Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

27 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of Danio rerio livers following chronic waterborne copper exposure

ABSTRACT: Zebrafish exposed to 2 waterborne copper concentrations (8 & 15 ug/L) in softwater for 21 days. Fish were terminally sampled and livers extracted for RNA extraction and hybridization to micorarrays

ORGANISM(S): Danio rerio

SUBMITTER: Paul Craig

PROVIDER: E-MEXP-2287 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Gene expression endpoints following chronic waterborne copper exposure in a genomic model organism, the zebrafish, Danio rerio.

Craig Paul M PM Hogstrand Christer C Wood Chris M CM McClelland Grant B GB

Physiological genomics 20090929 1

Although copper (Cu) is an essential micronutrient for all organisms, in excess, waterborne Cu poses a significant threat to fish from the cellular to population level. We examined the physiological and gene expression endpoints that chronic waterborne Cu exposure (21 d) imposes on soft-water acclimated zebrafish at two environmentally relevant concentrations: 8 microg/l (moderate) and 15 microg/l (high). Using a 16,730 65-mer oligonucleotide customized zebrafish microarray chip related to metal ...[more]

PMID: 19789285

Similar Datasets

Transcription profiling of Danio rerio livers following exposure to combinations of copper, sodium and calcium

Project description:Zebrafish (n=420; 70/treatment) were weighed and placed in 8L aerated tanks, served with flow-through soft-water at 25ml/min. A combination of Mariotte bottles were used to dose tanks with Cu (concentrated Cu solution made from CuSO4 dissolved in 0.05% HNO3), Na (concentrated NaCl solution), and Ca (concentrated CaCl2 solution) to 6 treatment regimes of either control (Ctrl), Cu only (Cu), high Ca only (Ca), Ca + Cu (CaCu), high Na only (Na), and Na + Cu (NaCu; See Table 1 for ion concentrations). Nitric acid had no measurable impact on water pH. Fish were fed 2% body weight of commercial tropical fish food, once per day. Tanks were monitored daily for mortality and cleaned of any food or waste that had accumulated. Water samples (10 ml) were taken from each tank, filtered though a 0.45?m filtration disc (Pall Corporation, East Hills, NY), added to a plastic tube containing 100?l HNO3 and kept at 4oC for analysis of ion content and Cu concentration. Throughout the experiment, there were no mortalities in any of the tanks. At the end of the exposure period, fish were quickly euthanized by overdose of buffered aesthetic (MS-222, Sigma) and sampled for gill, liver, and gut, which were immediately frozen in liquid N2 for further analysis of Cu burden, gene expression, and enzyme activity.

2009-09-01 | E-MEXP-2288 | biostudies-arrayexpress

Sebastes melanops array 5K v1

Project description:We used a reference design with a dye swap. We used 6 experimental probes grouped by treatment and sample day. "Treatment" fish consisted of rockfish exposed to forced decompression resulting in barotrauma, followed by subsequent recompression to their original depth. Control fish did not experience forced decompression. Fish were sampled at day 3, day 15 and day 31 post-decompression.

2012-01-02 | E-MEXP-3087 | biostudies-arrayexpress

Transcriptional Regulation in Testis Associated with Developmental and Reproductive Effects in Male Zebrafish Exposed to Natural Mixtures of Persistent Organic Pollutants from Mjosa Lake

Project description:Transcriptional Regulation in Testis Associated with Developmental and Reproductive Effects in Male Zebrafish Exposed to Natural Mixtures of Persistent Organic Pollutants from Mjosa Lake

2011-01-19 | E-MEXP-3061 | biostudies-arrayexpress

Transcriptional Regulation in liver Associated with Developmental and Reproductive Effects in Female Zebrafish Exposed to Natural Mixtures of Persistent Organic Pollutants from Lake Mjosa

Project description:Transcriptional Regulation in liver and ovary associated with developmental and reproductive effects in female Zebrafish exposed to natural mixtures of persistent organic pollutants from Lake Mjosa or Lake Losna

2011-01-19 | E-MEXP-3062 | biostudies-arrayexpress

Transcription profiling of zebra fish liver after water-borne exposure to polycyclic aromatic hydrocarbons and alkylphenols

Project description:Effect of 5.4 ppm polycyclic aromatic hydrocarbons (PAHs) and 18.2 ppm alkylphenols (APs) on gene expression in adult Zebrafish (Danio rerio) liver after 1 and 7 weeks of water-borne exposure.

