Ontology highlight
ABSTRACT:
PROVIDER: PRJNA562168 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:An European eel-specific microarray platform was developed to identify genes involved in response to pollutants. A comparative analysis of gene expression was conducted between European eel Anguilla anguilla individuals from lowly-polluted Wijmeers pond at Uitbergen (Belgium), highly-polluted Hazewinkel pond at Willebroek (Belgium), extremely-polluted Dessel-Schotel canal at the locations of Schotel (Belgium) and low polluted Bolsena lake (Italy) environments.
2013-05-22 | GSE41240 | GEO
Project description:An European eel-specific microarray platform was developed to identify genes involved in response to pollutants. A comparative analysis of gene expression was conducted between European eel Anguilla anguilla individuals from lowly-polluted Wijmeers pond at Uitbergen (Belgium), highly-polluted Hazewinkel pond at Willebroek (Belgium), extremely-polluted Dessel-Schotel canal at the locations of Schotel (Belgium) and low polluted Bolsena lake (Italy) environments. A comparative analysis of gene expression was conducted between European eel Anguilla anguilla individuals from lowly-polluted Wijmeers pond at Uitbergen (Belgium), highly-polluted Hazewinkel pond at Willebroek (Belgium), extremely-polluted Dessel-Schotel canal at the locations of Schotel (Belgium) and low polluted Bolsena lake (Italy) environments. Gene expression profiling was performed using an European eel-specific oligo-DNA microarray (GPL15124) of 14,913 probes based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.
2013-05-22 | E-GEOD-41240 | biostudies-arrayexpress
Project description:An European eel-specific microarray platform was developed to identify genes involved in response to pollutants A comparative analysis of gene expression was conducted between European eel Anguilla anguilla individuals from high (Tiber river, Italy) and low pollution (Bolsena lake, Italy) environments. Gene expression profiling was performed using an European eel-specific oligo-DNA microarray of 14,913 probes based on single-colour detection (Cyanine-3 only). Microarrays were scanned with Agilent scanner G2565BA (barcode on the left, DNA on the back surface, scanned through the glass) at a resolution of 5 microns; all slides were scanned twice at two different sensitivity settings (XDRHi 100% and XDRLo 10%); the scanner software created a unique ID for each pair of XDR scans and saved it to both scan image files. Feature Extraction (FE) 9.5 used XDR ID to link the pairs of scans together automatically when extracting data. The signal left after all the FE processing steps have been completed is ProcessedSignal that contains the Multiplicatively Detrended, Background-Subtracted Signal.
2013-05-22 | E-GEOD-35055 | biostudies-arrayexpress
Project description:We investigated salinity adaptation during the migration from freshwater to seawater of European eel (Anguilla anguilla) by examining the hypothesis that: The brain is the central organ for the co-ordination of environmental cues (day length, photoperiod, temperature and environmental salinity) with the anatomical and physiological adaptations which accompany pre-migrational morphogenesis and the osmoregulatory plasticity seen in post-migrational, salinity-adapted fish. We have characertised the mRNA expression profiles for the brains of fresh water and sea water adapted silver eel using a highly representative brain cDNA microarray. The array comprises 5760 cDNA clones from A.anguilla ranging from 0.5 -10 kb and an estimated redundancy of > 5 %.
