Oryza sativa
Ontology highlight
ABSTRACT:
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR165219_1.fastq.gz | Fastqsanger.gz | |||
| DRR165219_2.fastq.gz | Fastqsanger.gz | |||
| DRR165220_1.fastq.gz | Fastqsanger.gz | |||
| DRR165220_2.fastq.gz | Fastqsanger.gz | |||
| DRR165221_1.fastq.gz | Fastqsanger.gz |
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Project description:developing embryo gene expression in wild type and osmo25a mutant in rice
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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.
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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
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.
2016-07-20 | PXD004603 | JPOST Repository
Project description:Purpose: The goal of our study is to compare two different ecotypes of Oryza sativa L., PHS-susceptible rice trait and PHS-resistant rice trait under three different maturation stages in rice seed embryo with profile of miRNA-seq. Methods: Oryza sativa. L miRNA profiles of two different ecotypes with 3 different maturation stages of rice seed embryo were generated by NGS, in duplicate, following Illumina NGS workflow. Results: We found the differentially expressed microRNAs between PHS-susceptible rice trait and PHS-resistant rice trait according to the three different seed maturation stages. Target transcripts of differentially expressed microRNAs have been predicted via psRNATarget web server, and a part of those target genes are likely to be regulated by microRNAs, affecting overall responses to heat stress and the regulation of seed dormancy during maturation. Conclusions: Our study represents the analysis of rice seed small RNAs, specifically microRNAs, under two different ecotypes, three different seed maturation stages in rice seed embryo. Our results show that microRNAs are involved in response to heat stress and the regulation of seed dormancy. This study will provide a foundation for understanding dynamics of seed dormancy during the seed development and overcoming pre-harvest sprouting.
2021-07-04 | GSE175561 | GEO
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 RNA seq to investigate underlying molecular mechanism and to reveal functional role of AGO18 in rice.
2018-01-15 | GSE107903 | GEO
Project description:By comparing transcriptional profiling between a wild-type rice and an Al-sensitive rice mutant star1, we found that rice possesses novel mechanisms of Al-tolerance in addition to ART1-regulated mechanism in rice.
2012-09-19 | GSE40964 | GEO
Project description:We characterized a rice (Oryza sativa L ssp. indica cultivar 3037) semi-dwarf mutant sd37, in which CYP96B4 gene (Cytochrome P450 96B subfamily) was identified as the target gene by map-based cloning and complementation test. A point mutation in CYP96B4 leads to a substitution of Thr to Lys in the SRS2 region. The sd37 leaves, panicles and seeds are all smaller compared with those of wild-type, and histological analysis showed that the decreased cell number was the main reason for the dwarf phenotype. We used microarrays to detail the global programme of gene expression underlying cellularisation and identified distinct classes of up- and down- regulated genes during this process.
2013-07-09 | GSE48593 | GEO
Project description:Higher plants have developed sophisticated mechanisms to efficiently acquire and use micronutrients such as copper and iron. In the present work, we studied effects produced by the presence of a wide copper range in growth media and altered copper transport on iron homeostasis in Oryza sativa plants. The global analysis of gene expression in the rice seedlings grown under copper deficiency versus excess in the medium showed an increased expression of the genes involved in iron homeostasis. Different iron-related genes are expressed under either copper deficiency and excess, such as those that encode ferredoxin and transcriptional regulator IRON-RELATED TRANSCRIPTION FACTOR 2 (OsIRO2), respectively. As expected, the expression of OsCOPT1, which encodes a high affinity copper transport protein, was up-regulated under copper deficiency, and the expression of OsIRO2 targets were increased under copper excess. Arabidopsis COPT1 overexpression (C1OE) in rice causes root shortening under copper excess, modifies the expression of the putative Fe-sensing factor HEMERYTHRIN MOTIF-CONTAINING REALLY INTERESTING NEW GENE- AND ZINC-FINGER (OsHRZ1) and enhances the expression of OsIRO2 and its targets, which suggests a role of copper in iron signaling. Our studies conducted under simultaneous copper and iron deficiencies indicate that C1OE plants are more sensitive than the wild-type controls to root growth inhibition. The C1OE rice plants grown on soil contained higher endogenous iron concentration in grains than the wild-type plants (both brown and white grains). The results obtained herein showed the interaction between homeostatic networks of iron and copper, and suggest that strategies to obtain crops with optimized nutrient concentrations in edible parts should take into account this interaction.
2017-06-20 | GSE89109 | GEO
Project description:To understand the dynamics and global gene reprogramming in the early response to mechanical wounding in rice, the transcriptional response to mechanical injury was analyzed. A time-course experiment revealed the highly dynamic nature of the wound response in rice. Mechanical wounding triggered extensive gene expression reprogramming in the locally wounded leaf, affecting various physiological processes, including defense mechanisms and potentially tissue repair and regeneration. The rice response to mechanical wounding displayed both differences and similarities compared to the response to jasmonate treatment. These results highlight the importance of early JA signaling in response to mechanical stress in rice. This analysis provides an overview of the global transcriptional response to mechanical stress in rice, offering valuable insights for future studies on rice's response to injury, insect attack, and abiotic stresses.
2024-10-21 | GSE279814 | GEO