Ontology highlight
ABSTRACT:
PROVIDER: PRJNA747057 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15179200_1.fastq.gz | Fastqsanger.gz | |||
| SRR15179200_2.fastq.gz | Fastqsanger.gz | |||
| SRR15179201_1.fastq.gz | Fastqsanger.gz | |||
| SRR15179201_2.fastq.gz | Fastqsanger.gz | |||
| SRR15179202_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Acidification of seawater due to anthropogenic CO2, called as ocean acidification (OA), makes most coastal environments unfavorable for oysters. This is a serious socio-economical issue for China which is accounting for >70% of the world’s edible oyster supply. Understanding of OA effects at proteome level could lead to a better aquaculture management. Here, we present an iTRAQ based protein profiling analysis for the detection and quantification of proteome change under OA in one of the early life stages of a commercially important oyster species, Crassostrea hongkongensis. The completion of the genome sequence for oysters enabled us to confidently quantify over 1500 proteins in the larval oyster. Over 10% of proteome was altered in response to OA process at pH 7.6. Analysis of differentially expressed proteins and their associated pathways indicated that up-regulation of calcification, metabolic processes, cytoskeletal functions, oxidative stress and cell signaling processes might have been used by larvae to acclimate under OA. Although the expressions of cytoskeletal and signal transduction proteins were down-regulated in response to OA, there was no marked alternation in developmental processes such as metamorphic success. This study suggests that the estuarine edible oyster possess an adequate short-term adaptability or acclimation mechanism at proteome level to tolerate near-future OA scenario.
2015-10-29 | PXD002138 | Pride
Project description:In recent years, increasing levels of dissolved carbon dioxide in seawater have led to an increase of ocean acidification (OA), which constitutes a major threat to marine ecosystems. As an important economically marine bivalve, Mactra veneriformis is highly susceptible to ocean acidification. In this study, we recorded and observed the mortality rate, oxygen consumption rate and ammonia excretion rate of different shell colour groups of M. veneriformis under the stress of ocean acidification (pH=7.6), and conducted transcriptome analysis of the mantle tissues of M. veneriformis with white and purple shell colours in the acidified group (pH=7.6) and the control group (pH=8.1) under the two conditions, which showed that there was a significant difference in mortality rate between the acidified group and the control group at day 30, but there was a significant difference in mortality rate between the white colors group and the purple colors group at day 30, which was not significant. The results showed that there was a significant difference in mortality between the acidified and control groups at day 30, but the difference in mortality between the white and purple shell colour groups at day 30 was not significant. In the transcriptome analysis, fatty acid synthase gene was up-regulated in two shell colours of M. veneriformis under acidification stress, which may be a molecular compensatory mechanism to reduce the susceptibility of organisms to oxidative damage of lipids; tyrosinase gene was up-regulated, which may be a compensatory mechanism of Tyr's regulatory mechanism to the formation of shell damages under acidification; carbonic anhydrase gene was up-regulated in the purple group of M. veneriformis under acidification stress, which may be a compensatory mechanism for the acidity of M. veneriformis to cope with environmental stress; the white group of M. veneriformis under acidification stress was up-regulated. The carbonic anhydrase gene was up-regulated in the purple group under acidification stress, which may be an acidity compensation mechanism of M. veneriformis in response to the environmental stress.
2024-10-29 | GSE280202 | GEO
Project description:The filamentous diazotrophic cyanobacteria Trichodesmium spp. supply fixed nitrogen (N) to the N-depleted oligotrophic oceans where their growth is often limited by the low availability of phosphorus(P) and/or iron. Previous studies have mostly been focused on the effects of ocean acidification on Trichodesmium under nutrient sufficient or iron-limited conditions. Only a few studies have examined the impacts of ocean acidification on Trichodesmium grown at low P concentrations using non-steady-state batch cultures. Here we cultured Trichodesmium using P-limited continuous cultures (chemostat) to mimic steady-state oceanic low P condition, and used comparative NGS-derived Trichodesmium transcriptome profiling (RNA-seq) analysis to find differentially expressed genes and cellular pathways in response to acidification.
2022-10-13 | GSE181428 | GEO
Project description:Our paper presents the results of a study in which we used whole genome bisulfite sequencing (WGBS), RNA-Seq (i.e. transcriptomics), high-CO2 physiology experiments, and spatiotemporally separated samples isolated in situ (i.e. directly from the ocean) to examine the metabolic potential of genome-wide cytosine (5mC) methylation (i.e. epigenomics), its potential impacts to transcriptional dynamics under both present-day and future ocean acidification conditions, and its biogeographic conservation in the globally-significant, biogeochemically-critical marine cyanobacterium Trichodesmium.
2018-03-01 | GSE86991 | GEO
Project description:Our paper presents the results of a study in which we used whole genome bisulfite sequencing (WGBS), RNA-Seq (i.e. transcriptomics), high-CO2 physiology experiments, and spatiotemporally separated samples isolated in situ (i.e. directly from the ocean) to examine the metabolic potential of genome-wide cytosine (5mC) methylation (i.e. epigenomics), its potential impacts to transcriptional dynamics under both present-day and future ocean acidification conditions, and its biogeographic conservation in the globally-significant, biogeochemically-critical marine cyanobacterium Trichodesmium.