2008-12-11 | E-MEXP-1685 | biostudies-arrayexpress

Gene expression profiles after infection of zebrafish with Spring Viremia Carp Virus (SVCV)

Project description:We describe here transcripts induced after infection of zebrafish with Spring Viremia Carp Virus (SVCV). Two days after infection, differentially expressed transcript levels from selected immune-related zebrafish genes were studied in internal organs (pooled spleen, head kidney). Also, transcripts from resistant fishes to viral infection one month after inoculation were studied. Three different experiments were performed to get three biological replicates. Fishes were divided into two groups in each experiment. First group was infected by immersion with SVCV 10^7 pfu/ml, second group was used as a control of non-infected fishes. 6 fishes per group were sacrificed two days post infection, whereas the rest of the infected fishes from the three experiments were maintained for 30 days in the aquariums and then survivors (six for experiment) were sacrificed. This submission includes three biological replicate groups for the non-infected fish and the two days post-infected fish, and two biological replicate groups for the 30 days post-infected fish.

2013-11-04 | E-GEOD-42263 | biostudies-arrayexpress

Gene expression profile after Spring Viraemia Carpae Virus (SVCV) infection in zebrafish mutants rag1 -/- versus wt

Project description:Immune responses in higher vertebrates are classically separated into innate and adaptive (or specific) immunity. However, important gaps of knowledge about how adaptive responses are generated in lower vertebrates still remain unsolved. In order to explore the relative importance of adaptive and innate immune responses, we have studied zebrafish transcriptional responses to an infection with the Spring Viraemia of Carp virus (SVCV) in rag1-/- zebrafish mutants compared to wild type zebrafish by using both genome wide and immunological-targeted gene expression microarrays. Both wild type (wt) and mutant (rag1) zebrafish were divided in two groups with 3 individuals per group. First group was infected with 10^5 pfu per ml of SVCV, second group was mock-infected. Two days after challenge zebrafish were sampled, head kidney and spleen of each fish were extracted and pooled between each group. The experiment was repeated once to obtain two biological replicates.

2015-05-10 | E-GEOD-54096 | biostudies-arrayexpress

Transcription profiling of dorsal epaxial fast muscle from zebra fish at developmental stages where myotubes are still actively recruited (M+ stage) and where myotube production has ceased (M- stage)

Project description:Embryonic temperature modulates muscle fibre number in adult zebrafish: genome-wide changes in microRNA and mRNA expression and predicted miRNA-mRNA regulatory networks involved in the transition from hyperplastic to hypertrophic growth phenotypes.

2009-01-01 | E-TABM-552 | biostudies-arrayexpress

Transcription profiling by array of Danio rerio fast skeletal muscle from fish fed a single satiating meal

Project description:The F5 generation of a wild-caught population of zebrafish (Danio rerio) from Mymensingh, Bangladesh, were used in this study. Replicate experiments were carried out with adult male fish aged 9 months. Each group was maintained in a 50L tank at 27M-11.5M-:C and 12:12h dark:light photoperiod and fed bloodworms (Ocean NutritionM-^Y, Belgium) to satiety for one week. The experimental protocol involved fasting fish for 7 days and subsequent refeeding a single meal of bloodworms delivered over a 3h period, after which any uneaten food was removed from the tank. Seven fish were sampled at -156, -24, 0 (prior to the meal), 0.75, 3, 6, 7.5, 9, 11, 24, 36h and killed humanely by an overdose of ethyl 3-aminobenzoate methanesulfonate salt (MS-222). Six samples from the 0, 3, and 6h time-points were used in the microarray hybridization.

2011-03-11 | E-MEXP-2887 | biostudies-arrayexpress

Transcription profiling of Atlantic salmon gill epithelium from three different stocks migrating from freshwater river to lake (Saimaa stock, SS), brackish water (Neva stock, NS) or seawater (Teno stock, TS) were compared at three successive developmental stages (parr, smolt and postsmolt)

Project description:Transcripts of the gill epithelium from three different stocks of Atlantic salmon (Salmo salar) migrating from freshwater river to lake (Saimaa stock, SS), brackish water (Neva stock, NS) or seawater (Teno stock, TS) were compared at three successive developmental stages (parr, smolt and postsmolt) using the 16K GRASP cDNA microarray platform.

2010-06-01 | E-MEXP-2210 | 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