Uncultured euryarchaeote
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR014325.fastq.gz | Fastqsanger.gz | |||
| DRR014326.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
Project description:Tropospheric ozone (O3) is a secondary air pollutant and anthropogenic greenhouse gas. Concentrations of tropospheric O3 have more than doubled since the Industrial Revolution, and are high enough to damage plant productivity. Soybean (Glycine max L. Merr.) is the worldâs most important legume crop and is sensitive to O3. Current ground-level O3 are estimated to reduce global soybean yields by 6% to 16%. In order to understand transcriptional mechanisms of yield loss in soybean, we examined the transcriptome of soybean flower and pod tissues exposed to elevated O3 using RNA-Sequencing.
2015-01-31 | E-MTAB-5226 | biostudies-arrayexpress
Project description:High ozone (O3) concentration causes serious damages in plant productivity. Climate models forecast that ground O3 level in the future will reach phytotoxic range, resulting in crop yield losses. With an ultimate goal to screen molecular factors to minimize losses of crop production by the rise of O3 level, we have started an investigation on effects of O3 on rice using rice DNA chip. Herein, we have utilized the samples of dry mature rice seeds harvested in an ozone-sensitive rice cultivar (Oryza sativa L. indica cv. Takanari) and a tolerant cultivar (Oryza sativa L. japonica cv. Koshihikari) which were fumigated with ambient air (mean O3: 32.7 ppb) in small open-top chambers (OTCs). First, we extracted total RNA from dry mature rice seeds of Takanari and Koshihikari using a modified protocol based on cethyltrimethylammonium bromide extraction buffer and phenol-chloroform-isoamylalcohol treatment. Furthermore, to perform microarray analysis using the Agilent 4x44 rice DNA Chip and the dye-swap method, we designed a balanced block design comparing seeds in an ambient air-fumigated rice cultivar and those in a filtered air-fumigated rice cultivar. Direct comparison of Koshihikari and Takanari O3 transcriptomes in seeds of rice plants fumigated with ambient O3 in OTCs successfully showed that genes encoding proteins involved in jasmonic acid, GABA biosynthesis, cell wall and membrane modification, starch mobilization, and secondary metabolite biosynthesis are differently regulated in an O3-sensitive cv. Takanari and a tolerant cv. Koshihikari.
2013-08-20 | GSE49963 | GEO
Project description:High ozone (O3) concentration causes serious damages in plant productivity. Climate models forecast that ground O3 level in the future will reach phytotoxic range, resulting in crop yield losses. With an ultimate goal to screen molecular factors to minimize losses of crop production by the rise of O3 level, we have started an investigation on effects of O3 on rice using rice DNA chip. Herein, we have utilized the samples of dry mature rice seeds harvested in an ozone-sensitive rice cultivar (Oryza sativa L. indica cv. Takanari) and a tolerant cultivar (Oryza sativa L. japonica cv. Koshihikari) which were fumigated with ambient air (mean O3: 32.7 ppb) in small open-top chambers (OTCs). First, we extracted total RNA from dry mature rice seeds of Takanari and Koshihikari using a modified protocol based on cethyltrimethylammonium bromide extraction buffer and phenol-chloroform-isoamylalcohol treatment. Furthermore, to perform microarray analysis using the Agilent 4x44 rice DNA Chip and the dye-swap method, we designed a balanced block design comparing seeds in an ambient air-fumigated rice cultivar and those in a filtered air-fumigated rice cultivar. Direct comparison of Koshihikari and Takanari O3 transcriptomes in seeds of rice plants fumigated with ambient O3 in OTCs successfully showed that genes encoding proteins involved in jasmonic acid, GABA biosynthesis, cell wall and membrane modification, starch mobilization, and secondary metabolite biosynthesis are differently regulated in an O3-sensitive cv. Takanari and a tolerant cv. Koshihikari.
