Gene expression databases like Gene Expression Omnibus or ArrayExpress by now contain a wealth of toxicogenomic datasets. This is a offers great possibilities for advanced data analyses, like meta-analyses, co-expression studies, etc.However, automated retrieval of this data is still a challenge.With this computational pipeline we retrieve toxicogenomic data of the Danio rerio (zebrafish) embryo from GEO and ArrayExpress.To make the data as comparable as possible, we download the raw datasets, and re-map the probes or probesets to the most recent version.In the end a matrix with logFC in response to different chemical treatments is compiled.