Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19226712_1.fastq.gz | Fastqsanger.gz | |||
| SRR19226712_2.fastq.gz | Fastqsanger.gz | |||
| SRR19226713_1.fastq.gz | Fastqsanger.gz | |||
| SRR19226713_2.fastq.gz | Fastqsanger.gz | |||
| SRR19226714_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:a salmonid microarray was used to characterize environmentally-regulated shifts in gene expression between ocean and river habitats in gill and liver tissues of wild migrating adult Pacific sockeye salmon (Oncorhynchus nerka). To correlate gene expression with survival, non-lethal biopsy sampling of gill tissue and microarray-based profiling was combined with biotelemetry and genetic stock identification so that transcriptomic profiles could be compared between fish reaching spawning grounds and presumed mortalities. Fish were captured fish at two marine sampling sites, one within Johnstone Strait (JS), BC. Canada and one within Juan De Fuca Strait (JDFS), BC Canada. Ocean sites were contrasted to fish sampled within the Fraser River at Whonnock (W), BC, Canada. Gill and liver tissues were dissected at each of these sites. Non-lethal biopsy sampling was performed on migrating sockeye salmon intercepted within the Fraser River at Mission, BC, Canada and genetically-based stock ID was used to determine the stock-specific spawning grounds for each fish, giving an intended end-point of migration for each of the stocks investigated in this study.Gene expression levels were determined by comparing the amount of mRNA transcript in the experimental samples relative to a reference sample. A total of 123 microarrays were used to generate the dataset, corresponding to individual hybridizations of both gill and liver samples collected from JS (gill n=14; liver n=15), JDFS (gill n=15; liver n=13), W (gill n=11; liver n=10), and biopsy sampled gill tissue collected at Mission (n=45).Total RNA was amplified (1 round) with MessageAmpTMII-96 kit (Ambion, TX, USA), and reverse transcribed to cDNA before labelling with ALEXA dyes using the Invitrogen Indirect Labelling Kit. The reference contained the combined aRNA of all individuals used in the experiment, excluding bioposy sampled fish. Individual samples were labelled with Alexa 555 and the reference control with Alexa 647, and no dye swaps were perfromed.
2011-06-12 | E-GEOD-22346 | biostudies-arrayexpress
Project description:a salmonid microarray was used to characterize environmentally-regulated shifts in gene expression between ocean and river habitats in gill and liver tissues of wild migrating adult Pacific sockeye salmon (Oncorhynchus nerka). To correlate gene expression with survival, non-lethal biopsy sampling of gill tissue and microarray-based profiling was combined with biotelemetry and genetic stock identification so that transcriptomic profiles could be compared between fish reaching spawning grounds and presumed mortalities.
2011-06-12 | GSE22346 | GEO
Project description:In fish, the sex determining mechanisms can broadly be classified as genotypic (GSD), temperature-dependent (TSD), or genotypic plus temperature effects (GSD+TE). For the fish species with TSD or GSD+TE, extremely high or low temperature can affect its sex determination and differentiation. For long time, the underlying changes in DNA methylation that occur during high or low temperature induced sex reversal have not been fully clarified. In this study, we used Nile tilapia as a model to perform a genome-wide survey of differences in DNA methylation in female and male gonads between control and high temperature induced groups using methylated DNA immunoprecipitation (MeDIP). We identified the high temperature induction-related differentially methylated regions (DMRs), and performed functional enrichment analysis for genes exhibiting DMR. These identified differentially methylated genes were potentially involved in the connection between environmental temperature and sex reversal in Nile tilapia. In this study, four samples (control females, CF; control males, CM; induced females, IF; induced males, IM) were analyzed.
2015-08-27 | E-GEOD-72386 | biostudies-arrayexpress
Project description:Wild-type and isogenic H3K37R yeast cultures were grown in medium containing 2% raffinose as carbone source. Cells were synchronized in G1 with alpha factor. To half culture (100ml), glucose (2% final concentration) and 1.3ml BrdU (50mg/ml stock) and 1.3ml BrdU (50mg/ml stock) was added. To the other half, galactose (2% final concentration) and 1.3ml BrdU (50mg/ml stock). Both flasks were incubated for further 30min at 30C, then cell were collected by centrifugation and resuspended into 100ml of 30C warmed YPA-2%Glucose or YPA-2%Galactose medium containing 25ml HU (2M stock) plus 1.2 ml BrdU (50mg/ml stock) and incubated for 1 hour and 10minutes. YPA-Glucose and YPA-Galactose cultures were immediately transferred to ice/water bath and replication was stopped by addition of NaN3 and cells were processed for DNA immunoprecipitation with anti BrdU antibody.
