Ontology highlight
ABSTRACT:
PROVIDER: PRJNA750310 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR15276491_1.fastq.gz | Fastqsanger.gz | |||
| SRR15276491_2.fastq.gz | Fastqsanger.gz | |||
| SRR15276492_1.fastq.gz | Fastqsanger.gz | |||
| SRR15276492_2.fastq.gz | Fastqsanger.gz | |||
| SRR15276493_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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:Pacific geoduck (Panopea generosa) clams are found along the Northeast Pacific coast where they are significant components of coastal and estuarine ecosystems and the basis of a highly profitable aquaculture industry. The Pacific coastline, however, is also the sight of rapidly changing ocean habitat, including significant reductions in pH. To better understand the physiological impact of ocean acidification on geoduck clams, we characterized for the first time the proteomic profile of this bivalve during early larval development and compared it to that of larvae exposed to low pH.Geoduck larvae wer reared at pH 7.5 (ambient) or 7.1 in a commercial shellfish hatchery from day 6 to 19 post-fertilization , and sampled at six time points for an in-depth proteomics analysis using high-resolution data dependent analysis. We found that larvae reared at low pH were smaller than those reared at ambient pH, especially in the prodissoconch II phase of development, and displayed a delay in their competency for settlement. Proteomic profiles revealed that metabolic, cell cycle, and protein turnover pathways differed between the two pH, suggesting that differing phenotypic outcomes between pH 7.5 and 7.1 are likely due to environmental disruptions to the timing of molecular physiological events. In summary, ocean acidification likely caused an energetic stress on geoduck larvae, casuing a shift in physiological prioritization.
2019-05-04 | PXD013667 | Pride
Project description:In this study we investigated how changes in pH and ocean chemistry consistent with the scenarios of the Intergovernmental Panel on Climate Change (IPCC) drive major changes in gene expression, respiration, photosynthesis and symbiosis of the coral, Acropora millepora, long before they affect biomineralization. Changes in gene expression were consistent with metabolic suppression, an increase in oxidative stress, apoptosis and symbiont loss. Other expression patterns demonstrated up-regulation of membrane transporters, as well as the regulation of genes involved in membrane cytoskeletal interactions and cytoskeletal remodeling. These widespread changes in gene expression emphasize the need to expand future studies of ocean acidification to include a wider spectrum of cellular processes, many of which may occur well before impacts on calcification. We applied a reference microarray design for the experiment outlined in the study, which was a three condition experiment of ocean acidification: control pH 8.0-8.2, medium pH 7.8-7.9 and high pH 7.6-7.7, and across three time points: time zero, day 1 and day 28. Samples from time zero and control treatments were used to generate the reference sample for the microarray hybridization experiments. A total of 27 microarrays were used in the entire experiment, 3 biological replicates per treatment and timepoint. Reference samples in each array was labeled with Cy3, and the actual experimental samples with Cy5.
2012-07-29 | E-GEOD-28697 | biostudies-arrayexpress
Project description:In this study we investigated how changes in pH and ocean chemistry consistent with the scenarios of the Intergovernmental Panel on Climate Change (IPCC) drive major changes in gene expression, respiration, photosynthesis and symbiosis of the coral, Acropora millepora, long before they affect biomineralization. Changes in gene expression were consistent with metabolic suppression, an increase in oxidative stress, apoptosis and symbiont loss. Other expression patterns demonstrated up-regulation of membrane transporters, as well as the regulation of genes involved in membrane cytoskeletal interactions and cytoskeletal remodeling. These widespread changes in gene expression emphasize the need to expand future studies of ocean acidification to include a wider spectrum of cellular processes, many of which may occur well before impacts on calcification.
2012-07-30 | GSE28697 | 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: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: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
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:Rising atmospheric CO2 concentrations are leading to ocean acidification, altering the inorganic carbon buffer system with consequences for marine organisms. Here we applied RNA-seq and iTRAQ quantification to investigate the potential impacts of ocean acidification on the temperate coastal marine diatom Skeletonema marinoi.
2020-12-09 | PXD021416 | 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