Transcription profiling of Stickleback liver exposed to Cu, DbA (Dibezanthracene), EE2 (Ethinyl-estradiol) or relevant controls
Ontology highlight
ABSTRACT:
ORGANISM(S): Gasterosteus aculeatus
SUBMITTER: Tim Williams
PROVIDER: E-MAXD-43 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Identifying health impacts of exposure to copper using transcriptomics and metabolomics in a fish model.
Santos Eduarda M EM Ball Jonathan S JS Williams Tim D TD Wu Huifeng H Ortega Fernando F van Aerle Ronny R Katsiadaki Ioanna I Falciani Francesco F Viant Mark R MR Chipman James K JK Tyler Charles R CR
Environmental science & technology 20100101 2
Copper (Cu) is a micronutrient essential for the biochemical functioning of numerous processes in vertebrates but is also often present in the aquatic environment at concentrations able to cause adverse health effects in aquatic organisms. This study investigated the signaling pathways mediating the effects of exposure to Cu using a toxicogenomic approach in a fish model, the stickleback ( Gasterosteus aculeatus ). Freshwater-acclimated male fish were exposed via the water to Cu, including at en ...[more]
Similar Datasets
Project description:Stickleback were exposed to Cu, DbA (Dibezanthracene), EE2 (Ethinyl-estradiol) or relevant controls. Liver tissue from individual fish exposed to different doses were arrayed versus a common reference.
2009-07-10 | E-MAXD-42 | biostudies-arrayexpress
Project description:Sticklebacks were caught from the River Aire (Yorkshire, UK) and Siblyback reservoir (Cornwall, UK), depurated for 4 months at Exeter University, split into groups of 20 individuals before exposure. Fish were exposed to either control conditions, three concentrations of copper (3.2, 32, 128 µg/L; prepared using copper sulphate), three concentrations of ethinyl-estradiol (EE2) (1, 10, 32 ng/L) and three mixtures (3.2 µg Cu/L and 32 ng EE2/L; 128 µg Cu/L and 1 ng EE2/L; 128 µg Cu/L and 32 ng EE2/L) in duplicate tanks for 4 days. After sampling liver of male fish were stored at -80C for transcriptomics. Total RNA was prepared from fish livers, aliquots of all samples were pooled and labeled with Cy3-dCTP as a common reference, individual samples were labeled with Cy5-dCTP. Each hybridisation to the stickleback PGPS2 cDNA microarray consisited of one Cy5-labeled individual sample and one aliquot of the Cy3 labeled commmon reference sample. Data were captured with an Axon scanner using Genepix software.
2017-06-01 | E-MTAB-4907 | biostudies-arrayexpress
Project description:Adult female three-spined stickleback fish (Gasterosteus aculeatus) were exposed to 10 individual chemicals, 26 mixtures of these chemicals, or control conditions in a flow-through system for 4 days. Transcriptomics was performed on liver samples by microarray. The main aims were to determine molecular signatures induced by these chemicals in the three-spined stickleback, discover whether these persisted in chemical mixtures and identify non-additive molecular responses in chemical mixtures exposures.
2018-03-01 | E-MTAB-5581 | biostudies-arrayexpress
Project description:Male and five female sticklebacks were exposed to the single compounds dibenzanthracene (DbA, Sigma Aldrich, Cat No D-31400) (40ug/L DbA in 0.0125% acetone) and oestradiol (E2, Sigma, Cat No E-8875) (50 ng/L E2 in 0.0125% acetone) or binary DbA + E2 (40ug/L DbA + 50ng/L E2 in 0.0125% acetone) in addition to a solvent control (acetone, 0.0125%), over a period of 48 hours. In this experiment RNA was pooled from 4 males or 4 females for each sex/exposure group. Pools of treated fish samples were compared with the relevant solvent controls. Dye swaps were carried out such that a total of 12 microarrays were analysed.
2008-02-08 | E-MAXD-39 | biostudies-arrayexpress
Project description:A Platichthys flesus cDNA microarray (GENIPOL) comprised of 12,700 clones, was used to determine and characterize gene expression profiles of environmentally sampled flounders from sites of different pollution status in Northern Europe.
