We have conducted an immune challenge experiment on 48h zebrafish embryos, which were previously treated with the immunosuppressive drug clobetasol propionate (CP). The embryos' immune system was challenged by injection of a mix of different pathogen associated molecular patterns (PAMPs). RNA sequencing was performed in order to detect altered molcular expression levels induced by CP, PAMPs and a combination of both. The data was published in Essfeld et al. 2022. The uploaded data archive (7-zip compressed) consists of three major data types:1. MultiQC reports from raw RNA-Seq read processing and QC (50bp SR)2. Result tables from differential gene expression analysis (DGEA) with DESEq23. Result tables from Overrespresentation Analysis (ORA) with clusterProfiler Gene count normalization and DGEA was conducted with DESeq2 (Love et al., 2014, DOI 10.1186/s13059-014-0550-8) . Three biological replicates per condition, exposure treatments were compared with respect to the control group in a pairwise fashion, applying Wald’s t-test. P values were corrected for multiple testing with independent hypothesis weighting (IHW) (Ignatiadis et al., 2016, DOI 10.1038/nmeth.3885 ) after Benjamini-Hochberg (BH). To improve the signal to statistical noise ratio, the obtained log2-fold change (lfc) values were shrunk with the apeglm method described by Zhu and colleagues (2019, DOI 10.1093/bioinformatics/bty895 ) before DGEA result tables were subjected to ORA via clusterProfiler (Yu et al., 2012, DOI 10.1089/omi.2011.0118). The ArrayExpress accession number E-MTAB-11092, provides access to the raw and DESeq2 normalized gene count matrices upon which these analysis were performed. Genes were annotated through the biomaRt package (Durinck et al., 2009, DOI 10.1038/nprot.2009.97 ) in R (R Core Team 2021).