Oryza sativa
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA124359 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The present study used microarray approach to identify the genomewide response to cholera toxin in the presence of nitrate. Considering that fact that the possibility of the existence of multiple Gα genes/proteins in plants has not been conclusively ruled out, analysis of the genomewide impact of RGA1 mutation in rice and GPA1 mutation in Arabidopsis reveal only those genes that are under their direct control. On the other hand, assuming that all those different Gα subunits in any given plant are regulated by cholera toxin, analysis of the genomwide response to cholera toxin could capture the entire G-protein responsive transcriptome, beyond what can be revealed by the mutant approach. This could reveal even those genes that respond to other, as yet unidentified Gα subunits, as well as reveal some genes that are non-specifically regulated by cholera toxin, independent of any G-proteins.
2010-12-01 | GSE20924 | GEO
Project description:The present study used microarray approach to identify the genomewide response to cholera toxin in the presence of nitrate. Considering that fact that the possibility of the existence of multiple GM-NM-1 genes/proteins in plants has not been conclusively ruled out, analysis of the genomewide impact of RGA1 mutation in rice and GPA1 mutation in Arabidopsis reveal only those genes that are under their direct control. On the other hand, assuming that all those different GM-NM-1 subunits in any given plant are regulated by cholera toxin, analysis of the genomwide response to cholera toxin could capture the entire G-protein responsive transcriptome, beyond what can be revealed by the mutant approach. This could reveal even those genes that respond to other, as yet unidentified GM-NM-1 subunits, as well as reveal some genes that are non-specifically regulated by cholera toxin, independent of any G-proteins. Total RNA was isolated from 10 day old excised rice leaves treated with or without cholera toxin in the presence of nitrate.Total RNA was first converted into cDNA and then into cRNA labeled with Cy3 and Cy5 dyes. These were hybridized on the 44K 60-mer whole genome arrays on glass slides. The slides were washed and scanned on an Agilent scanner (G2565B) at 100 % laser power. Data extraction was carried out with Agilent Feature Exiraction software (version 9.1). The experiment was repeated with a biological-cum-technical replicate where total RNA samples were isolated from a fresh batch of rice plants and the cRNAs were labeled with opposite dyes (dye-swap).
2010-12-01 | E-GEOD-20924 | biostudies-arrayexpress
Project description:Transcriptional profiling of MIT knockdown plants. MIT is a mitochondrial Fe transporter essential for rice growth and development. The goal was to determine the effects of MIT on global rice gene expression.
2011-04-07 | GSE28428 | GEO
Project description:Whole Genome Segregation of light and nitrate effect in rice plants
| PRJNA110963 | ENA
Project description:Cross-kingdom molecular exchange between hosts and interacting microbes is essential for the survival of both plants and their pathogens. Recent studies showed plants transfer their small RNAs (sRNAs) and massager RNAs (mRNAs) into fungal pathogens to suppress infection. However, whether and how plants send defense proteins into pathogen cells remains unknown. Here, we show that rice plants send defense proteins into the fungal pathogen Rhizoctonia solani via extracellular vesicles (EVs). These vesicles enrich host defense proteins and are taken up by the fungal cells. Reducing EV-mediated host protein transfer leads to increased disease susceptibility. Thus, plants send defense proteins via EVs into fungal pathogens to combat infection, providing a mechanism of protein exchange between plants and pathogens that helps reduce crop disease.
2025-01-06 | PXD048458 | Pride
Project description:The goal of this work is to identify the gene regulatory hubs that control nitrogen-use in Oryza sativa, one of the most important crop plants, by using a combination of genomics, bioinformatics and systems biology approaches. Here, we evaluate the role of bZIP1, a transcription factor involved in light and nitrogen sensing, by exposing wild-type (WT) and bZIP1 T-DNA null mutant plants to a combinatorial space of N and L treatment conditions. We use ANOVA analysis combined with clustering and Boolean modeling, to evaluate the role of bZIP1 in mediating L and N signaling genome-wide. We also study the interspecies conservation, comparing rice with Arabidopsis thaliana nitrogen transcriptomes, to help identify conserved nitrogen regulation.
2015-06-10 | E-GEOD-38102 | biostudies-arrayexpress
Project description:Rice is one of the most important global food crops, and is also a model organism for cereal research 31 . Complete genome sequencing of rice, together with advances in transcriptomics and proteomics, has had a dramatic impact on plant growth and 5 breeding programs 32 . Genomic analysis of DNA methylation in rice has revealed methylation patterns associated with gene bodies and promoters, and the occurrence of high levels of DNA methylation in the centromeric domain 33 . A genome-wide investigation of acetylation in rice revealed that H3K9ac and H3K27ac are mainly enriched at transcription start sites associated with active transcription 34 . Furthermore, global proteome analysis has shown that phosphorylation and succinylation are involved in diverse cellular and metabolic processes 35, 36 . However, despite these considerable advances in our knowledge, additional large-scale analysis of the lysine acetylome in rice is expected to identify many more Kac sites and acetylated proteins in this improtant crop plant. In this study, affinity enrichment and high-resolution LC-MS/MS were used for large-scale analysis of the lysine acetylome in rice variety Nipponbare. In total, 1353 lysine acetylation sites were detected in 866 protein groups in rice seedlings. Proteomic analysis showed that Kac occurs in proteins involved in diverse biological processes with varied cellular functions and subcellular localization.
2017-11-13 | PXD004870 | Pride
Project description:Fairy rings are zones of stimulated grass growth by the interaction between the fungi and the plant. In the previous research, we reported the identification of the “fairy”, 2-azahypoxanthine (AHX), produced by the fairy ring-forming fungus and the mechanism of its growth-promoting activity using DNA microarray. We discovered AOH, a common metabolite of AHX in plants. We investigate expression profiling of rice seedlings treated with AHX or AOH for the mechanism of their growth-promoting activity.
2014-01-01 | GSE38844 | GEO
Project description:In this study, we used a cross-species network approach to uncover nitrogen (N)-regulated network modules conserved across a model and a crop species. By translating gene network knowledge from the data-rich model Arabidopsis (Arabidopsis thaliana, ecotype Columbia-0) to a crop, rice (Oryza sativa spp. japonica (Nipponbare)), we identified evolutionarily conserved N-regulatory modules as targets for translational studies to improve N use efficiency in transgenic plants.
2015-06-10 | GSE38102 | GEO
Project description:To reveal the underlying molecular mechanism of jasmonate inhibits gibberellins signaling in rice, we performed transcriptional profiling of wild type nipponbare and mutant coi1-13 plants on a global scale using the Affymetrix GeneChip Rice Genome Array
2011-12-01 | GSE29577 | GEO