2011-03-01 | E-MTAB-396 | biostudies-arrayexpress
Project description:Structural analogues are assumed to elicit toxicity via similar predominant modes of action (MOAs). Currently, MOA categorization of chemicals in environmental risk assessment is mainly based on the physico-chemical properties of potential toxicants. It is often not known whether such classification schemes are also supported by mechanistic biological data. In this study, the toxic effects of two groups of structural analogues (alcohols and anilines) with predefined MOA (narcotics and polar narcotics) were investigated at different levels of biological organization (gene transcription, energy reserves and growth). Chemical similarity was not indicative of a comparable degree of toxicity and a similar biological response. Categorization of the test chemicals based on the different biological responses (growth, energy use and gene transcription) did not result in a classification of the predefined narcotics versus the predefined polar narcotics. Moreover, gene transcription based clustering profiles were indicative of the observed effects at higher level of biological organization. Furthermore, a small set of classifier genes could be identified that was discriminative for the clustering pattern. These classifier genes co-varied with the organismal and physiological responses. Compared to the physico-chemistry based MOA classification, integrated biological multi-level effect assessment can provide the necessary MOA information that is crucial in high-quality environmental risk assessment. Our findings support the view that transcriptomics tools hold considerable promise to be used in biological response based mechanistic profiling of potential (eco)toxicants. The hybridization design was a universal reference design (a mixture of aliquots from control and exposed samples), which is recommended when class discovery is the main purpose of the experiment. One of the three biological replicates of each exposure condition was labeled with one dye, the remaining two samples were labeled with the second dye.
2012-02-01 | E-GEOD-29864 | biostudies-arrayexpress
Project description:Structural analogues are assumed to elicit toxicity via similar predominant modes of action (MOAs). Currently, MOA categorization of chemicals in environmental risk assessment is mainly based on the physico-chemical properties of potential toxicants. It is often not known whether such classification schemes are also supported by mechanistic biological data. In this study, the toxic effects of two groups of structural analogues (alcohols and anilines) with predefined MOA (narcotics and polar narcotics) were investigated at different levels of biological organization (gene transcription, energy reserves and growth). Chemical similarity was not indicative of a comparable degree of toxicity and a similar biological response. Categorization of the test chemicals based on the different biological responses (growth, energy use and gene transcription) did not result in a classification of the predefined narcotics versus the predefined polar narcotics. Moreover, gene transcription based clustering profiles were indicative of the observed effects at higher level of biological organization. Furthermore, a small set of classifier genes could be identified that was discriminative for the clustering pattern. These classifier genes co-varied with the organismal and physiological responses. Compared to the physico-chemistry based MOA classification, integrated biological multi-level effect assessment can provide the necessary MOA information that is crucial in high-quality environmental risk assessment. Our findings support the view that transcriptomics tools hold considerable promise to be used in biological response based mechanistic profiling of potential (eco)toxicants. The hybridization design was a universal reference design (a mixture of aliquots from control and exposed samples), which is recommended when class discovery is the main purpose of the experiment. One of the three biological replicates of each exposure condition was labeled with one dye, the remaining two samples were labeled with the second dye.
