Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

41 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Whole organism transcriptomic analysis provides mechanistic insight into the acute toxicity of emamectin benzoate in Daphnia magna

ABSTRACT: This experiment was conducted to study the short-term (12h) transcriptional responses in Daphnia magna after exposure to the anti-sea lice chemical emamectin benzoate (EMB). The microarray results were further vefiried using qPCR. The gene exression responses were linked to adverse effects after 48h exposure, in order to supply knowledge for environmental hazard assessment of this chemical in non-target crustaceans. Neonatal (<24h) Daphnia magna were exposed to 7.8-2000 pM waterborne emamectin benzoate for 12h. Microarray analysis was performed using pooled whole-organism D. magna (8 individuals) and 4 biological replicates were analyzed for each treatment group.

ORGANISM(S): Daphnia magna

SUBMITTER: Knut Erik Tollefsen

PROVIDER: E-GEOD-83859 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Whole organism transcriptomic analysis provides mechanistic insight into the acute toxicity of emamectin benzoate in Daphnia magna

Project description:This experiment was conducted to study the short-term (12h) transcriptional responses in Daphnia magna after exposure to the anti-sea lice chemical emamectin benzoate (EMB). The microarray results were further vefiried using qPCR. The gene exression responses were linked to adverse effects after 48h exposure, in order to supply knowledge for environmental hazard assessment of this chemical in non-target crustaceans.

2016-06-30 | GSE83859 | GEO

Daphnia magna exposed to narcotics and polar narcotics

Project description:This SuperSeries is composed of the following subset Series: GSE29854: Daphnia magna exposed to narcotics and polar narcotics - aniline GSE29856: Daphnia magna exposed to narcotics and polar narcotics - 4-chloroaniline GSE29857: Daphnia magna exposed to narcotics and polar narcotics - 3,5-dichloroaniline GSE29858: Daphnia magna exposed to narcotics and polar narcotics - 2,3,4-trichloroaniline GSE29862: Daphnia magna exposed to narcotics and polar narcotics - ethanol GSE29864: Daphnia magna exposed to narcotics and polar narcotics - isopropanol GSE29867: Daphnia magna exposed to narcotics and polar narcotics - methanol Refer to individual Series

2012-02-01 | E-GEOD-29993 | biostudies-arrayexpress

Gene expression profiles of Daphnia magna exposed to Cd at the 1/10 LC50

Project description:Cadmium (Cd) is a toxic metal causing sublethal and chronic effects in crustaceans. Omic technologies offer unprecedented opportunities to better understand modes of toxicity by providing a holistic view of the molecular changes underlying physiological disruption. We sought to use gene expression and metabolomic analyses to reveal the processes leading to chronic Cd toxicity in the indicator species, Daphnia magna, after a 24-h sublethal exposure (18 ug/L, corresponding to 1/10 LC50). We first confirmed that metabolites can be detected and identified in small volumes (~3-6 ul) of D. magna hemolymph using Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry and NMR spectroscopy. We then compared the altered metabolite levels from a mass spectrometry metabolomics study to differentially expressed genes identified by a D. magna 44k oligonucleotide microarray. Metabolomics identified several essential amino acids, nucleotides and fatty acids as decreased in D. magna hemolymph following Cd exposure. Transcriptional changes included decreased levels of digestive enzymes and increased expression of genes related to embryonic development. The integration of metabolomic and transcriptomic profiles, as well as incorporation of results from previous studies, has enabled construction of a conceptual model detailing how sublethal Cd disrupts energy reserves and reproduction resulting in chronic toxicity. Daphnia magna were exposed to 18 micrograms/L Cadmium sulfate for 24 hours. RNA was extracted and hybridized to a custom Daphnia magna microarray to determine genes differentially expressed by the treatment. Two treament experiment:Unexposed and Cd treatment, 6 replicates for each condition

2010-12-31 | E-GEOD-20218 | biostudies-arrayexpress

Daphnia pulex_Lysine acetylation

Project description:Daphnia (Daphnia pulex) is a small planktonic crustacean and a key constituent of aquatic ecosystems. It is commonly used as a model organism for studying environmental toxic challenges. In the past decade, a Daphnia genomic information and proteomic dataset has been developed. This dataset has expanded the opportunity to relate toxicological effects with “Daphnia proteomics” as it integrates proteomic knowledge in Daphnia, those approach will provide greater insights for toxicological research. In order to exploit Daphnia for ecotoxicological research, information on the post-translational modification (PTM) of proteins is necessary as this is a critical regulator of biological processes. Acetylation of lysine (Kac) is a reversible and highly regulated PTM that is associated with diverse biological functions. However, a comprehensive description of Kac in Daphnia is not yet available. Here, to understand the cellular distribution of lysine acetylation in Daphnia, we identified 98 acetylation sites in 65 proteins by immunoprecipitation using an anti-acetyllysine antibody and an liquid chromatography system supported by mass spectroscopy. We identified 28 acetylated sites connected with metabolic proteins and 6 acetylated enzymes associated with the TCA cycle in Daphnia. From GO and KEGG enrichment analyses, we showed that Kac in D. pulex is highly enriched in proteins associated with metabolic processes. Our data provide the first global analysis of lysine acetylation in D. pulex. The expanded proteomic dataset will be an important resource for the functional analysis of Kac in D. pulex and it will be nice to have a first step done using a promising future model organism.

