Supplemental dataset accompanying the paper: Comprehensive and functional analysis of horizontal gene transfer events in diatoms, Vancaester et al. MBE (https://doi.org/10.1093/molbev/msaa182). This dataset contains the generated gene expression matrix for the diatoms Phaeodactylum tricornutum, Seminavis robusta, Fragilariopsis cylindrus and Thalassiosira pseudonana. Relevant experiments were queried using Curse (Vaneechoutte and Vandepoele 2019), which also allows the user to identify and curate replicates. Next, the atlas was generated using Prose (Vaneechoutte and Vandepoele 2019), which uses the SRA toolkit to download the raw data locally, FastQC (Andrews 2010) to perform quality control and adapter detection, Trimmomatic (Bolger et al. 2014) for automatic read trimming and finally kallisto (Bray et al. 2016) for expression quantification in transcripts per million (TPM). Finally, also the co-expression clusters defined based on the gene expression for Phaeodactylum tricornutum is included. The dataset containing all detected phylogenetic trees of diatom genes of horizontal descent can be found on (https://zenodo.org/record/3889669#.XyB-E-dCdPY).