Ontology highlight
ABSTRACT:
PROVIDER: PRJEB86960 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14828364_cleaned.contigs.fa.gz | Other | |||
| SRR14828365_cleaned.contigs.fa.gz | Other | |||
| SRR14828367_cleaned.contigs.fa.gz | Other | |||
| SRR14828368_cleaned.contigs.fa.gz | Other | |||
| SRR14828376_cleaned.contigs.fa.gz | Other |
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Project description:Effluent from geoduck clam larval rearing tanks at two different pH (8.2 and 7.1) was collected at 4 time points (Days 1, 5, 8, and 12) over 12 days in a shellfish hatchery in Washington state, USA. The water was filtered to 0.2 microns to retain the bacterial fraction.
2021-04-21 | PXD020692 | Pride
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:The shellfish aquaculture industry provides a sustainable food source and jobs for a growing population. Oysters are the primary aquaculture species produced in the United States and account for a significant portion of seafood exports. Shellfish hatcheries have been experiencing frequent mass mortality events over the last couple of decades that occur approximately 10-14 days after oyster settlement. Settlement is a process that shellfish such as oysters undergo in which they transform from a free-swimming pelagic larvae to a sessile juvenile oyster. In order for this energy-intensive process to be successful, the oyster has to undergo behavioral and morphological changes. This is a vulnerable period in the oyster life cycle and conditions need to be such that they aren’t creating added stress. However, due to the oysters’ vulnerability, this is often a time when bacterial infections can occur, which when occurring with environmental conditions that are unfavorable, can prove to be fatal. In order to help oysters survive this process, scientists at the Taylor Shellfish Hatchery in Quilcene, WA has experimented with altering abiotic and biotic factors such as algal diet densities, pH, water flow rate, among others. At this hatchery, Pacific oysters are typically reared at 23˚C, however preliminary research results have suggested that oysters may have a higher survival rate when held at 29˚C during the settlement period. This pilot experiment attempts to identify differences in protein expression between oyster seed held at 23˚C and 29˚C during the settlement period using novel proteomic technology. Our proteomic results, paired with survival data, suggest that holding oyster seed at 29˚C during the settlement period results in higher survival rates.
2022-03-03 | PXD015434 | Pride
Project description:Samples from different locations within a shellfish hatchery Metagenome
| PRJNA1173763 | ENA
Project description:To identify gene expression differences between Oncorhynchus mykiss that migrate and those that reside in freshwater, we compared gill transcriptomes of fish prior to release from a hatchery with those of fish recaptured eight days post-release while all fish were still in freshwater, but some were captured next to the hatchery (non-migrants) and others were captured moving toward the ocean (migrants). The in-hatchery sampling method represents a highly similar environment for all the fish, and allows for the determination of activated genes predictive of smolting programs prior to release into streams. Morphological (e.g. color) and physiological (gill NaCl-ATPase activity) data were also obtained and correlated to gene expression differences to aid in predictions. Gill tissue was sampled for transcriptome profiling 13 days prior to two different releases from the hatchery (total sampled within hatchery n = 19). Samples were also taken eight days after the two releases near-hatchery (total in-creek n = 20) or migrating towards the ocean but still in freshwater (second release only n = 20). Finally, 48 days after the second release a final set of resident fish were sampled near the hatchery (n =10). In terms of time after release, the most parallel comparison is the second 8 day post release sample in-creek and migrating. Although all samples were obtained in freshwater, the samples with the most similar local environment are the pre-release samples.
2014-03-04 | E-GEOD-48844 | biostudies-arrayexpress
Project description:Here we map the molecular response of a synthetic community of 32 human gut bacteria to three non-antibiotic drugs by using five omics layers, namely 16S rRNA gene profiling, metagenomics, metatranscriptomics, metaproteomics, and metabolomics. Using this controlled setting, we find that all omics methods with species resolution in their readouts are highly consistent in estimating relative species abundances across conditions. Furthermore, different omics methods can be complementary in their ability to capture functional changes in response to the drug perturbations. For example, while nearly all omics data types captured that the antipsychotic drug chlorpromazine selectively inhibits Bacteroidota representatives in the community, the metatranscriptome and metaproteome suggested that the drug induces stress responses related to protein quality control and metabolomics revealed a decrease in polysaccharide uptake, likely caused by Bacteroidota depletion. Taken together, our study provides insights into how multi-omics datasets can be utilised to reveal complex molecular responses to external perturbations in microbial communities.
2022-12-13 | PXD036445 | Pride
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
2008-02-08 | GSE10119 | GEO
Project description:The study was designed to investigate the impacts of hatchery spawning and rearing on steelhead trout (Oncorhynchus mykiss) versus the wild fish on a molecular level. Additionally, epigenetic differences between feeding practices that allow slow growth and fast growth hatchery trout were investigated. The sperm and RBC DNA both had a large number of DMRs when comparing the hatchery versus wild steelhead trout populations. Interestingly, the DMRs were cell type specific with negligible overlap. Slow growth compared to fast growth steelhead also had a larger number of DMRs in the RBC samples. Observations demonstrate a major epigenetic programming difference between the hatchery and wild fish populations, but negligible genetic differences. Therefore, hatchery conditions and growth rate can alter the epigenetic developmental programming of the steelhead trout, which may correlate to the phenotypic variations observed.
2020-05-24 | GSE145887 | GEO