2012-02-01 | E-GEOD-29867 | biostudies-arrayexpress
Project description:Structural analogues are assumed to elicit toxicity via similar predominant modes of action (MOAs). Currently, MOA categorization of chemicals in environmental risk assessment is mainly based on the physico-chemical properties of potential toxicants. It is often not known whether such classification schemes are also supported by mechanistic biological data. In this study, the toxic effects of two groups of structural analogues (alcohols and anilines) with predefined MOA (narcotics and polar narcotics) were investigated at different levels of biological organization (gene transcription, energy reserves and growth). Chemical similarity was not indicative of a comparable degree of toxicity and a similar biological response. Categorization of the test chemicals based on the different biological responses (growth, energy use and gene transcription) did not result in a classification of the predefined narcotics versus the predefined polar narcotics. Moreover, gene transcription based clustering profiles were indicative of the observed effects at higher level of biological organization. Furthermore, a small set of classifier genes could be identified that was discriminative for the clustering pattern. These classifier genes co-varied with the organismal and physiological responses. Compared to the physico-chemistry based MOA classification, integrated biological multi-level effect assessment can provide the necessary MOA information that is crucial in high-quality environmental risk assessment. Our findings support the view that transcriptomics tools hold considerable promise to be used in biological response based mechanistic profiling of potential (eco)toxicants. The hybridization design was a universal reference design (a mixture of aliquots from control and exposed samples), which is recommended when class discovery is the main purpose of the experiment. One of the three biological replicates of each exposure condition was labeled with one dye, the remaining two samples were labeled with the second dye.
2012-02-01 | E-GEOD-29862 | biostudies-arrayexpress
Project description:Structural analogues are assumed to elicit toxicity via similar predominant modes of action (MOAs). Currently, MOA categorization of chemicals in environmental risk assessment is mainly based on the physico-chemical properties of potential toxicants. It is often not known whether such classification schemes are also supported by mechanistic biological data. In this study, the toxic effects of two groups of structural analogues (alcohols and anilines) with predefined MOA (narcotics and polar narcotics) were investigated at different levels of biological organization (gene transcription, energy reserves and growth). Chemical similarity was not indicative of a comparable degree of toxicity and a similar biological response. Categorization of the test chemicals based on the different biological responses (growth, energy use and gene transcription) did not result in a classification of the predefined narcotics versus the predefined polar narcotics. Moreover, gene transcription based clustering profiles were indicative of the observed effects at higher level of biological organization. Furthermore, a small set of classifier genes could be identified that was discriminative for the clustering pattern. These classifier genes co-varied with the organismal and physiological responses. Compared to the physico-chemistry based MOA classification, integrated biological multi-level effect assessment can provide the necessary MOA information that is crucial in high-quality environmental risk assessment. Our findings support the view that transcriptomics tools hold considerable promise to be used in biological response based mechanistic profiling of potential (eco)toxicants. The hybridization design was a universal reference design (a mixture of aliquots from control and exposed samples), which is recommended when class discovery is the main purpose of the experiment. One of the three biological replicates of each exposure condition was labeled with one dye, the remaining two samples were labeled with the second dye.
2012-02-01 | E-GEOD-29856 | biostudies-arrayexpress
Project description:Structural analogues are assumed to elicit toxicity via similar predominant modes of action (MOAs). Currently, MOA categorization of chemicals in environmental risk assessment is mainly based on the physico-chemical properties of potential toxicants. It is often not known whether such classification schemes are also supported by mechanistic biological data. In this study, the toxic effects of two groups of structural analogues (alcohols and anilines) with predefined MOA (narcotics and polar narcotics) were investigated at different levels of biological organization (gene transcription, energy reserves and growth). Chemical similarity was not indicative of a comparable degree of toxicity and a similar biological response. Categorization of the test chemicals based on the different biological responses (growth, energy use and gene transcription) did not result in a classification of the predefined narcotics versus the predefined polar narcotics. Moreover, gene transcription based clustering profiles were indicative of the observed effects at higher level of biological organization. Furthermore, a small set of classifier genes could be identified that was discriminative for the clustering pattern. These classifier genes co-varied with the organismal and physiological responses. Compared to the physico-chemistry based MOA classification, integrated biological multi-level effect assessment can provide the necessary MOA information that is crucial in high-quality environmental risk assessment. Our findings support the view that transcriptomics tools hold considerable promise to be used in biological response based mechanistic profiling of potential (eco)toxicants. The hybridization design was a universal reference design (a mixture of aliquots from control and exposed samples), which is recommended when class discovery is the main purpose of the experiment. One of the three biological replicates of each exposure condition was labeled with one dye, the remaining two samples were labeled with the second dye.
2012-02-01 | E-GEOD-29854 | biostudies-arrayexpress