Project description:Whole transcriptome analysis of dechorinated zebrafish embryos after (static?) exposure to one of five smoke dyes from 6 hours post-fertilization (hpf) to 48 hpf. Smoke dyes tested are Disperse Blue 14, Disperse Red 9, Solvent Red 169, Solvent Violet 47, and Solvent Yellow 33. Results provide insight into the molecular mechanisms of immunological response to the dyes.
Project description:Investigation of microRNA expression profile of 12, 24, 36 and 48 hours post-fertilization Danio rerio embryos developmentally exposed to retinoic acid. A twelve chip study using total RNA recovered from pools of 75 tropical 5D zebrafish embryos at 12, 24, 36, and 48 hours post fertilization (hpf). Embryos were exposed to control embryo medium or 5 nM retinoic acid from 6-24 hpf, with two biological replicates per condition. Control samples were pooled and hybridized to a single array. 12 miRZebrafish arrays (based on MirBase release 12.0) were used to measure the expression level of 218 mature miRNA from Danio rerio.
Project description:To test wether endocrine disruption is detectable in zebrafish at the transcriptome level, we exposed newly fertilized zebrafish embryos to low doses of genistein (EC10 and EC20) for 48 hours.
Project description:The purpose of this study was to identify transcripts differentially expressed in zebrafish embryos exposed to two oxygenated PAHs, 1,9-benz-10-anthrone and benzanthracene-7,12-dione, which cause abnormal development. We used RNA-seq (Illumina HiSeq) to identify mRNA profiles of whole zebrafish embryos exposed to 10 μM 1,9-benz-10-anthrone, benzanthracene-7,12-dione or vehicle control (1% DMSO) from 6-48 hours post fertilization
Project description:Transcriptomic profiling of the response to dioxin in developing zebrafish embryos, at 24, 48, 72, 96, and 120 h post-fertilization. The goal was to elucidate mechanisms by which dioxin causes toxicity in zebrafish; this dose was previously shown to induce teratogenesis.
Project description:Environmental metals are known to cause harmful effects to fish of which many molecular mechanisms still require elucidation. Particularly concentration dependence of gene expression effects is unclear. Focusing on this matter, zebrafish embryo toxicity tests were used in combination with transcriptomics. Embryos were exposed to three concentrations of copper (CuSO4), cadmium (CdCl2) and cobalt (CoSO4) from just after fertilization until the end of the 48 hpf pre- and 96 hpf post-hatch stage. The RNA was then analyzed on Agilent’s Zebrafish (V3, 4x44K) arrays. Enrichment for GO terms of biological processes illustrated for cadmium that most affected GO terms were represented in all three concentrations, while for cobalt and copper most GO terms were represented in the lowest test concentration only. This suggested a different response to the non-essential cadmium than cobalt and copper. In cobalt and copper treated embryos, many developmental and cellular processes as well as the Wnt and Notch signaling pathways were found significantly enriched. Also, different exposure concentrations affected varied functional networks. In contrast, the largest clusters of enriched GO terms for all three concentrations of cadmium included responses to cadmium ion, metal ion, xenobiotic stimulus, stress and chemicals. However, concentration dependence of mRNA levels was evident for several genes in all metal exposures. Some of these genes may be indicative of the mechanisms of action of the individual metals in zebrafish embryos.
Project description:During early neurogenesis, multiple whole animal gene expression profiling studies revealed widespread changes in developmental mRNA and miRNA abundance in ethanol-exposed embryos. Consistent with a role for miRNAs in neurobehavioral development, miRNA target prediction analyses identified multiple miRNAs misexpressed in the ethanol exposed cohorts that were also predicted to target inversely expressed transcripts known to influence brain morphogenesis. [mRNA] A twelve chip study using total RNA recovered from pools of 75 tropical 5D zebrafish embryos at 24 hours post fertilization (hpf). Embryos were exposed to control embryo medium, 100 mM ethanol, or 300 mM ethanol from 4-24 hpf, with four-fold biological redundancy per condition. A single 12x135K Nimblegen array was used to measure the expression level of 38,489 genes from Danio rerio using 60-mer probes, with three-fold technical redundancy. [miRNA] A twelve chip study using miRNA recovered from pools of 75 tropical 5D zebrafish embryos at 12, 24, 36, and 48 hours post fertilization (hpf). Embryos were exposed to control embryo medium or 300 mM ethanol from 4-24 hpf, with two-fold biological redundancy per condition. Control samples were pooled and hybridized to a single array. 12 miRZebrafish arrays (based on MirBase release 12.0) were used to measure the expression level of 218 mature miRNA from Danio rerio, with 12-fold technical redundancy.