2012-05-01 | GSE37650 | GEO
Project description:Paddy rice with husk can be availbale for chicken dietary resource instead of yellow corn. Ingestion of paddy rice potentially affects on gastrointestinal physiology and function including digestion/absorption of nutrients and gut barrier function such as mucosal immunity, but the details of changes is unknown. To obtain insight into the physiological modifications in the small intestine of chickens fed paddy rice, we conducted a comprehensive analysis of gene expression in small intestine by DNA microarray. In the paddy rice group, a total of 120 genes were elevated >1.5-fold in the paddy rice group, whereas a total of 159 genes were diminished < 1.5-fold. Remarkably, the gene expression levels of IGHA (immunoglobulin heavy chain α), IGJ (immunoglobulin J chain), and IGLL1 (immunoglobulin light chain λ chain region), which constitute immunoglobulin A, decreased 3 to 10 times in the paddy rice group.
2024-09-22 | GSE277733 | GEO
Project description:High ozone (O3) concentration causes serious damages in plant productivity. Climate models forecast that ground O3 level in the future will reach phytotoxic range, resulting in crop yield losses. With an ultimate goal to screen molecular factors to minimize losses of crop production by the rise of O3 level, we have started an investigation on effects of O3 on rice using rice DNA chip. Herein, we have utilized the samples of dry mature rice seeds harvested in an ozone-sensitive rice cultivar (Oryza sativa L. indica cv. Takanari) and a tolerant cultivar (Oryza sativa L. japonica cv. Koshihikari) which were fumigated with ambient air (mean O3: 32.7 ppb) in small open-top chambers (OTCs). First, we extracted total RNA from dry mature rice seeds of Takanari and Koshihikari using a modified protocol based on cethyltrimethylammonium bromide extraction buffer and phenol-chloroform-isoamylalcohol treatment. Furthermore, to perform microarray analysis using the Agilent 4x44 rice DNA Chip and the dye-swap method, we designed a balanced block design comparing seeds in an ambient air-fumigated rice cultivar and those in a filtered air-fumigated rice cultivar. Direct comparison of Koshihikari and Takanari O3 transcriptomes in seeds of rice plants fumigated with ambient O3 in OTCs successfully showed that genes encoding proteins involved in jasmonic acid, GABA biosynthesis, cell wall and membrane modification, starch mobilization, and secondary metabolite biosynthesis are differently regulated in an O3-sensitive cv. Takanari and a tolerant cv. Koshihikari.
2012-04-30 | E-GEOD-37650 | biostudies-arrayexpress
Project description:Ozone (O3) is known to cause lung injury, which can influence the health and function of resident immune and non-immune cells of the respiratory tract. Alveolar macrophages (AMs), a highly plastic lung resident cell population, are among the first responders to the inhaled O3 and ozonized products. However, the complete understanding of how AMs respond to O3, particularly to different concentrations, remains elusive. Through single cell RNA sequencing (scRNA-seq), we aimed to profile AM transcriptome from O3-exposed mice and understand the relevance of these transcriptomic changes to the population and functional heterogeneity. Accordingly, we exposed C57BL/6J male mice to filtered air (FA), 1 ppm O3, or 1.5 ppm O3 for 3 hours. After 24h of exposure, bronchoalveolar lavage (BAL) was performed to harvest immune cells, which were subjected to ScRNA-seq. As compared to FA-exposed mice, O3-exposed mice exhibited increased alveolar macrophages and neutrophils in the lung airspaces, consistent with the elevated levels of macrophage and neutrophil chemokines, i.e., MIP-2, MCP-3, MCP-5. The ScRNA-Seq data analyses were performed to identify distinct and annotate distinct cellular clusters. AM clusters were analyzed for the alterations in gene expression and associated enrichment of biological pathways. Although the O3 exposure did not result in the appearance of a distinct cellular cluster, there was a significant difference in the number of differentially expressed genes (DEGs) between AMs from mice exposed to 1 ppm and 1.5 ppm O3, relative to those exposed to FA. As compared to AMs from FA-exposed group, AMs from 1 ppm and 1.5 ppm O3-exposed groups displayed enrichment of pathways including oxidative phosphorylation, EIF2 signaling, and non-canonical NF-kB signaling. Furthermore, AMs from 1 ppm O3-exposed mice were uniquely activated in IL-10 signaling pathway. On the other hand, AMs from 1.5 ppm O3-exposed mice were uniquely enriched in pathways including DNA damage bypass and repair pathways. Interestingly, UMAP analyses on annotated AMs resulted in five distinct subclusters. DEGs and IP analyses for each subcluster revealed O3 concentration-dependent enrichment of pathways relevant to protein translation, cholesterol biosynthesis and mitochondrial biogenesis. Further analyses revealed that O3 exposure results in cluster-specific alterations to the expression of gene signatures associated with macrophage activation. Finally, AMs from 1.5 ppm O3-exposed mice displayed elevated expression of proliferation associated gene signatures. Taken together, this study identified O3 concentration-dependent alterations in AMs transcriptomes and associated functional modulations at single cell resolution.