2018-03-01 | GSE86979 | GEO
Project description:Pacific oysters (Crassostrea gigas) were exposed to either 400 µatm (control) or 2800 µatm (ocean acidification) of pCO2 for 1 month. At the end of 1 month, half of the oysters from each pCO2 treatment were subjected to an additional mechanical stimulation. Gill (ctenidia) tissue was excised from 4 oysters from each of 4 treatments - 400 and 2800 µatm with and without mechanical stimulation. Tandem mass spectrometry was performed on all 16 samples on a LTQ Orbitrap XL with 3 technical replicates per biological sample.
2014-05-15 | PXD000835 | Pride
Project description:Increasing atmospheric CO2 raises sea surface temperatures and results in ocean acidification, which will impact upon calcifying marine organisms, such as the commercially and ecologically important Pacific oyster (Crassostrea gigas). Larval stages of development are particularly sensitive to such stressors and may represent population bottlenecks. A two-dimensional electrophoresis (2-DE) proteomic approach was used to investigate the response of 40 hour C. gigas larvae to ocean acidification and warming, and to relate protein expression to phenotypic variation in size and calcification. Larvae were reared at two pHs (8.1 and 7.9) and two temperatures (20°C and 22°C), and comparisons carried out between the four possible treatment combinations. In total 22 differentially expressed spots, corresponding to 18 proteins, were identified by nano-liquid chromatography tandem mass spectrometry. These proteins had roles in metabolism, biomineralisation, intra- and extra-cellular matrix formation and as molecular chaperones. Thirteen of these spots responded to acidification, of which 11 showed reduced expression during acidification. Declines in ATP synthase, arginine kinase and other metabolic proteins suggest metabolic depression occurred during acidification and reduced protein synthesis. In contrast, 6 of 7 proteins that were differentially expressed during warming showed increased expression. Among these were molecular chaperones including protein disulphide isomerase (PDI) and Grp78. Concurrent acidification and warming appeared to mitigate some proteomic changes and negative phenotypic effects observed in acidification at 20°C; however, differential expression of nine proteins and other temperature-independent effects on calcification phenotypes suggest that larval responses to multiple stressors will be complex.
2022-03-01 | PXD002316 | Pride
Project description:Increasing atmospheric CO2 concentrations are causing decreased pH over vast expanses of the ocean. This decreasing pH may alter biogeochemical cycling of carbon and nitrogen via the microbial process of nitrification, a key process that couples these cycles in the ocean, but which is often sensitive to acidic conditions. Recent reports indicate a decrease in oceanic nitrification rates under experimentally lowered pH. How composition and abundance of ammonia oxidizing bacteria (AOB) and archaea (AOA) assemblages respond to decreasing oceanic pH, however, is unknown. We sampled microbes from two different acidification experiments and used a combination of qPCR and functional gene microarrays for the ammonia monooxygenase gene (amoA) to assess how acidification alters the structure of ammonia oxidizer assemblages. We show that despite widely different experimental conditions, acidification consistently altered the community composition of AOB by increasing the relative abundance of taxa related to the Nitrosomonas ureae clade. In one experiment this increase was sufficient to cause an increase in the overall abundance of AOB. There were no systematic shifts in the community structure or abundance of AOA in either experiment. These different responses to acidification underscore the important role of microbial community structure in the resiliency of marine ecosystems. amoA gene diversity from two ocean acidification experiments, Monterey Bay experiment (two time points, ambient and acidified) and Vineyard Sound experiment (ambient and acifidied, with and without nutrients) examined with 2 two-color arrays (Cy3 and Cy5): the universal standard 20-mer oligo is printed to the slide with a 70-mer oligo (an archetype). Environmental DNA sequences (fluoresced with Cy3) within 15% of the 70-mer conjugated to a 20-mer oligo (fluoresced with Cy5) complementary to the universal standard will bind to the oligo probes on the array. Signal is the ratio of Cy3 to Cy5.
2013-08-27 | E-GEOD-49956 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE22171: Pacific salmon gill samples: fate tracking in river, sampled in ocean GSE22177: Pacific salmon gill samples: fate tracking in river GSE22347: Pacific salmon gill samples: fate tracking at spawning grounds Refer to individual Series
2010-12-31 | E-GEOD-22179 | biostudies-arrayexpress
Project description:ESTs in which transcription levels in oyster gill differed among sampling times after heat shock and between families with high or low survival of heat shock were identified through expression profiling of 1,675 spot pairs Keywords: comparison of families characterized by low or high survival after heat shock Oyster families were characterized by survival after heat shock, exposed to a sub-lethal heat shock, and gill was collected before and at 1, 3, 6, and 24 h afterwards. Differences among sampling times and between family types were assessed using a 2-way analysis of variance. In total, 1,675 ESTs were included in the analysis.
2009-01-12 | E-GEOD-12070 | biostudies-arrayexpress