search DOI 10.17882/52864

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

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).

Disciplines

Biological oceanography

Keywords

Crassostrea gigas, Alexandrium minutum, Paralytic Shellfish Toxins, R, Transcriptomic, Differential expression, Elastic-net regression, Script

Data

FileSizeFormatProcessingAccess
R script for analyses of genes differentially expressed.
33 KoR script
Download
R script for regression analysis
9 KoR script
Download
How to cite
Mat Audrey (2018). Codes used to study the Crassostrea gigas oyster transcriptome response to Alexandrium exposure. SEANOE. https://doi.org/10.17882/52864
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. https://doi.org/10.1016/j.aquatox.2018.03.030

Copy this text

Related documents
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. https://doi.org/10.1016/j.aquatox.2018.03.030
AboutContactLegal noticeCreditsRSSTwitterOAI-PMH
Certified by