuroscience, Karolinska Institute, SE-171 77 Stockholm, Sweden.
authors.forename: Jan
authors.initials: J
authors.lastname: Mulder
authors.affiliation: Department of Cell and Molecular Biology, Karolinska Institute, SE-171 77 Stockholm, Sweden.
authors.forename: Olaf
authors.initials: O
authors.lastname: Bergmann
authors.affiliation: Science for Life Laboratory, Division of Gene Technology, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden. joakim.lundeberg@scilifelab.se.
authors.forename: Joakim
authors.initials: J
authors.lastname: Lundeberg
authors.affiliation: Department of Cell and Molecular Biology, Karolinska Institute, SE-171 77 Stockholm, Sweden.
authors.forename: Jonas
authors.initials: J
authors.lastname: Frisén
mesh_terms: D000818:Animals; D001921:Brain / Q000378:metabolism; D001943:Breast Neoplasms / Q000378:metabolism; D018076:DNA, Complementary / Q000096:biosynthesis; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D051379:Mice; D009928:Organ Specificity; D012333:RNA, Messenger / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D059467:Transcriptome
chemical_list: D018076:DNA, Complementary; D012333:RNA, Messenger