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4 results for “Dinophysis”
Data and analysis code for a toxin induction study on two species of Dinophysis dinoflagellates
<h3>General description</h3> <p>This repository contains the datasets, analysis code and output generated and used in the manuscript "Effects of copepod chemical cues on intra- and extracellular toxins in two species of <em>Dinophysis</em>", which has been published as a research article in Harmful Algae (https://doi.org/10.1016/j.hal.2024.102793).</p> <h3>Files</h3> <p><strong>HRMS_data_Dinophysis_induction_experiment.zip </strong>contains the source high-resolution mass-spectroscopy endometabolomics data in open file formats.</p> <p><strong>Put_annot_sign_affect_feat_metabol_data.xlsx</strong> (corresponds to <strong>Supplementary spreadsheet 1</strong> in the main manuscript) contains putative annotations of significantly affected features from the metabolomics data, for each <em>Dinophysis </em>species (<em>D.</em> <em>sacculus </em>and <em>D. acuminata</em>) and each mode of ionization. Notably, results obtained from GNPS (Global Natural Products Social Molecular Networking, <a href="https://gnps.ucsd.edu/" target="_blank" rel="noopener noreferrer">https://gnps.ucsd.edu/</a>), and SIRIUS (<a href="https://bio.informatik.uni-jena.de/sirius/" target="_blank" rel="noopener noreferrer">https://bio.informatik.uni-jena.de/sirius/</a>) were mentionned. When available, MS/MS spectra were also provided. </p> <p><strong>Tabl_sign_affect_feat.xlsx</strong> (corresponds to <strong>Supplementary spreadsheet 3</strong> in the main manuscript) contains tables of significantly affected features (ANOVA, Tukey’s post hoc test, adjusted p-value cut-offs of 0.001 or 0.01) from the metabolomics data, for each <em>Dinophysis </em>species (<em>sacculus </em>and <em>acuminata</em>) and each mode of ionization. A visual representation (heatmaps) of these significant fetures are available as Figs S3-S6 in the supplementary information of the main mauscript. </p> <p><strong>Toxin_analysis_code_output.Rmd</strong> is the R-markdown file that produces the interactive analysis output output (<strong>Toxin_analysis_code_output.html</strong>, corresponds to <strong>Supplementary code & output </strong>in the main manuscript) of the toxin analysis, and uses the datasets <strong>Toxin_analysis_data.csv</strong>,<strong> pca_score_sacculus.csv</strong>,<strong> </strong>and<strong> pca_score_acuminata.csv</strong> source datasets to perform the statistical analyses and generate figures (details for each dataset below).</p> <p><strong>Toxin_analysis_data.csv</strong> (corresponds to <strong>Supplementary spreadsheet 2</strong> in the main manuscript) contains the main data used to statistically analyse the toxin and growth dynamics of both <em>Dinophysis</em> species in response to different grazer treatments, and to produce the majority of the figures in the main manuscript (Figs. 2-6) and supplementary information (Figs. S1-S2). </p> <p><strong>pca_score_sacculus.csv</strong> & <strong>pca_score_acuminata.csv</strong> contain the scores of the first two principal components of the PCA performed on LC-HRMS derived metabolomic profiles of <em>D. sacculus </em>and <em>D. acuminata</em> respectively, in both positive and negative ion mode. These are used to produce PCA score plots (Fig. 6 in the main manuscript and Fig. S2 in the supplementary information).</p> <p><strong>custom.css</strong> is a custom html style sheet file that formats the <strong>Toxin_analysis_code_output.html</strong> to display scrollable tables correctly. It is used by <strong>Toxin_analysis_code_output.Rmd </strong>and is necessary for true reproduction of the output (<strong>.html</strong>) file.</p>
Functional annotation of the reference transcriptome of Dinophysis acuminata strain DAVA01
<p>Raw reads were pre-processed by removing the adaptors and low-quality reads using BBMap. The filtered reads were normalized for depth based on kmer counts using BBNorm function. De novo transcriptomes were generated using both Trinity and velvet-oases. CD-HIT-EST was used to merge the two de novo transcriptomes and reduce the transcript redundancy to 98% similarity and generate unique genes. Transcriptome assembly completeness was evaluated with BUSCO (Benchmarking Universal Single Copy Orthologs) database. Functional annotation was done using blastp function of ncbi-blast using the nr database with evalue 1E-20 and num_alignments 3.</p>
Functional annotation of the reference transcriptome of Dinophysis ovum strain DoSS3195
<p>Raw reads were pre-processed by removing the adaptors and low-quality reads using BBMap. The filtered reads were normalized for depth based on kmer counts using BBNorm function. De novo transcriptomes were generated using both Trinity and velvet-oases. CD-HIT-EST was used to merge the two de novo transcriptomes and reduce the transcript redundancy to 98% similarity and generate unique genes. Transcriptome assembly completeness was evaluated with BUSCO (Benchmarking Universal Single Copy Orthologs) database. Functional annotation was done using blastp function of ncbi-blast using the nr database with evalue 1E-20 and num_alignments 3.</p>
Data for Dinophysis induction experiment
<p>This is data</p>
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