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

STAR Protoc. 2021 Mar 30;2(2):100411. doi: 10.1016/j.xpro.2021.100411. eCollection 2021 Jun 18.

Authors

Erik S Schild¹, Jonas Mars¹, Annabel Ebbing¹, Judith Vivié², Marco Betist¹, Hendrik C Korswagen^{1

3}

Affiliations

¹ Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
² Single Cell Discoveries B.V., Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
³ Institute of Biodynamics and Biocomplexity, Developmental Biology, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Caenorhabditis elegans* / chemistry
Caenorhabditis elegans* / genetics
Caenorhabditis elegans* / metabolism
Gene Expression Profiling / methods*
RNA, Messenger / analysis
RNA, Messenger / genetics
RNA, Messenger / metabolism
Sequence Analysis, RNA / methods
Single-Cell Analysis / methods*
Tomography / methods*
Transcriptome / genetics

Substances

RNA, Messenger