Oryza sativa
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA114877 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Microarray analysis of gene expression in rice lacking cytosolic glutamine synthetase 1 2
| PRJNA263251 | ENA
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:Goal of the study is to characterize distinct function(s) of two cytosolic glutamine synthetase (GS) in rice plants. We grew rice lacking GS1;1 and GS1;2 under the ammonium sufficient condition. We harvested roots from the two mutants as well as those of the corresponding control.
2019-04-01 | E-MTAB-6303 | biostudies-arrayexpress
Project description:Goal of the study is to characterize specific function(s) of the cytosolic glutamine synthetase (GS) 1;2 for apical meristem induction in rice plants. To address the issue, we conducted transcript profiling toward basal parts of the knockout mutant lacking GS1;2. We used microarrays conduct transcript profiling of gs1;2 plants. Wild-type samples were used as control.
2014-11-28 | GSE62124 | GEO
Project description:Pollen tube growth is essential for successful fertilization and stable crop yields. We constructed loss-of-function/knock-out mutants that simultaneously target two rice genes using the CRISPR/Cas9 mutagenesis system. The selected OsRALF17 and OsRALF19 genes are strongly expressed in rice bicellular/tricellular pollen and have essential functions in the pollen tube growth. For the corresponding transcriptomic analysis, we sampled mature pollen anthers from a control group and an OsRALF17/19 knock-out mutant.
2023-09-29 | E-MTAB-12295 | biostudies-arrayexpress
Project description:Microarray analysis of gene expression in rice lacking cytosolic glutamine synthetase 1 1 and 1 2 grown under the ammonium sufficient condition
| PRJNA214911 | ENA
Project description:Nitrogen (N) is a critical limiting element in the provision of important components, e.g., chlorophylls, to plants. Organic N synthesized by glutamine synthetase (GS) may help regulate metabolic networks for plant growth and development. However, how multiple isoforms of cytosolic GSs act for metabolic regulation remain unclear. Using the knockout mutants, Osgs1;1 and Osgs1;2, we compared the effects of two cytosolic GSs on metabolism and cell differentiation in rice roots using reverse genetic-, metabolite- and transcript profiling- and microscopic analyzes together with integrated metabolite-transcript network analysis. We used microarrays to detail the global programme of gene expression in rice Osgs1;1 and Osgs1;2 roots.
2020-04-20 | GSE49789 | GEO
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:Here, we present OryzaPG-DB, a rice proteome database based on shotgun proteogenomics, which incorporates the genomic features of experimental shotgun proteomics data. This version of the database was created from the results of 27 nanoLC-MS/MS runs on a hybrid ion trap-orbitrap mass spectrometer, which offers high accuracy for analyzing tryptic digests from undifferentiated cultured rice cells. Peptides were identified by searching the product ion spectra against the protein, cDNA, transcript and genome databases from Michigan State University, and were mapped to the rice genome. Approximately 3200 genes were covered by these peptides and 40 of them contained novel genomic features. Users can search, download or navigate the database per chromosome, gene, protein, cDNA or transcript and download the updated annotations in standard GFF3 format, with visualization in PNG format. In addition, the database scheme of OryzaPG was designed to be generic and can be reused to host similar proteogenomic information for other species. OryzaPG is the first proteogenomics-based database of the rice proteome, providing peptide-based expression profiles, together with the corresponding genomic origin, including the annotation of novelty for each peptide.
| PXD004603 | JPOST Repository
Project description:Artificial miRNA mediated knock-down ago18 transgenic lines [ago18(1), ago18(2)] showed developmentally compromised phenotype in both vegetative and reproductive tissues compared to wild-type control. We have performed small RNA seq to investigate underlying molecular mechanism and to reveal functional role of AGO18 in rice.
2018-01-15 | GSE107904 | GEO