An European eel-specific microarray platform was developed to identify genes involved in response to pollutants
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ABSTRACT:
ORGANISM(S): Anguilla anguilla
PROVIDER: GSE41240 | GEO | 2013/05/22
SECONDARY ACCESSION(S): PRJNA176301
REPOSITORIES: GEO
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. 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:Gene expression analyses have been performed on brain, liver and muscle of eels (Anguilla anguilla) sampled in three different segment of the Canal des Etangs ( artificial canal linking Arcachon Basin and Lacanau Lake). The present study relies on intraspecific differences of glass eels encountered below and above the water dams. Eels were collected using electric fishing under similar climatic and hydrological conditions. Individuals were sampled below the obstacle, close to the fishway entry in segment 1 (Pas du Bouc; +44° 50' 27.95, -1° 9' 8.09) and 2 (Langouarde, +44° 51' 32.92, -1° 9' 5.03). Fish from the segment 3 (Joncru; +44° 52' 57.13, -1° 8' 11.70) were sampled on the fishway, as water depth before the obstacle, approximately 2 meters, precluded the use of electro-fishing technique. Ten individuals were selected from each site according to their body size (between 83 and 155 mm) and health status (no externally visible pathogens) criteria. Internal parasites such as Anguilicola crassus were taken into account. Sampled and selected fish were immediately sacrified by decapitation and the whole brain, liver and muscle tissue (posterior bottom body part) were dissected and stored at -80°C in separate tubes with RNAlater buffer (Quiagen) for gene expression analysis. Microarray analysis was conducted using an European eel-specific array consisting of a total of 14,913 probes based on a large collection of high-throughput transcriptomic sequences (Pujolar et al. 2012). Probe sequences and further details on the microarray platform can be found on the GEO database under accession number GPL15124.
2014-11-20 | GSE56040 | GEO
Project description:Gene expression analyses have been performed on brain, liver and muscle of eels (Anguilla anguilla) sampled in three different segment of the Canal des Etangs ( artificial canal linking Arcachon Basin and Lacanau Lake). The present study relies on intraspecific differences of glass eels encountered below and above the water dams. Eels were collected using electric fishing under similar climatic and hydrological conditions. Individuals were sampled below the obstacle, close to the fishway entry in segment 1 (Pas du Bouc; +44° 50' 27.95, -1° 9' 8.09) and 2 (Langouarde, +44° 51' 32.92, -1° 9' 5.03). Fish from the segment 3 (Joncru; +44° 52' 57.13, -1° 8' 11.70) were sampled on the fishway, as water depth before the obstacle, approximately 2 meters, precluded the use of electro-fishing technique. Ten individuals were selected from each site according to their body size (between 83 and 155 mm) and health status (no externally visible pathogens) criteria. Internal parasites such as Anguilicola crassus were taken into account. Sampled and selected fish were immediately sacrified by decapitation and the whole brain, liver and muscle tissue (posterior bottom body part) were dissected and stored at -80°C in separate tubes with RNAlater buffer (Quiagen) for gene expression analysis. Microarray analysis was conducted using an European eel-specific array consisting of a total of 14,913 probes based on a large collection of high-throughput transcriptomic sequences (Pujolar et al. 2012). Probe sequences and further details on the microarray platform can be found on the GEO database under accession number GPL15124. A comparative analysis of gene expression was conducted between eels sampled in differents segments of Canal des Etangs. Total RNAs were extracted from the whole liver,muscle and brain using the Absolutely RNA RT-PCR Miniprep kit (Agilent) according to the manufacturer’s instructions. Three independent RNA pools, each consisting of three individuals RNA samples, were prepared for each sampling site and tissues. Due to technical problems, it was no possible to perform microarray analyses in muscle of eels sampled in forebay 3. Accordingly, DNA microarray analysis has been performed in a total of 24 pools. RNAs’ quality was evaluated by electrophoresis on a 1% agarose gel and their concentrations were determined by spectrophotometry. Total RNA was stored in RNAse free water at -80° C. Sample labelling and hybridization were conducted following the details in Pujolar et al. (2012). Hybridized slides were scanned at 5 µm resolution using an Agilent DNA microarray scanner. Slides were scanned at two different sensitivity levels (XDR Hi 100% and XDR Lo 10%) and the two linked images generated were analysed together. Data were extracted and background subtracted using the standard procedure in Agilent Feature Extraction (FE) software v. 9.5.1. Data were normalized separately for each tissue using a quantile normalization procedure using R (http://www.r-project.org).
2014-11-20 | E-GEOD-56040 | 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
Project description:Diet assessment of European eel (Anguilla anguilla) leptocephali in the Sargasso Sea
| PRJEB20115 | ENA
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:The goal of this study was to gain a better understanding of the genetic background of gonadal maturation of the European eel and to use gene expression profiles to identify predictive markers for broodstock selection that can be measured in blood samples. To find leads for maturation markers we performed a pilot deep-sequencing transcriptome analysis of ovarian tissue derived from a yellow eel, a prepubertal silver eel and a post-spawning matured eel. Among the best leads were two key players in steroidogenesis, namely pP450c17 and liver receptor homolog-1.
2015-06-30 | GSE70381 | GEO
Project description:In spite of many decades of research, the spawning migration of the European eel Anguilla anguilla from the European coast to the Sargasso Sea remains a mystery. In particular, the role of the swimbladder as a buoyancy regulating structure is not yet understood. In this study, we exercised silver eels in a swim tunnel under elevated hydrostatic pressure. The transcriptome of gas gland tissue of these exercised eels was then compared to the known transcriptome of not exercised (control) silver eel gas gland cells. Due to the high infection rate of the eel population with the swimbladder parasite Anguillicola crassus, the comparison also included an exercised group of silver eels with a heavily damaged swimbladder, and we compared the previously published transcriptome of not exercised silver eels with a highly damaged swimbladder with the exercised group of silver eels with a heavily damaged swimbladder. The comparisons of unexercised (control) silver eels with exercised silver eels with functional swimbladder (EF), as well as with exercised silver eels with damaged swimbladder(ED), both showed a significant elevation in transcripts related to glycolytic enzymes. This could also be observed within the comparison of unexercised silver eels with a highly infected swimbladder with exercised eels with a damaged swimbladder (DED). In contrast to EF, in ED a significant elevation in transcript numbers of mitochondrial NADH dehydrogenase was observed. While in EF the transcriptional changes suggested that acid production and secretion was enhanced, in ED these changes appeared to be related to thickened tissue and thus elevated diffusion distances. The remarkable number of differentially expressed transcripts coding for proteins connected to cAMP-dependent signaling pathways indicated that metabolic control in gas gland cells includes cAMP-dependent pathways. In contrast to ED, in EF significant transcriptional changes could be related to the reconstruction of the extracellular matrix, while in ED tissue repair and inflammation was more pronounced. Surprisingly, in exercised eels hypoxia inducible transcription factor expression was elevated. In EF, a large number of genes related to the circadian clock were transcriptionally modified, which may be connected to the circadian vertical migrations observed during the spawning migration.
2020-09-14 | GSE150340 | GEO