2016-01-05 | PXD002441 | Pride

Gene expression profiling in Daphnia magna, Part III: Uncovering Biomarkers for Metal and ORC exposures

Project description:To determine toxicant specific effects of Ordnance Related Compound (ORC) exposure we performed microarray hybridizations with RNA isolated from Daphnia magna following different ORC exposures at the 1/10 LC50. The gene expression profiles revealed toxicant specific gene expression profiles allowed for the identification of specific biomarkers of exposure. Keywords: ecotoxicogenomic exposure study We exposed Daphnia magna the 1/10 LC50 of different Ordnance Related Compounds (Cu, Zn, Pb, WO4, RDX, TNT, 2-ADNT, 2-ADNT, TNB, DNB, 2,4-DNT, and 2,6-DNT) for 24 hours. For each exposure condition, we performed 3 exposures and 2 technical replicates (as dye swap) for each exposure (6 microarrays total, except TNT and Cu). All exposures were compared to a unexposed laboratory control (MHRW media).

2010-05-18 | E-GEOD-13169 | biostudies-arrayexpress

Transcription profiling of juvenile Daphnia manga following exposure to the pesticides methomyl and propanil

Project description:Juvenile daphnia magna (<24hrs old, n=25 / test vessel) were exposed to methomyl (M) a carbamate insecticide (10.52ug/l), propanil (P), an analide herbicide (363ug/l), an independent action (IA) mixture of M (10.52ug/l and P (363ug/l) representing effect concentration 1 (EC1) for each chemical, based on standard immobility assay (OECD) or to control (untreated medium). All exposures were carried out in reconstituted water (see protocol GROWTH). Treated vessels were spiked with stock solutions of pesticides dissolved directly into reconstituted water. Test vessels were 1L glass beakers arranged in a randomised block design. Transcriptomic screening was used to assess the mechanism of toxicity of the two single pesticides and to explain (in part) the interaction of methomyl and propanil in an independent action (IA) EC1 mixture.

2010-09-15 | E-TABM-793 | biostudies-arrayexpress

Transcription profiling of juvenile Daphnia manga following exposure to various doses of Lufenuron, a benzoylphenylurea growth inhibitor (no RNA amplification)

Project description:Juvenile (<24hr old) Daphnia magna populations (n=250) were exposed (24hr) to Benzoylphenylurea growth inhibitor (14C labeled) lufenuron. Treatments were 0.15 ug/L, 0.33 ug/L, 0.65 ug/L lufenuron solvent control was 100 ul/L acetone carrier . Transcriptomic responses were screened using a D.magna cDNA microarray and the regulation of gene expression via log fold-change in transcript abundance, assessed. Genes involved in the synthesis of chitin were expected to respond to lufenuron, given the mode of action

2010-10-13 | E-TABM-798 | biostudies-arrayexpress

The Molecular Toxicity Identification Evaluation (mTIE) Approach Predicts Chemical Exposure in Daphnia magna

Project description:Daphnia magna is a bio-indicator organism accepted by several international water quality regulatory agencies. Current approaches for assessment of water quality rely on acute and chronic toxicity that provide no insight into the cause of toxicity. Recently, molecular approaches, such as genome wide gene expression responses, are enabling an alternative mechanism based approach to toxicity assessment. While these genomic methods are providing important mechanistic insight into toxicity, statistically robust prediction systems that allow the identification of chemical contaminants from the molecular response to exposure are needed. Here we apply advanced machine learning approaches to develop predictive models of contaminant exposure using a D. magna gene expression dataset for 36 chemical exposures. We demonstrate here that we can discriminate between chemicals belonging to different chemical classes including endocrine disruptors, metals and industrial chemicals based on gene expression. We also show that predictive models based on indices of whole pathway transcriptional activity can achieve comparable results while facilitating biological interpretability. D. magna were exposed to 36 Chemicals and 5 control series in quadruplicate.

2013-01-17 | E-GEOD-43564 | biostudies-arrayexpress

Transcriptomic responses to emamectin benzoate in Pacific and Atlantic Canada salmon lice Lepeophtheirus salmonis with differing levels of drug resistance

Project description:This study investigates the baseline or inducible differences in between populations of Atlantic salmon lice Lepeophtheirus salmonis with differing levels of resistance to the parasiticidal drug emamectin benzoate (EMB), as well as the induced effects of EMB exposure to Pacific salmon lice. F1 generation lice were exposed in bioassays to a dilution series of emamectin benzoate.

2014-11-17 | GSE56024 | GEO

Daphnia genotoxicity experiment

Project description:Daphnia neonates (100 individuals, 24h post-hatch) and adults (20 individuals, 168h post-hatch) were exposed to DMSO carrier (0.002%), low (0.25 uM sodium dichromate, 0.01 uM benzo-a-pyrene) or high (0.75 uM soduium dichromate, 0.1 uM benzo-a-pyrene) concentrations of a genotoxicant mixture, or were untreated. Untreated controls were sampled at the initial time point, exposed Daphnia were sampled at 6h and 24h post-exposure. Transcriptional profiles were determined using an Agilent oligonucleotide microarray.

2011-03-01 | E-MTAB-551 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data