Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1129077 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:DNA oligonucleotide microarrays were designed with 307 probes for 96 internal transcribed spacer (ITS1, located between 18S and 26S rRNA genes) sequences of known species and strains from the genus Pseudo-nitzschia (Bacillariophyceae). In addition, microarrays also carried 1893 probes targeting ITS1 aequences of marine Crenarchaeota and Alphaproteobacteria of SAR11 clade. In order to assign microarray profiles to Pseudo-nitzschia ribotypes and species and to 'train' the data analysis system, we grew cultures of Pseudo-nitzschia in the laboratory with identities confirmed through rDNA sequence analysis. In total, 9 cultures and 35 environmental water samples were hybridized to microarrays, in some cases, in duplicate or triplicate. Analysis of microarray data allowed us to identify and map Pseudo-nitzschia spp. in the coastal waters along Washington and Oregon coast of the Eastern Pacific Ocean, and to observe seasonal changes in diatom community composition.
2012-06-01 | GSE27141 | GEO
Project description:The oceanic diatom Pseudo-nitzschia granii was cultured in the laboratory under steady-state iron-replete and iron-limited conditions. Transcriptomic and proteomic analyses were performed to determine how this organism reorganizes major metabolic processes as a function of iron supply.
2018-08-21 | PXD009698 | Pride
Project description:DNA oligonucleotide microarrays were designed with 307 probes for 96 internal transcribed spacer (ITS1, located between 18S and 26S rRNA genes) sequences of known species and strains from the genus Pseudo-nitzschia (Bacillariophyceae). In addition, microarrays also carried 1893 probes targeting ITS1 aequences of marine Crenarchaeota and Alphaproteobacteria of SAR11 clade. In order to assign microarray profiles to Pseudo-nitzschia ribotypes and species and to 'train' the data analysis system, we grew cultures of Pseudo-nitzschia in the laboratory with identities confirmed through rDNA sequence analysis. In total, 9 cultures and 35 environmental water samples were hybridized to microarrays, in some cases, in duplicate or triplicate. Analysis of microarray data allowed us to identify and map Pseudo-nitzschia spp. in the coastal waters along Washington and Oregon coast of the Eastern Pacific Ocean, and to observe seasonal changes in diatom community composition. Total DNA was isolated from 9 Pseudo-nitzschia laboratory cultures and 35 environmental water samples collected during 7 field campaigns in 2007-2009. The environmental samples were collected at distances of 5 to 55 km from the coast, along the following transects in the Pacific Ocean covering over 300 km of the coastline: La Push (LP), Grays Harbor (GH), Columbia River (CR), and Newport Hydroline (NH). The DNA samples were subjected to PCR amplification with the primers specific for ITS1 sequences. The resultant biotin-labeled target samples were analyzed using microarray hybridization with the CombiMatrix ElectraSense 4X2K format. Out of 44 analyzed samples, 40, 2, and 2 were used for single, duplicate and triplicate hybridizations, respectively.
2012-05-31 | E-GEOD-27141 | biostudies-arrayexpress
Project description:Pseudo-nitzschia multiseries (Ps-n) is a toxigenic marine diatom that produces the neurotoxin, domoic acid. We screened for candidate genes that may be involved in domoic acid production by determining changes in transcript profiles in Ps-n cultures that were in late exponential (low-domoic-acid-producing) vs. stationary (high-domoic-acid-producing) growth states. We also identified a number of candidate reference genes for future RT-qPCR studies, based on their stability in this study.
2013-09-08 | GSE46845 | GEO
Project description:Genome sequencing of a harmful algal bloom forming cyanobacterium Planktothrix agardhii NIES-204
| PRJDB4739 | ENA
Project description:Metatranscriptome profiling of a harmful algal bloom.
| PRJNA241185 | ENA
Project description:Harmful algal blooms are induced largely by nutrient enrichment common in warm waters. An increasingly frequent phenomenon is the “red tide”: blooms of dinoflagellate microalgae that accumulate toxins lethal to other organisms in high doses. Here, we present the de novo assembled genome (~4.75 Gbp) of Prorocentrum cordatum, a globally abundant, bloom-forming dinoflagellate, and the associated transcriptome, proteome, and metabolome data from axenic cultures to elucidate the microalgal molecular responses to heat stress. We discovered, in a high-G+C genome with long introns and extensive genetic duplication, a complementary mechanism between RNA editing and exon usage that regulates dynamic expression and functional diversity of genes and proteins, and metabolic profiles that reflect reduced capacities in photosynthesis, central metabolism, and protein synthesis. These results based on multi-omics evidence demonstrate the genomic hallmark of a bloom-forming dinoflagellate, and how the complex gene structures combined with multi-level transcriptional regulation underpin concerted heat-stress responses.
2023-10-18 | PXD046193 | Pride
Project description:<p>In annually reoccurring patterns, microalgae form blooms that persist and decline thereby contributing massively to global biogeochemical cycles. The decline of blooms is mainly caused by nutrient limitation and goes ahead with the aging of individual algal cells. Nutrient intake can re-initiate proliferation, but the processes involved are poorly understood. By investigating the bloom-forming diatom Coscinodiscus radiatus, we demonstrate how algae recover after nutrient influx. The rejuvenation physiology of the algae is characterized by metabolomic re-organization and the formation of extracellular vesicles. Regulated pathways mediating aging are centered around the methionine cycle in C. radiatus. Vesicles shuttle reactive oxygen species, oxylipins and other harmful metabolites out of the old cells, thereby re-enabling their proliferation. Metabolic processes involved in aging and vesicle production are modulated by bacteria. Using chemical signaling bacteria can trigger vesicle production thereby releasing organic nutrients for their growth and supporting algal growth as well.</p><p><br></p><p><strong>Metabolomics analysis</strong> is reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS5368' rel='noopener noreferrer' target='_blank'><strong>MTBLS5368</strong></a>.</p><p><strong>Metabolomics profiling of FACS purified EVs</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS5401' rel='noopener noreferrer' target='_blank'><strong>MTBLS5401</strong></a>.</p>
2024-05-07 | MTBLS5368 | MetaboLights
Project description:<p>In annually reoccurring patterns, microalgae form blooms that persist and decline thereby contributing massively to global biogeochemical cycles. The decline of blooms is mainly caused by nutrient limitation and goes ahead with the aging of individual algal cells. Nutrient intake can re-initiate proliferation, but the processes involved are poorly understood. By investigating the bloom-forming diatom Coscinodiscus radiatus, we demonstrate how algae recover after nutrient influx. The rejuvenation physiology of the algae is characterized by metabolomic re-organization and the formation of extracellular vesicles. Regulated pathways mediating aging are centered around the methionine cycle in C. radiatus. Vesicles shuttle reactive oxygen species, oxylipins and other harmful metabolites out of the old cells, thereby re-enabling their proliferation. Metabolic processes involved in aging and vesicle production are modulated by bacteria. Using chemical signaling bacteria can trigger vesicle production thereby releasing organic nutrients for their growth and supporting algal growth as well.</p><p><br></p><p><strong>Metabolomics profiling of FACS purified EVs</strong> is reported in the current study <a href='https://www.ebi.ac.uk/metabolights/MTBLS5401' rel='noopener noreferrer' target='_blank'><strong>MTBLS5401</strong></a>.</p><p><strong>Metabolomics analysis</strong> is reported in <a href='https://www.ebi.ac.uk/metabolights/MTBLS5368' rel='noopener noreferrer' target='_blank'><strong>MTBLS5368</strong></a>.</p>
2024-05-07 | MTBLS5401 | MetaboLights