Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1196326 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR31663815_1.fastq.gz | Fastqsanger.gz | |||
| SRR31663815_2.fastq.gz | Fastqsanger.gz | |||
| SRR31663816_1.fastq.gz | Fastqsanger.gz | |||
| SRR31663816_2.fastq.gz | Fastqsanger.gz | |||
| SRR31663817_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 12 |
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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: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:The comparision between gradual ocean acidification (GC) and one way ocean acidification (HC) of physiological and molecular responses on diatom Skeletonema costatum
2025-01-01 | GSE253819 | GEO
Project description:Sequencing the metatranscriptome can provide information about the response of organisms to varying environmental conditions. We present a methodology for obtaining random whole-community mRNA from a complex microbial assemblage using Pyrosequencing. The metatranscriptome had, with minimum contamination by ribosomal RNA, significant coverage of abundant transcripts, and included significantly more potentially novel proteins than in the metagenome. Keywords: metatranscriptome, mesocosm, ocean acidification This experiment is part of a much larger experiment. We have produced 4 454 metatranscriptomic datasets and 6 454 metagenomic datasets. These were derived from 4 samples. The experiment is an ocean acidification mesocosm set up in a Norwegian Fjord in 2006. We suspended 6 bags containing 11,000 L of sea water in a Coastal Fjord and then we bubbled CO2 through three of these bags to simulate ocean acidification conditions in the year 2100. The other three bags were bubbled with air. We then induced a phytoplankton bloom in all six bags and took measurements and performed analyses of phytoplankton, bacterioplankton and physiochemical characteristics over a 22 day period. We took water samples from the peak of the phytoplankton bloom and following the decline of the phytoplankton bloom to analyses using 454 metagenomics and 454 metatranscriptomics. Day 1, High CO2 Bag and Day 1, Present Day Bag, refer to the metatranscriptomes from the peak of the bloom. Day 2, High CO2 Bag and Day 2, Present Day Bag, refer to the metatranscriptomes following the decline of the bloom. Obviously High CO2 refers to the ocean acidification mesocosm and Present Day refers to the control mesocosm. Raw data for both the metagenomic and metatranscriptomic components are available at NCBI's Short Read Archive at ftp://ftp.ncbi.nlm.nih.gov/sra/Studies/SRP000/SRP000101
2008-02-08 | E-GEOD-10119 | biostudies-arrayexpress
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:Coastal upwelling regions are among the most productive marine ecosystems but may be threatened by amplified ocean acidification. Increased acidification is hypothesized to reduce iron bioavailability for phytoplankton thereby expanding iron limitation and impacting primary production. Here we show from community to molecular levels that phytoplankton in an upwelling region respond to short-term acidification exposure with iron uptake pathways and strategies that reduce cellular iron demand. A combined physiological and multi-omics approach was applied to trace metal clean incubations that introduced 1200 ppm CO2 for up to four days. Although variable, molecular-level responses indicate a prioritization of iron uptake pathways that are less hindered by acidification and reductions in iron utilization. Growth, nutrient uptake, and community compositions remained largely unaffected suggesting that these mechanisms may confer short-term resistance to acidification; however, we speculate that cellular iron demand is only temporarily satisfied, and longer-term acidification exposure without increased iron inputs may result in increased iron stress.
2023-11-14 | PXD038549 | Pride
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:In this research we present a transcriptomics analysis of the physiological response of a marine calcifier, Strongylocentrotus purpuratus, to ocean acidification, a decline in ocean pH that results from the absorption of anthropogenic carbon dioxide (CO2). Larvae were raised from fertilization to prism stage in seawater with elevated CO2 conditions based upon IPCC emissions scenario B1 (540ppm CO2) and A1FI (1020ppm CO2).
2009-08-14 | GSE13777 | GEO