Dataset Information

MRNA-Seq of zebrafish embryos (96hpf) exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups

ABSTRACT: mRNA-Seq of zebrafish embryos (96hpf) exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups

PROVIDER: PRJEB41695 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR4910710.fastq.gz	Fastqsanger.gz
	ERR4910701.fastq.gz	Fastqsanger.gz
	ERR4910711.fastq.gz	Fastqsanger.gz
	ERR4910702.fastq.gz	Fastqsanger.gz
	ERR4910712.fastq.gz	Fastqsanger.gz

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Project description:The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish (Danio rerio) embryos as aquatic vertebrate non-target model exposed to sub lethal concentrations of Abamectin (CAS 71751-41-2). Abamectin is a heavily used insecticide applied for crop protection against sucking insects (i.e. Acari). The Insecticide Resistance Action Committee (IRAC) classified Abamectin after its mode of action (MoA) in the target organism as a Glutamate-gated chloride channel (GluCl) allosteric modulator (Group 6). In vertebrates, GluCl do not exist, but they are closely related to vertebrate glycine receptors (Wolstenholme 2012). The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events (KE) explaining upstream adverse effects in aquatic non-target organisms. This will provide useful information to refine and improve existing adverse outcome pathways (AOP). Furthermore, integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects, based on similarly altered transcriptomic and proteomic profiles. In a modified version of the zebrafish embryo toxicity test (OECD 236), 15 fertilized eggs were exposed to two different sub lethal concentrations of Abamectin for 96 hours under semi-static conditions. Each test comprised of a low exposure (LE, 0.11 mg/L), mid exposure (ME, 0.22 mg/L), high exposure (HE, 0.44 mg/L) and negative control (NC) group and was performed in triplicates. At 96 hours post fertilization (hpf), 10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit (Macherey-Nagel). RNA quality was assessed with a 2100 Bioanalyzer system (Agilent) before coding RNA was purified (PolyA selection with TruSeq RNA Library Prep Kit v2) and sequenced on an Illumina HiSeq 4000 System (Illumina) in 50 bp single read mode, producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.

Project description:The aim of this mRNA expression profiling experiment was to screen for ecotoxicogenomic fingerprints in zebrafish (Danio rerio) embryos as aquatic vertebrate non-target model exposed to sub lethal concentrations of the heavily used organophosphate insecticide Fipronil (CAS 2921-88-2). The Insecticide Resistance Action Committee (IRAC) classified Fipronil after its mode of action (MoA) in the target organism as an acetylcholinesterase (AChE) inhibitor (Group 1B). The goal is to identify toxicogenomic profiles with predictive character and potential molecular key events (KE) explaining upstream adverse effects in aquatic non-target organisms. This will provide useful information to refine and improve existing adverse outcome pathways (AOP). Furthermore, integrating the obtained profiles for this and other tested chemicals in a collective database will enable us in the future to derive predictions about the ecotoxicological hazard for chemcials with unknown apical effects, based on similarly altered transcriptomic and proteomic profiles. In a modified version of the zebrafish embryo toxicity test (OECD 236), 15 fertilized eggs were exposed to two different sub lethal concentrations of Fipronil for 96 hours under semi-static conditions. Each test comprised of a low exposure (LE, 0.075 mg/L), high exposure (HE, 0.3 mg/L) and negative control (NC) group and was performed in triplicates. At 96 hours post fertilization (hpf), 10 larvae were randomly picked for each sample and pooled for RNA and protein extraction with NucleoSpin RNA/Protein kit (Macherey-Nagel). RNA quality was assessed with a 2100 Bioanalyzer system (Agilent) before coding RNA was purified (PolyA selection with TruSeq RNA Library Prep Kit v2) and sequenced on an Illumina HiSeq 4000 System (Illumina) in 50 bp single read mode, producing roughly 30 million reads per sample. Adapter sequences were removed with trimmomatic and sequences were aligned to the D.rerio reference genome GRCz11 with STAR. Counting of feature mapped reads was performed through featureCounts. Library gene count tables were then merged to a single count matrix as input for differential gene expression analysis with DESeq2.

Dataset Information

MRNA-Seq of zebrafish embryos (96hpf) exposed to different concentrations of Abamectin below acute toxicity levels against untreated control groups

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