2026-02-01 | GSE302132 | GEO
Project description:High ozone (O3) concentration causes serious damages in plant productivity. Climate models forecast that ground O3 level in the future will reach phytotoxic range, resulting in crop yield losses. With an ultimate goal to screen molecular factors to minimize losses of crop production by the rise of O3 level, we have started an investigation on effects of O3 on rice using rice DNA chip. Herein, we have utilized the samples of dry mature rice seeds harvested in an ozone-sensitive rice cultivar (Oryza sativa L. indica cv. Takanari) and a tolerant cultivar (Oryza sativa L. japonica cv. Koshihikari) which were fumigated with ambient air (mean O3: 32.7 ppb) in small open-top chambers (OTCs). First, we extracted total RNA from dry mature rice seeds of Takanari and Koshihikari using a modified protocol based on cethyltrimethylammonium bromide extraction buffer and phenol-chloroform-isoamylalcohol treatment. Furthermore, to perform microarray analysis using the Agilent 4x44 rice DNA Chip and the dye-swap method, we designed a balanced block design comparing seeds in an ambient air-fumigated rice cultivar and those in a filtered air-fumigated rice cultivar. Direct comparison of Koshihikari and Takanari O3 transcriptomes in seeds of rice plants fumigated with ambient O3 in OTCs successfully showed that genes encoding proteins involved in jasmonic acid, GABA biosynthesis, cell wall and membrane modification, starch mobilization, and secondary metabolite biosynthesis are differently regulated in an O3-sensitive cv. Takanari and a tolerant cv. Koshihikari. Comparison between O. sativa L. indica cv. Takanari and japonica cv. Koshihikari grown under ozone for their lifetime was performed. Controls were plants grown under filtered air. Three biological replicates (4 plants in each biological replicate in each small open top chamber - seed; pooled) were used, and dye-swaped.
2013-08-20 | E-GEOD-49963 | biostudies-arrayexpress
Project description:Ozone at an elevated level is an important environmental stress factor that limits plant growth and development. To test how O3-induced ROS signalling interacts with the ABA pathway we present a global characterization of O3-responsive genes in the abi1td mutant. To understand better ABA signalling and the interactions between stress-response pathways we also performed a microarray analysis of drought-treated abi1td and WT plants. Since ABA signalling is well known to mediate defined responses based on the WT and different mutants analysis in drought stress conditions, the comparison of the O3 and drought stress response in abi1td enabled the identification of new processes depending on ABA-related pathways in O3-treated plants. Altogether, our findings indicate that ABI1 plays the role of a general signal transducer linking diferrent hormone signalling pathways to O3 stress tolerance.<br><br><br><br>Key words: ROS signalling; ABA signalling; ozone stress; drought stress; environmental stress; gene knockout;
2009-08-27 | E-MEXP-1863 | biostudies-arrayexpress
Project description:uncultured methanogenic archaeon overview
| PRJNA851135 | ENA