Code for "Transcriptomic responses of adult versus juvenile atlantids to ocean acidification"

Date: 01-02-2022 Update:03-06-2022

Citation

This code accompanies the manuscript Ramos-Silva P, Odendaal M, Wall-Palmer D, Mekkes L, Peijnenburg KTCA. Transcriptomic Responses of Adult Versus Juvenile Atlantids to Ocean Acidification. Front Mar Sci 2022; 9: 1–12. https://doi.org/10.3389/fmars.2022.801458

Description

This repository contains the Rmd-scripts (scripts/) used to generate (results). The aim of this project was to study the transcriptomic responses of adult and juvenile Atlanta ariejansseni to past, present and future ocean chemistry.

Reads used in this study were deposited at NCBI BioProject PRJNA742523. The Transcriptome Shotgun Assembly has been deposited at DDBJ/EMBL/GenBank under the accession GJHI00000000. Formatted input-files are available upon request.

The included code was ran in R version 4.0.4.

File description

(scripts/)

• differential_gene_expression.Rmd: Differential gene expression analysis with DESeq2
• correlation_analysis.Rmd: Pearson correlation analysis
• enrichment_analysis.Rmd: Visualization of the GO enrichment analysis

The .(html) -output of these scripts can be found in the (results) -folder. Raw figures are stored in the (figures) folder.

Input R-objects and files used in each of the scripts are stored in the (input) folder.