Ontology highlight
ABSTRACT:
PROVIDER: PRJNA562167 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR25708943_1.fastq.gz | Fastqsanger.gz | |||
| SRR25708943_2.fastq.gz | Fastqsanger.gz | |||
| SRR25708944_1.fastq.gz | Fastqsanger.gz | |||
| SRR25708944_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 34 |
Similar Datasets
Project description:Anableps anableps (Largescale four-eyed fish) genome, fAnaAna1, primary haplotype
| PRJNA561985 | ENA
Project description:Anableps anableps (Largescale four-eyed fish) genome, fAnaAna1, alternate haplotype
| PRJNA561986 | ENA
Project description:Toxic compounds such as organochlorine pesticides (OCs), polychlorinated biphenyls (PCBs), and polybrominated diphenyl ether flame retardants (PBDEs) have been detected in fish, birds, and aquatic mammals that live in the Columbia River or use the river as a food source. We developed a custom microarray for largescale suckers (Catostomus macrocheilus) and used it to investigate the molecular effects of contaminant exposure on wild fish in the Columbia River. Using Significance Analysis of Microarrays (SAM) we identified 72 probes representing 69 unique genes with expression patterns that correlated with hepatic tissue levels of OCs, PCBs, or PBDEs. These genes were involved in many biological processes previously shown to respond to contaminant exposure, including drug and lipid metabolism, apoptosis, cellular transport, oxidative stress, and cellular chaperone function. The relation between gene expression and contaminant burden suggests that these genes may respond to environmental contaminant exposure and are promising candidates for further field and laboratory studies to develop biomarkers for monitoring exposure of wild fish to contaminant mixtures found in the Columbia River Basin Correlation between contaminant exposure and gene expression profiles of wild largescale suckers collected from three different sites in the Columbia River. At each site, liver samples of six to eight different fish were analyzed using microarrays.
2013-12-04 | E-GEOD-41016 | biostudies-arrayexpress
Project description:During early stages of development, juvenile fish must rely on their innate immune system to defend against pathogens. At these early stages, the immune system is immature and is unlikely to express the full repertoire of genes that control defences. Although vulnerable, these larval fish can still fight of infections, indicating there are active defence mechanisms. Using rainbow trout as a model, we have taken a transcriptomics approach to determine the antibacterial (Aeromonas salmonicida) and antiviral (VHSV) responses to infection at four early life history stages, eyed egg, post-hatch, first feeding and three weeks post-first feeding. We performed microarray analysis using an Agilent 4x44K custom designed array, using a common RNA reference hybridization design. We show that all stages of the developing fish respond to the disease challenge at 3 days post-challenge, but the number and complexity of the response increases with developmental stage. Specifically, the response to virus at eyed egg and hatch stages does not show the full interferon response as is found at first feeding and 3 weeks post-first feeding. The experiments were carried out with a custom-designed Agilent (Agilent design ID: 028918) oligonucleotide microarray (A-MEXP-2315) named Trout_imm_v1. In total, 46 hybridisations were performed on individual animals, with 4 biological replicates per sampling point (apart from Bacteria infected eyed eggs for which two hybridizations were not used). This work was funded by the European Community’s seventh framework programme (FP7/2007-2013), under grant agreement no. 222719 (LIFECYCLE).
2016-03-03 | E-MTAB-3401 | biostudies-arrayexpress
Project description:Anableps anableps isolate:Para Raw sequence reads
| PRJNA369037 | ENA
Project description:Toxic compounds such as organochlorine pesticides (OCs), polychlorinated biphenyls (PCBs), and polybrominated diphenyl ether flame retardants (PBDEs) have been detected in fish, birds, and aquatic mammals that live in the Columbia River or use the river as a food source. We developed a custom microarray for largescale suckers (Catostomus macrocheilus) and used it to investigate the molecular effects of contaminant exposure on wild fish in the Columbia River. Using Significance Analysis of Microarrays (SAM) we identified 72 probes representing 69 unique genes with expression patterns that correlated with hepatic tissue levels of OCs, PCBs, or PBDEs. These genes were involved in many biological processes previously shown to respond to contaminant exposure, including drug and lipid metabolism, apoptosis, cellular transport, oxidative stress, and cellular chaperone function. The relation between gene expression and contaminant burden suggests that these genes may respond to environmental contaminant exposure and are promising candidates for further field and laboratory studies to develop biomarkers for monitoring exposure of wild fish to contaminant mixtures found in the Columbia River Basin
2013-12-04 | GSE41016 | GEO