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

Ståhl PL, Salmén F, Vickovic S, Lundmark A, Navarro JF, Magnusson J, Giacomello S, Asp M, Westholm JO, Huss M, Mollbrink A, Linnarsson S, Codeluppi S, Borg Å, Pontén F, Costea PI, Sahlén P, Mulder J, Bergmann O, Lundeberg J, Frisén J

Science 353 (6294) 78-82 [2016-07-01; online 2016-07-02]

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.

Bioinformatics Compute and Storage [Service]

Bioinformatics Long-term Support WABI [Collaborative]

Fluorescence Tissue Profiling [Collaborative]

NGI Stockholm (Genomics Applications) [Collaborative]

NGI Stockholm (Genomics Production) [Service]

Tissue Profiling [Collaborative]

QC bibliography QC xrefs

PubMed 27365449

DOI 10.1126/science.aaf2403

Crossref 10.1126/science.aaf2403