Gene biomarkers for the assessment of thyroid-disrupting activity in zebrafish embryos

We have conducted an exposure study on zebrafish embryos using thyroidal active compounds. Based on OECD guideline 236, freshly fertilized zebrafish embryos were exposed to two sublethal concentrations of triiodothyronine (T3), 6-Propyl-2-thiouracil (6-PTU), methimazole (MMI) and iopanoic acid (IOP) until 96 hours post fertilization. RNA was extracted and sequenced to identify thyroid-related gene expression patterns. .

The uploaded data archive consists of three major data types:1. MultiQC reports from raw RNA-Seq read processing and QC2. Result tables from differential gene expression analysis (DGEA) with DESeq2 (apeglm shrunk results indicated by "reslfs")3. 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 numbers E-MTAB-14185 (IOP), E-MTAB-14184 (MMI), E-MTAB-14183 (T3) and E-MTAB-9054 (6-PTU), provide 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).