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Preparation of plant tissue to enable Spatial Transcriptomics profiling using barcoded microarrays
KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH Royal Inst Technol, Dept Gene Technol, Sci Life Lab, Stockholm, Sweden.;Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Natl Bioinformat Infrastruct Sweden, Stockholm, Sweden..ORCID iD: 0000-0003-0738-1574
KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Gene Technology. KTH Royal Inst Technol, Dept Gene Technol, Sci Life Lab, Stockholm, Sweden..ORCID iD: 0000-0003-4313-1601
2018 (English)In: Nature Protocols, ISSN 1754-2189, E-ISSN 1750-2799, Vol. 13, no 11, p. 2425-2446Article in journal (Refereed) Published
Abstract [en]

Elucidation of the complex processes involved in plant growth requires analysis of the spatial gene expression patterns in all affected tissues. This protocol extension is an adaptation of a protocol that describes how to use barcoded oligo-dT microarrays to evaluate spatial global gene expression profiles in mammalian tissue to enable it to be applied to plant material. Here, we explain the required adjustments for preparing and treating plant tissue sections on the array surface, specifically in regard to how to permeabilize and remove the tissue. Once the tissue has been removed, the cDNA-mRNA hybrid that is left on the slide is processed in the same way as cDNA obtained during experiments on mammalian tissue; thus the later stages of the protocol are not included here, and readers should follow the accompanying protocol for those. We have previously used our protocol to generate high-quality sequencing libraries for Arabidopsis thaliana inflorescence, Populus tremula developing and dormant leaf buds, and Picea abies female cones. However, we anticipate that the protocol can be adapted to other tissue types and species. The entire protocol for preparing samples and processing libraries can be completed in 3-4 d.

Place, publisher, year, edition, pages
Nature Publishing Group, 2018. Vol. 13, no 11, p. 2425-2446
National Category
Biological Sciences
Identifiers
URN: urn:nbn:se:kth:diva-239077DOI: 10.1038/s41596-018-0046-1ISI: 000448980400001PubMedID: 30353173Scopus ID: 2-s2.0-85055524579OAI: oai:DiVA.org:kth-239077DiVA, id: diva2:1264927
Funder
Knut and Alice Wallenberg FoundationSwedish Research Council
Note

QC 20181121

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

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Giacomello, StefaniaLundeberg, Joakim

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