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

<p>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. .</p> <p>The uploaded data archive consists of three major data types:<br>1. MultiQC reports from raw RNA-Seq read processing and QC<br>2. Result tables from differential gene expression analysis (DGEA) with DESeq2 (apeglm shrunk results indicated by "reslfs")<br>3. Result tables from Overrespresentation Analysis (ORA) with clusterProfiler</p> <p>Gene count normalization and DGEA was conducted with DESeq2 (<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8">Love et al., 2014</a>, 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&rsquo;s t-test. P values were corrected for multiple testing with independent hypothesis weighting (IHW) (<a href="https://www.nature.com/articles/nmeth.3885">Ignatiadis et al., 2016</a>, 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 (<a href="https://academic.oup.com/bioinformatics/article/35/12/2084/5159452?login=true">2019</a>, DOI 10.1093/bioinformatics/bty895 ) before DGEA result tables were subjected to ORA via clusterProfiler (<a href="https://www.liebertpub.com/doi/10.1089/omi.2011.0118">Yu et al., 2012</a>, DOI 10.1089/omi.2011.0118).</p> <p>The ArrayExpress accession&nbsp;numbers&nbsp;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 (<a href="https://www.nature.com/articles/nprot.2009.97.pdf?origin=ppub">Durinck et al., 2009</a>, DOI 10.1038/nprot.2009.97 ) in R (<a href="https://www.r-project.org/">R Core Team 2021</a>).</p>