Raw RNA-sequencing and ISO-sequencing data, and the transcriptome assembly (fasta file) can be found at NCBI BioProject PRJNA798187 (this is embargoed until peer-reviewed publication) (Thomas et al. , 2022). Raw gene count data, raw water sampling data, all scripts used for bioinformatic analyses, the annotated transcriptome assembly (OmicsBox and csv files), R code used for the statistical analyses (differential expression and gene set analyses), and data files to accompany the statistical analyses are available from DOI 10.25903/ha66-mm11 (this DOI is embargoed until peer-reviewed publication) (Thomaset al. , 2023b). All R code for the statistical analyses (correlating gene expression profiles with CO2 treatment and OA-affected behaviours), as well as accompanying data files for the statistical analyses, can be found at DOI 10.25903/7dcz-th66 (this DOI is embargoes until peer-reviewed publication) (Thomaset al. , 2023a).