2021-04-30 | E-MTAB-9999 | biostudies-arrayexpress
Project description:Genoe survey sequencing of fish louse Argulus japonicus
| PRJDB10088 | ENA
Project description:We report the application of Solexa/IlluminaM-bM-^@M-^Ys RNA-seq sequencing approaches for transcriptome in a marine fish under different conditions (bacterial- and mock-challenged conditions). By obtaining over four billion bases of sequence from the cDNA, we generated 169,950 none-redundant consensus sequences, from which 44842 functional transcripts with complete or various length of encoding regions were identified. More than 52% of these transcripts could be enriched in approximately 219 known metabolic or signaling pathways, among of which 2673 transcripts were found to be associated with immune-relevant genes. Besides, about 8% of the transcripts seemed fish-specific genes that have never been described before. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations. Our study provided a global survey of the gene activities in host defense against bacterial infection in a non-model marine fish. Examination of different transcriptome in baterial- and mock challenged fish.
2012-08-09 | E-GEOD-21721 | biostudies-arrayexpress
Project description:A large-scale functional genomics study revealed shifting energy generating processes in white muscle during the final 1,300 km migration of wild sockeye salmon to their spawning grounds in the Fraser River, British Columbia. In 2006, Lower Adams stock sockeye salmon ceased feeding after passing the Queen Charlotte Islands, 850 km from the Fraser River. Enhanced protein turnover and reduced transcription of actin, muscle contractile and heme-related proteins were early starvation responses in saltwater. Arrival to the estuarine environment triggered massive protein turnover through induction of proteasoma and lysosomal proteolysis and protein biosynthesis, and a shift from anaerobic glycolysis to oxidative phosphorylation. Response to entry into freshwater was modest, with up-regulation of heat shock proteins and nitric oxide biosynthesis. High river temperatures resulted in a strong defense/immune response and high mortalities in 50% of fish. Arrival to the spawning grounds triggered further up-regulation of oxidative phosphorylation and proteolysis, down-regulation of protein biosynthesis and helicase activity, and continued down-regulation of muscle proteins and most glycolytic enzymes. However, sharp up-regulation of PFK-I indicated induction of glycolytic potential at the spawning grounds. The identification of potential environmental cues triggering genome-wide transcriptional shifts in white muscle associated with migration and the strong activation of proteasomal proteolysis were both novel findings. Keywords: Functional genomics study on wild-caught fish The experiment was based on expression profiles of white muscle tissue collected from wild migrating adult sockeye salmon during their return spawning migration back to the Fraser River. Fish were collected from seven sites along the final 1,300 km migration path, and white muscle samples were quickly frozen in liquid nitrogen upon capture. Marine sampling sites included (from north to south) the Queen Charlotte Islands (QCI), Johnstone Strait (JS), Juan de Fuca Strait (JDFS), and the Strait of Georgia (SOG). Freshwater sampling sites included Whonnock (W), Savona (SV) and the Lower Adams Spawning Grounds. Genetically-based stock ID was used to identify the natal sites of fish collected from the wild. The experiment was designed to profile the transcriptional shifts associated with migration of the Adams River stock complex. The total experiment included 80 microarray slides, with a minimum biological replicate size per site of 6 (SV), and maximum of 18 (JS) (see supplemental table for details). Additional intra-site variables, which could only be addressed in some sites, included sex (female biased) and river entry timing (for JS, JDFS and W sites; identified through radio-tracking of marine collected fish). Total RNA was amplified (1 round) with MessageAmpTMII-96 kit (Ambion, TX, USA), and reverse transcribed to cDNA before labelling with ALEXA dyes using the Invitrogen Indirect Labelling Kit. The experiment was based on a reference design, with the reference containing the combined aRNA of all individuals used in the experiment. Individual samples were labelled with Alexa 555 and the reference control with Alexa 647, with no dye flips included. A single technical replicate of one SV fish (replicate 5) was included in the experimental design. This experiment is part of a larger white muscle experiment containing additional sockeye salmon stocks.
2010-05-15 | E-GEOD-13657 | biostudies-arrayexpress
Project description:We report the application of Solexa/Illumina’s RNA-seq sequencing approaches for transcriptome in a marine fish under different conditions (bacterial- and mock-challenged conditions). By obtaining over four billion bases of sequence from the cDNA, we generated 169,950 none-redundant consensus sequences, from which 44842 functional transcripts with complete or various length of encoding regions were identified. More than 52% of these transcripts could be enriched in approximately 219 known metabolic or signaling pathways, among of which 2673 transcripts were found to be associated with immune-relevant genes. Besides, about 8% of the transcripts seemed fish-specific genes that have never been described before. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations. Our study provided a global survey of the gene activities in host defense against bacterial infection in a non-model marine fish.
2012-08-09 | GSE21721 | GEO