GSE230213 Identifying suitable experimental designs to determining differentially expressed genes and benchmark doses from transcriptomic dose-response studies in zebrafish embryos

Contributors : Hyojin Lee ; John Stead ; Andrew Williams ; Ella Atlas ; Jan Mennigen ; Jason O'Brien ; Carole YaukSeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioTo identify suitable experimental designsfor toxicology experiments (i.e., sample size, pool size, number of biological replicates, and number of doses), we exposed zebrafish embryos to 0.1% dimethyl sulfoxide for 4-120 hours post fertilization. We then created 96 samples to examine the impact of pool size comprised of 1, 5, 10, and 20 zebrafish embryos each (n = 24). From these, total RNA extraction was extracted and transcriptomic analyses were done using the TempO-Seq S1500+ Surrogate Assay platform. Samples were sequencing on an Illumina NextSeq 2000. The data were simulated to conduct power analyses exploring suitable study designs for identification of differentially expressed genes and for benchmark dose analysis. The aim was to identify a feasible pool size and sample size that would yield an acceptable false discovery rate for these analyses.

Source: GEO: Gene Expression Omnibus - April 17, 2024 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Danio rerio Source Type: research