A Revised Adaptation of the Smart-Seq2 Protocol for Single-Nematode RNA-Seq

Dennis Chang; Lorrayne Serra; Dihong Lu; Ali Mortazavi; Adler Dillman

doi:10.1007/978-1-0716-0743-5_6

A Revised Adaptation of the Smart-Seq2 Protocol for Single-Nematode RNA-Seq

Methods Mol Biol. 2021:2170:79-99. doi: 10.1007/978-1-0716-0743-5_6.

Authors

Dennis Chang¹, Lorrayne Serra², Dihong Lu¹, Ali Mortazavi³, Adler Dillman⁴

Affiliations

¹ Department of Nematology, University of California, Riverside, CA, USA.
² Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, CA, USA.
³ Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, CA, USA. ali.mortazavi@uci.edu.
⁴ Department of Nematology, University of California, Riverside, CA, USA. adlerd@ucr.edu.

PMID: 32797452
DOI: 10.1007/978-1-0716-0743-5_6

Abstract

The advancement of transcriptomic studies in plant parasitic nematodes will greatly benefit from the development of single-nematode RNA-seq methods. Since many plant parasitic nematodes are obligate parasites, it is often difficult to efficiently obtain sufficient amounts of nematodes for transcriptomic studies. Here we have adapted SMART-Seq2 for single-nematode RNA-seq requiring only an individual nematode for a sample replicate. This protocol provides a detailed step-by-step procedure of the RNA-seq workflow starting from lysis of the nematode to quantification of transcripts using a user-friendly online platform.

Keywords: Nematode; RNA-seq; Smart-seq2.

Publication types

Research Support, N.I.H., Extramural

MeSH terms

Animals
Computational Biology
High-Throughput Nucleotide Sequencing
Nematoda / genetics*
RNA / chemistry*
RNA / genetics
RNA-Seq / methods*
Sequence Analysis, RNA / methods
Single-Cell Analysis / methods

Substances

RNA