Codes used to study the Crassostrea gigas oyster transcriptome response to Alexandrium exposure

Date 2018-01-11
Author(s) Mat AudreyORCID1
Affiliation(s) 1 : Ifremer, LEMAR UMR 6539 CNRS/UBO/IRD/Ifremer, CS 10070, 29280 Plouzané, France
DOI 10.17882/52864
Publisher SEANOE
Keyword(s) Crassostrea gigas, Alexandrium minutum, Paralytic Shellfish Toxins, R, Transcriptomic, Differential expression, Elastic-net regression, Script

R scripts written for differential analysis and regression analysis to investigate the molecular basis of Paralytic Shellfish Toxins load in the oyster Crassostrea gigas exposed to the toxigenic alga Alexandrium minutum. Differentially expressed genes were analyzed with R (version 3.2.3, Gentry et al. (2004) Genome Biol 5:R80) using the packages DESeq2 (version 1.10.0; Love et al. (2014) Genome Biol 15:1-21) and edgeR (version 3.12.0, Robinson et al. (2010) Bioinformatics 26:139-140). Elastic-net regression was run with R using the package glmnet (version 2.0-2, Friedman et al. (2010) J Stat Softw 33:1-22).

Licence CC-BY-NC-SA
File Size Format Processing Access
R script for analyses of genes differentially expressed. 33 KB R script Open access
R script for regression analysis 9 KB R script Open access
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How to cite 

Mat Audrey (2018). Codes used to study the Crassostrea gigas oyster transcriptome response to Alexandrium exposure. SEANOE.

In addition to properly cite this dataset, it would be appreciated that the following work(s) be cited too, when using this dataset in a publication :

Mat Audrey, Klopp Christophe, Payton Laura, Jeziorski Celine, Chalopin Morgane, Amzil Zouher, Tran Damien, Wikfors Gary H., Hegaret Helene, Soudant Philippe, Huvet Arnaud, Fabioux Caroline (2018). Oyster transcriptome response to Alexandrium exposure is related to saxitoxin load and characterized by disrupted digestion, energy balance, and calcium and sodium signaling. Aquatic Toxicology, 199, 127-137.