Ontology highlight
ABSTRACT:
PROVIDER: PRJEB21584 | ENA |
REPOSITORIES: ENA
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Project description:We present the draft genome of Nitrospirae bacterium Nbg-4 as a representative of this clade and couple this to in situ protein expression under sulfate-enriched and sulfate-depleted conditions in rice paddy soil. The proteins were extracted from the soil and analysed via LC-MS/MS measurements.
2018-01-08 | PXD007817 | Pride
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:Diurnal time-course transcriptional profiling of rice leaf in the field comparing a circadian clock related mutant, osgi, with the wild-type (WT). Two sample experiments (WT vs. osgi) : 13 time-points (2h interval), 8 replicates (2leaves from individual plants x 4stages(each staggered by tranplanting dates with one week interval)): sampled on Aug. 12th 7:00-Aug.13th 7:00 (2008) at a paddy field in Tsukuba (Japan)
2011-05-18 | E-GEOD-18685 | biostudies-arrayexpress
Project description:Rice has evolved regulatory programs and specialized cell types that allow the plant to withstand different environments. To understand how rice root systems cope with water stresses, we profiled translatomes (ribosome-associated mRNAs) and accessible chromatin of developmentally-defined root cell populations from well-watered and drained control (aerobic control), water deficit, waterlogged, fully submerged plants and recovery conditions. Whereas, the waterlogging responses are limited to specific root domains, water deficit and submergence signatures are extensive, and mostly reversible after 1 day of recovery, relative to control roots. Root systems were also evaluated in rice cultivated in a paddy field. Specific responses include a halt in the cell-cycle and DNA synthesis-related genes translation in meristematic tissue under submergence and exo/endodermis suberin-related pathways bolstering under water deficit. Chromatin accessibility and translatome data integration was used to generate inferred regulatory networks that are dynamically regulated by changing water availability. The data collection is further enriched by translatome and chromatin accessibility data for the root systems of plate-grown seedlings (7 day old) and those cultivated in a paddy field (49 day old). An atlas of eight cell population translatomes for field-grown plants exhibited robust cell type expression. Collectively, these data for specific cell populations at multiple developmental ages and in multiple environments including growth two limiting water stresses will serve as a community resource.
2022-05-02 | GSE180100 | GEO
Project description:Arsenic (As) is a carcinogenic metalloid that is a contaminant widely polluting rice paddy soils around the world. In order to gain better insight into molecular mechanism of rice exposed to As(III) stress, we used next-generation sequencing technology to acquire global transcriptome alteration and miRNA regulation in rice upon As(III) treatments. Our results suggest time course and As(III)-dosing treatments were devised. Cluster analyses show that root and shoot samples were differentially grouped. For roots, sub-clusters were more distinct in the dosage course whereas for shoots they were most recognizable for the time course treatments. Other than the significantly regulated gene expression in the heavy metal-responsive sulfur and glutathione metabolism pathways, the expression of genes related to heavy metal transportation, jasmonate biosynthesis and signaling pathways, lipid metabolism and gene transcription were sharply regulated, indicating that rice allocates energy and resources from growth to stress response under As(III) stress. In addition to the detection of previously identified stress-related miRNAs, we further discovered 36 new As(III)-responsive miRNAs. These results expand our understanding of As(III) stress mechanism to the As(III)-responsive mRNA and miRNA transcriptomes, which provide a foundation for subsequent functional research. 10 mRNA samples examined 10 miRNA samples examined
2013-01-09 | E-GEOD-36696 | biostudies-arrayexpress
Project description:Rice grown in paddy fields prefers to use ammonium ions as a major source of inorganic nitrogen. Glutamine synthetase (GS) catalyzes the conversion of ammonium ions to glutamine. In three cytosolic GS in rice, OsGS1;1 has the critical role for normal growth and grain filling. To understand a role of GS1;1, we performed transcriptional profiling of wild type Nipponbare and GS1;1 mutant plants in seedling using the Agilent Rice Oligo Microarray.
2010-03-01 | GSE15122 | GEO
Project description:Time-course transcriptional profiling of rice leaf in the field in 2009. This experiment was performed to validate the results of field transcriptomic modeling. Using 461 field transcriptome data obtained in 2008 (GSE36040; GSE36042; GSE36043; GSE36044; GSE18685) and the corresponding meteorologicla dara, we perfomred statistical modeling of transcriptome. Rice leaves (Norin8 vs. osgi) in the paddy field were collected on Aug. 10 - 12, 24 - 25, 31, Oct. 8 - 9 in 2009.
2012-12-07 | E-GEOD-36777 | biostudies-arrayexpress
Project description:Rice anthers at the anthesis stage were collected from the wild type (Dongjin cultivar) and far1-1 mutant grown in the paddy field located in the KyungHee University. The collected samples were immediately frozen with liquid nitrogen. RNA from these samples was extracted with RNeasy plant mini kit according to the manufacture's documentation.
2022-12-31 | E-MTAB-10106 | biostudies-arrayexpress
Project description:Macronutrients are pivotal elements for proper plant growth and development. We performed microarray analysis of rice leaves under nitrogen (N), phosphorus (P), and potassium (K) deficiency conditions in paddy field to obtain a global view of gene regulations associated with plant response to essential nutrients.
2019-10-06 | GSE73766 | GEO