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Spatially resolved transcriptome profiling in model plant species
KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab. Stockholm University, Sweden.
KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.ORCID iD: 0000-0001-8728-3709
KTH, School of Biotechnology (BIO), Gene Technology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
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2017 (English)In: Nature Plants, ISSN 2055-0278, Vol. 3, 17061Article in journal (Refereed) Published
Abstract [en]

Understanding complex biological systems requires functional characterization of specialized tissue domains. However, existing strategies for generating and analysing high-throughput spatial expression profiles were developed for a limited range of organisms, primarily mammals. Here we present the first available approach to generate and study high-resolution, spatially resolved functional profiles in a broad range of model plant systems. Our process includes high-throughput spatial transcriptome profiling followed by spatial gene and pathway analyses. We first demonstrate the feasibility of the technique by generating spatial transcriptome profiles from model angiosperms and gymnosperms microsections. In Arabidopsis thaliana we use the spatial data to identify differences in expression levels of 141 genes and 189 pathways in eight inflorescence tissue domains. Our combined approach of spatial transcriptomics and functional profiling offers a powerful new strategy that can be applied to a broad range of plant species, and is an approach that will be pivotal to answering fundamental questions in developmental and evolutionary biology.

Place, publisher, year, edition, pages
Palgrave Macmillan, 2017. Vol. 3, 17061
National Category
Bioinformatics and Systems Biology
Identifiers
URN: urn:nbn:se:kth:diva-209734DOI: 10.1038/nplants.2017.61Scopus ID: 2-s2.0-85019067549OAI: oai:DiVA.org:kth-209734DiVA: diva2:1114005
Funder
Science for Life Laboratory - a national resource center for high-throughput molecular bioscience
Note

QC 20170622

Available from: 2017-06-22 Created: 2017-06-22 Last updated: 2017-06-22Bibliographically approved

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Giacomello, StefaniaSalmén, FredrikVickovic, SanjaMcKee, Lauren S.Bulone, VincentLundeberg, Joakim
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CiteExportLink to record
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Cite
Citation style
  • apa
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More styles
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Output format
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