Spatial transcriptomics of the nematode Caenorhabditis elegans using RNA tomography

Erik S. Schild; Jonas Mars; Annabel Ebbing; Judith Vivié; Marco Betist; Hendrik C. Korswagen

doi:10.1016/j.xpro.2021.100411

Spatial transcriptomics of the nematode Caenorhabditis elegans using RNA tomography

Erik S. Schild^*
, Jonas Mars
, Annabel Ebbing
, Judith Vivié
, Marco Betist
, Hendrik C. Korswagen

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

1 Citation (Scopus)

2 Downloads (Pure)

Abstract

RNA tomography or tomo-seq combines mRNA sequencing and cryo-sectioning to spatially resolve gene expression. We have adapted this method for the nematode Caenorhabditis elegans to generate anteroposterior gene expression maps at near-cellular resolution. Here, we provide a detailed overview of the method and present two approaches: one that includes RNA isolation for maximum sensitivity and one that is suitable for partial automatization and is therefore less time-consuming. For complete details on the use and execution of this protocol, please refer to Ebbing et al. (2018).

Original language	English
Article number	100411
Pages (from-to)	1-21
Journal	STAR protocols
Volume	2
Issue number	2
DOIs	https://doi.org/10.1016/j.xpro.2021.100411
Publication status	Published - 18 Jun 2021

Keywords

Model Organisms
RNA-seq
Sequence analysis

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10.1016/j.xpro.2021.100411Licence: CC BY

1-s2.0-S2666166721001180-mainFinal published version, 4.14 MBLicence: CC BY

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title = "Spatial transcriptomics of the nematode Caenorhabditis elegans using RNA tomography",

abstract = "RNA tomography or tomo-seq combines mRNA sequencing and cryo-sectioning to spatially resolve gene expression. We have adapted this method for the nematode Caenorhabditis elegans to generate anteroposterior gene expression maps at near-cellular resolution. Here, we provide a detailed overview of the method and present two approaches: one that includes RNA isolation for maximum sensitivity and one that is suitable for partial automatization and is therefore less time-consuming. For complete details on the use and execution of this protocol, please refer to Ebbing et al. (2018).",

keywords = "Model Organisms, RNA-seq, Sequence analysis",

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note = "Funding Information: This work is part of the research program (14NOISE01) of the Foundation for Fundamental Research on Matter (FOM), which is financially supported by the Netherlands Organization for Scientific Research ( NWO ). Publisher Copyright: {\textcopyright} 2021 The Authors",

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doi = "10.1016/j.xpro.2021.100411",

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AU - Vivié, Judith

AU - Betist, Marco

AU - Korswagen, Hendrik C.

N1 - Funding Information: This work is part of the research program (14NOISE01) of the Foundation for Fundamental Research on Matter (FOM), which is financially supported by the Netherlands Organization for Scientific Research ( NWO ). Publisher Copyright: © 2021 The Authors

PY - 2021/6/18

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N2 - RNA tomography or tomo-seq combines mRNA sequencing and cryo-sectioning to spatially resolve gene expression. We have adapted this method for the nematode Caenorhabditis elegans to generate anteroposterior gene expression maps at near-cellular resolution. Here, we provide a detailed overview of the method and present two approaches: one that includes RNA isolation for maximum sensitivity and one that is suitable for partial automatization and is therefore less time-consuming. For complete details on the use and execution of this protocol, please refer to Ebbing et al. (2018).

AB - RNA tomography or tomo-seq combines mRNA sequencing and cryo-sectioning to spatially resolve gene expression. We have adapted this method for the nematode Caenorhabditis elegans to generate anteroposterior gene expression maps at near-cellular resolution. Here, we provide a detailed overview of the method and present two approaches: one that includes RNA isolation for maximum sensitivity and one that is suitable for partial automatization and is therefore less time-consuming. For complete details on the use and execution of this protocol, please refer to Ebbing et al. (2018).

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KW - Sequence analysis

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ER -

Spatial transcriptomics of the nematode Caenorhabditis elegans using RNA tomography

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Keywords

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