Transcriptomic Analysis in the Sea Anemone Nematostella Vectensis

Overview

Journal Methods Mol Biol

Specialty Molecular Biology

Date 2020 Oct 19

PMID 33074544

Citations 4

Authors

Jacob F Warner

Eric Rottinger

Affiliations

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Abstract

The sea anemone Nematostella vectensis is an emerging research model to study embryonic development and regeneration at the molecular and global transcriptomic level. Transcriptomics analysis is now routinely used to detect differential expression at the genome level. Here we present the latest procedures for isolating high-quality RNA required for next generation sequencing, as well as methods and resources for quantifying transcriptomic data.

Citing Articles

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Creating a User-Friendly and Open-Access Gene Expression Database for Comparing Embryonic Development and Regeneration in Nematostella vectensis.

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References

Hand C, Uhlinger K . The Culture, Sexual and Asexual Reproduction, and Growth of the Sea Anemone Nematostella vectensis. Biol Bull. 2018; 182(2):169-176. DOI: 10.2307/1542110. View

Bossert P, Dunn M, Thomsen G . A staging system for the regeneration of a polyp from the aboral physa of the anthozoan Cnidarian Nematostella vectensis. Dev Dyn. 2013; 242(11):1320-31. PMC: 6889817. DOI: 10.1002/dvdy.24021. View

Amiel A, Johnston H, Nedoncelle K, Warner J, Ferreira S, Rottinger E . Characterization of Morphological and Cellular Events Underlying Oral Regeneration in the Sea Anemone, Nematostella vectensis. Int J Mol Sci. 2015; 16(12):28449-71. PMC: 4691047. DOI: 10.3390/ijms161226100. View

Putnam N, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A . Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science. 2007; 317(5834):86-94. DOI: 10.1126/science.1139158. View

Schwaiger M, Schonauer A, Rendeiro A, Pribitzer C, Schauer A, Gilles A . Evolutionary conservation of the eumetazoan gene regulatory landscape. Genome Res. 2014; 24(4):639-50. PMC: 3975063. DOI: 10.1101/gr.162529.113. View

Rentzsch F, Fritzenwanker J, Scholz C, Technau U . FGF signalling controls formation of the apical sensory organ in the cnidarian Nematostella vectensis. Development. 2008; 135(10):1761-9. DOI: 10.1242/dev.020784. View

Rottinger E, Dahlin P, Martindale M . A framework for the establishment of a cnidarian gene regulatory network for "endomesoderm" specification: the inputs of ß-catenin/TCF signaling. PLoS Genet. 2013; 8(12):e1003164. PMC: 3531958. DOI: 10.1371/journal.pgen.1003164. View

Layden M, Rottinger E, Wolenski F, Gilmore T, Martindale M . Microinjection of mRNA or morpholinos for reverse genetic analysis in the starlet sea anemone, Nematostella vectensis. Nat Protoc. 2013; 8(5):924-34. PMC: 4805419. DOI: 10.1038/nprot.2013.009. View

Servetnick M, Steinworth B, Babonis L, Simmons D, Salinas-Saavedra M, Martindale M . Cas9-mediated excision of disrupts endoderm development, pharynx formation and oral-aboral patterning. Development. 2017; 144(16):2951-2960. PMC: 5592810. DOI: 10.1242/dev.145839. View

10.

Kraus Y, Aman A, Technau U, Genikhovich G . Pre-bilaterian origin of the blastoporal axial organizer. Nat Commun. 2016; 7:11694. PMC: 4895019. DOI: 10.1038/ncomms11694. View

11.

Ikmi A, McKinney S, Delventhal K, Gibson M . TALEN and CRISPR/Cas9-mediated genome editing in the early-branching metazoan Nematostella vectensis. Nat Commun. 2014; 5:5486. DOI: 10.1038/ncomms6486. View

12.

Tulin S, Aguiar D, Istrail S, Smith J . A quantitative reference transcriptome for Nematostella vectensis early embryonic development: a pipeline for de novo assembly in emerging model systems. Evodevo. 2013; 4:16. PMC: 3748831. DOI: 10.1186/2041-9139-4-16. View

13.

Helm R, Siebert S, Tulin S, Smith J, Dunn C . Characterization of differential transcript abundance through time during Nematostella vectensis development. BMC Genomics. 2013; 14:266. PMC: 3680055. DOI: 10.1186/1471-2164-14-266. View

14.

Warner J, Guerlais V, Amiel A, Johnston H, Nedoncelle K, Rottinger E . NvERTx: a gene expression database to compare embryogenesis and regeneration in the sea anemone . Development. 2018; 145(10). DOI: 10.1242/dev.162867. View

15.

Wingett S, Andrews S . FastQ Screen: A tool for multi-genome mapping and quality control. F1000Res. 2018; 7:1338. PMC: 6124377. DOI: 10.12688/f1000research.15931.2. View

16.

Bolger A, Lohse M, Usadel B . Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15):2114-20. PMC: 4103590. DOI: 10.1093/bioinformatics/btu170. View

17.

Kelman L, SAUNDERS S, Wicht S, Frith L, Corrigall A, KIRSCH R . The effects of amino acids on albumin synthesis by the isolated perfused rat liver. Biochem J. 1972; 129(4):805-9. PMC: 1174225. DOI: 10.1042/bj1290805. View

18.

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

19.

ROYER C, Tauc P, Herve G, Brochon J . Ligand binding and protein dynamics: a fluorescence depolarization study of aspartate transcarbamylase from Escherichia coli. Biochemistry. 1987; 26(20):6472-8. DOI: 10.1021/bi00394a027. View

20.

Bernstein I, Bernstein D, Balakrishnan K, Korbee L . Infertility treated with donor specific lymphocytes in recurrent idiopathic spontaneous abortion. Transplant Proc. 1989; 21(1 Pt 1):565. View