2008-12-31 | E-MAXD-29 | biostudies-arrayexpress
Project description:Anguilla anguilla (European eel) genome, fAngAng1, alternate haplotype
| PRJNA561984 | ENA
Project description:Anguilla anguilla (European eel) genome, fAngAng1, primary haplotype
| PRJNA561979 | ENA
Project description:Ecotoxicogenomic studies face the problem of the lack of gene sequence information available for toxicologically relevant non-model pollution sentinel species. In this sense, next generation sequencing technologies allow obtaining deep de novo sequence information cost-effectively. We have thus employed the platform GS-FLX of Roche technologies, in order to sequence the multitissue transcriptome of a fish species under severe population decline, the European eel (Anguilla anguilla), using normalized cDNA (Evrogen). The European eel could be successfully employed in pollution biomonitoring studies as it is a euryhaline teleost that is quite resistant to chemical exposure. We have completed a one whole plate sequencing-run using the Titanium kit of Roche from which a total of 7.8x105 reads were obtained with a length average of 303.53 bp. Annotated genes, for instance, could be further assessed as biomarkers of exposure to specific chemical compounds in marine, estuarine and river waters. Designed tool will be thus useful, in the study of: a.- the mode of action of chemical compounds in active monitoring studies using caged eels, b.- the physiological processes that are specific to freshwater eels such as the one of sexual development and reproduction, c.- reasons that could explain the disappearance of the species from European waters. In the first context, a caging experiment was performed to measure the putative effects of a paper industry effluent on eel hepatic transcription levels. For this purpose, eels were caged upstream and downstream to the SMURFFIT-KAPPA paper industry in Iurreta (Biscay, Basque Country). Thus, hepatic transcription profiles reflect the stress levels suffered by eels.
2016-07-31 | GSE53345 | GEO
Project description:Ecotoxicogenomic studies face the problem of the lack of gene sequence information available for toxicologically relevant non-model pollution sentinel species. In this sense, next generation sequencing technologies allow obtaining deep de novo sequence information cost-effectively. We have thus employed the platform GS-FLX of Roche technologies, in order to sequence the multitissue transcriptome of a fish species under severe population decline, the European eel (Anguilla anguilla), using normalized cDNA (Evrogen). The European eel could be successfully employed in pollution biomonitoring studies as it is a euryhaline teleost that is quite resistant to chemical exposure. We have completed a one whole plate sequencing-run using the Titanium kit of Roche from which a total of 7.8x105 reads were obtained with a length average of 303.53 bp. Annotated genes, for instance, could be further assessed as biomarkers of exposure to specific chemical compounds in marine, estuarine and river waters. Designed tool will be thus useful, in the study of: a.- the mode of action of chemical compounds in active monitoring studies using caged eels, b.- the physiological processes that are specific to freshwater eels such as the one of sexual development and reproduction, c.- reasons that could explain the disappearance of the species from European waters. In the first context, a caging experiment was performed to measure the putative effects of a paper industry effluent on eel hepatic transcription levels. For this purpose, eels were caged upstream and downstream to the SMURFFIT-KAPPA paper industry in Iurreta (Biscay, Basque Country). Thus, hepatic transcription profiles reflect the stress levels suffered by eels. The experiment contains a time serial sampling: T0 = before sampling; T1 = after 3 days of exposure; T2=after 15 days of exposure. In addition, caged eels were placed in 2 sites, Upstream (Up) and Downstream (Do) of the hotspot. 6 samples were dissected per sampling group (5 groups= ToUP; T1UP; T1Do; T2Up; T2Do), 30 samples in total
2016-07-31 | E-GEOD-53345 | biostudies-arrayexpress
Project description:Since the early 1980s, the population of European eels (Anguilla anguilla) has dramatically declined. Nowadays, the European eel is listed on the red list of threatened species (IUCN Red List) and is considered as critically endangered of extinction. Pollution is one of the explanations of the collapse of this species. Among their possible effects, pollutants gradually accumulated in eels during their somatic growth phase (yellow eel stage) would be remobilized during their reproductive migration leading to potential toxic events in gonads. The aim of this study was to investigate the potential effect of pollution on the gonad development of wild female silver eels. Female silver eels from two sites with differing contamination levels were artificially matured. Transcriptomic analyses by means of a 1000 candidate gene cDNA microarray were performed on gonads after 11 weeks of maturation. The results showed that the transcription levels of several genes that were associated to the gonadosomatic index (GSI) were involved in mitotic cell division but also in spermatogenesis. Genes associated to pollution were mainly involved in the mechanisms of protection against oxidative stress, in DNA repair, in the purinergic signaling pathway and in steroidogenesis, suggesting an impairment of gonad development in eels from the polluted site. This was in agreement with the fact that eels from the reference site showed a higher gonad growth in comparison to contaminated fish.
2015-01-01 | GSE64278 | GEO