This Zenodo entry refers to a study using metabolomics and transcriptomic data analysis to analyse chemical interactions between two microalgae: Skeletonema marinoi and Prymnesium parvum p_parvum_Eukaryota_augustus_gene_prediction.faa file contains the predicted protein sequences from the transcriptome of Prymnesium parvum using Augustus. This list is generated from a non-restrictive Busco Analysis. s_costatum_Stramenopiles_augustus_gene_prediction.faa file contains the predicted protein sequences from the transcriptome of Skeletonema marinoi using Augustus. This list is generated from a restrictive Busco Analysis. The files p_parvum_deseq2_results_all.csv and s_marinoi_deseq2_results_all.csv contain differential gene expression analysis, while p_parvum_deseq2_result_sorted_regulated_with_proteins.csv and s_marinoi_deseq2_result_sorted_regulated_with_proteins.csv contain only upregulated protein sequences in co-culture conditions. The genes_read.R script is used to generate the p_parvum_deseq2_result_sorted_regulated_with_proteins.csv and s_marinoi_deseq2_result_sorted_regulated_with_proteins.csv. The code for analysis from RAW reads to differential gene expression analysis is available on: https://github.com/Bioinformatics-Core-Facility-Jena/SE20220705_97. The RAW files are available on BioProject: PRJNA1006530