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Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections
KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology.
KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0002-2207-7370
KTH, Centres, Science for Life Laboratory, SciLifeLab.
KTH, Centres, Science for Life Laboratory, SciLifeLab.
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2018 (English)In: Nature Protocols, ISSN 1754-2189, E-ISSN 1750-2799, Vol. 13, no 11, p. 2501-2534Article in journal (Refereed) Published
Abstract [en]

Spatial resolution of gene expression enables gene expression events to be pinpointed to a specific location in biological tissue. Spatially resolved gene expression in tissue sections is traditionally analyzed using immunohistochemistry (IHC) or in situ hybridization (ISH). These technologies are invaluable tools for pathologists and molecular biologists; however, their throughput is limited to the analysis of only a few genes at a time. Recent advances in RNA sequencing (RNA-seq) have made it possible to obtain unbiased high-throughput gene expression data in bulk. Spatial Transcriptomics combines the benefits of traditional spatially resolved technologies with the massive throughput of RNA-seq. Here, we present a protocol describing how to apply the Spatial Transcriptomics technology to mammalian tissue. This protocol combines histological staining and spatially resolved RNA-seq data from intact tissue sections. Once suitable tissue-specific conditions have been established, library construction and sequencing can be completed in similar to 5-6 d. Data processing takes a few hours, with the exact timing dependent on the sequencing depth. Our method requires no special instruments and can be performed in any laboratory with access to a cryostat, microscope and next-generation sequencing.

Place, publisher, year, edition, pages
Nature Publishing Group, 2018. Vol. 13, no 11, p. 2501-2534
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:kth:diva-239078DOI: 10.1038/s41596-018-0045-2ISI: 000448980400004PubMedID: 30353172Scopus ID: 2-s2.0-85055531492OAI: oai:DiVA.org:kth-239078DiVA, id: diva2:1264921
Funder
Knut and Alice Wallenberg FoundationSwedish Research CouncilSwedish Foundation for Strategic Research Swedish Cancer SocietyTorsten Söderbergs stiftelseÅke Wiberg FoundationRagnar Söderbergs stiftelse
Note

QC 20181121

Available from: 2018-11-21 Created: 2018-11-21 Last updated: 2019-05-17Bibliographically approved

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Salmén, FredrikStåhl, PatrikMollbrink, AnnelieNavarro Fernandez, José CarlosVickovic, SanjaLundeberg, Joakim

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Salmén, FredrikStåhl, PatrikMollbrink, AnnelieNavarro Fernandez, José CarlosVickovic, SanjaLundeberg, Joakim
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