RNA Sequencing Experimental Analysis Workflow Using Caenorhabditis Elegans

Overview

Journal Methods Mol Biol

Specialty Molecular Biology

Date 2024 Jul 27

PMID 39068359

Authors

Jose Robledo

Saifun Ripa Nahar

Manuel A Ruiz

Raymond J Hendricks

David J Burks

Mary L Ladage

Taegun Kwon

Rajeev K Azad

Pamela A Padilla

Affiliations

Soon will be listed here.

Abstract

RNA sequencing is an approach to transcriptomic profiling that enables the detection of differentially expressed genes in response to genetic mutation or experimental treatment, among other uses. Here we describe a method for the use of a customizable, user-friendly bioinformatic pipeline to identify differentially expressed genes in RNA sequencing data obtained from C. elegans, with attention to the improvement in reproducibility and accuracy of results.

References

Stark R, Grzelak M, Hadfield J . RNA sequencing: the teenage years. Nat Rev Genet. 2019; 20(11):631-656. DOI: 10.1038/s41576-019-0150-2. View

Brenner S . The genetics of Caenorhabditis elegans. Genetics. 1974; 77(1):71-94. PMC: 1213120. DOI: 10.1093/genetics/77.1.71. View

Aranda P, LaJoie D, Jorcyk C . Bleach gel: a simple agarose gel for analyzing RNA quality. Electrophoresis. 2012; 33(2):366-9. PMC: 3699176. DOI: 10.1002/elps.201100335. View

Chen S, Zhou Y, Chen Y, Gu J . fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018; 34(17):i884-i890. PMC: 6129281. DOI: 10.1093/bioinformatics/bty560. View

Dobin A, Davis C, Schlesinger F, Drenkow J, Zaleski C, Jha S . STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2012; 29(1):15-21. PMC: 3530905. DOI: 10.1093/bioinformatics/bts635. View

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N . The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25(16):2078-9. PMC: 2723002. DOI: 10.1093/bioinformatics/btp352. View

Chen Y, Lun A, Smyth G . From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. F1000Res. 2016; 5:1438. PMC: 4934518. DOI: 10.12688/f1000research.8987.2. View

Klosin A, Casas E, Hidalgo-Carcedo C, Vavouri T, Lehner B . Transgenerational transmission of environmental information in . Science. 2017; 356(6335):320-323. DOI: 10.1126/science.aah6412. View

Miersch C, Doring F . Paternal dietary restriction affects progeny fat content in Caenorhabditis elegans. IUBMB Life. 2012; 64(7):644-8. DOI: 10.1002/iub.1042. View

10.

Du Preez G, Fourie H, Daneel M, Miller H, Hoss S, Ricci C . Oxygen consumption rate of Caenorhabditis elegans as a high-throughput endpoint of toxicity testing using the Seahorse XF96 Extracellular Flux Analyzer. Sci Rep. 2020; 10(1):4239. PMC: 7060326. DOI: 10.1038/s41598-020-61054-7. View

11.

Whiteman M, Spencer J, Szeto H, Armstrong J . Do mitochondriotropic antioxidants prevent chlorinative stress-induced mitochondrial and cellular injury?. Antioxid Redox Signal. 2007; 10(3):641-50. DOI: 10.1089/ars.2007.1879. View

12.

Melnick M, Gonzales P, Cabral J, Allen M, Dowell R, Link C . Heat shock in C. elegans induces downstream of gene transcription and accumulation of double-stranded RNA. PLoS One. 2019; 14(4):e0206715. PMC: 6453478. DOI: 10.1371/journal.pone.0206715. View

13.

Gimenez G, Stockwell P, Rodger E, Chatterjee A . Strategy for RNA-Seq Experimental Design and Data Analysis. Methods Mol Biol. 2022; 2588:249-278. DOI: 10.1007/978-1-0716-2780-8_16. View

14.

Chatterjee A, Ahn A, Rodger E, Stockwell P, Eccles M . A Guide for Designing and Analyzing RNA-Seq Data. Methods Mol Biol. 2018; 1783:35-80. DOI: 10.1007/978-1-4939-7834-2_3. View