Protocol for nuclear dissociation of the adult C. elegans for single-nucleus RNA sequencing and its application for mapping environmental responses

Max T Levenson; Rio Barrere-Cain; Lisa Truong; Yen-Wei Chen; Karissa Shuck; Blake Panter; Ella Reich; Xia Yang; Patrick Allard

doi:10.1016/j.xpro.2023.102756

Protocol for nuclear dissociation of the adult C. elegans for single-nucleus RNA sequencing and its application for mapping environmental responses

STAR Protoc. 2023 Dec 15;4(4):102756. doi: 10.1016/j.xpro.2023.102756. Epub 2023 Dec 2.

Authors

Max T Levenson¹, Rio Barrere-Cain², Lisa Truong³, Yen-Wei Chen¹, Karissa Shuck², Blake Panter², Ella Reich², Xia Yang⁴, Patrick Allard⁵

Affiliations

¹ Molecular Toxicology Inter-Departmental Program, UCLA, Los Angeles, CA 90095, USA.
² Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA.
³ Human Genetics Graduate Program, UCLA, Los Angeles, CA 90095, USA.
⁴ Molecular Toxicology Inter-Departmental Program, UCLA, Los Angeles, CA 90095, USA; Integrative Biology and Physiology Department, UCLA, Los Angeles, CA 90095, USA.
⁵ Molecular Toxicology Inter-Departmental Program, UCLA, Los Angeles, CA 90095, USA; Institute for Society & Genetics, UCLA, Los Angeles, CA 90095, USA; Molecular Biology Institute, UCLA, Los Angeles, CA 90095, USA. Electronic address: pallard@ucla.edu.

Abstract

Caenorhabditis elegans is a valuable model to study organ, tissue, and cell-type responses to external cues. However, the nematode comprises multiple syncytial tissues with spatial coordinates corresponding to distinct nuclear transcriptomes. Here, we present a single-nucleus RNA sequencing (snRNA-seq) protocol that aims to overcome difficulties encountered with single-cell RNA sequencing in C. elegans. We describe steps for isolating C. elegans nuclei for downstream applications including snRNA-seq applied to the context of alcohol exposure. For complete details on the use and execution of this protocol, please refer to Truong et al. (2023).¹.

Keywords: Gene Expression; Model Organisms; RNA-seq; Single Cell.

MeSH terms

Animals
Base Sequence
Caenorhabditis elegans* / genetics
Cell Nucleus* / genetics
RNA, Small Nuclear
Sequence Analysis, RNA

Substances

RNA, Small Nuclear

Abstract

MeSH terms

Substances

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