Spatial transcriptomics of the nematode Caenorhabditis elegans using RNA tomography

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

Research output: Contribution to journal/periodicalArticleScientificpeer-review


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 languageEnglish
Pages (from-to)100411
JournalSTAR protocols
Issue number2
Publication statusPublished - 18 Jun 2021


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