Oryza sativa
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-40549
PROVIDER: PRJNA174253 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Spatial transcriptomes of iron-deficient and cadmium-stressed rice
2015-12-04 | E-GEOD-40549 | ExpressionAtlas
Project description:Several metals are essential nutrients for plants but metals are toxic in excess, deleteriously affecting crop yield and quality. Various kinds of genes involved in metal homeostasis have been investigated in detail over the past few decades and the mechanisms of how metals are absorbed from soil and distributed in plants have been elucidated. However, numerous genes related to metal homeostasis remain to be investigated and a comprehensive analysis of the expressions of these genes is required. In the present study, we investigated the spatial gene expression profile of iron (Fe)-deficient and cadmium (Cd)-stressed rice by a combination of laser capture microdissection and microarray analysis. We performed comprehensive microarray analysis of a rice root using laser microdissection and collected a total of 13 samples (3 replicates for each sample, 39 total microarray data). Roots of normal, Fe-deficient (-Fe) and Cd-stressed (+Cd) rice were separated into the vascular bundle (VB), cortex (Cor), and epidermis plus exodermis (EP). In addition, vascular bundles from new leaves (newDC) and old leaves (oldDC) at the lowest node, which are important for metal distribution, were separately analyzed.
2013-12-31 | E-GEOD-40549 | biostudies-arrayexpress
Project description:Several metals are essential nutrients for plants but metals are toxic in excess, deleteriously affecting crop yield and quality. Various kinds of genes involved in metal homeostasis have been investigated in detail over the past few decades and the mechanisms of how metals are absorbed from soil and distributed in plants have been elucidated. However, numerous genes related to metal homeostasis remain to be investigated and a comprehensive analysis of the expressions of these genes is required. In the present study, we investigated the spatial gene expression profile of iron (Fe)-deficient and cadmium (Cd)-stressed rice by a combination of laser capture microdissection and microarray analysis.
2013-12-31 | GSE40549 | 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:We used RNA-Seq to systematically investigate the global transcriptomes of rice which was inoculated with viruliferous SBPH, or inoculated with insect-derived RSV or plant-derived RSV by mechanical inoculation, and generated a useful resource for the immune reaction of rice in face of different kinds of RSV. The changes in the expression of candidate transcripts may provide valuable information for future studies on molecular mechanisms of rice stripe disease.
2015-10-18 | E-MTAB-5025 | biostudies-arrayexpress
Project description:A biological phenomenon in which hybrids exhibit superior phenotypes from its parental inbred lines known as heterosis, has been widely exploited in plant breeding and extensively used in crop improvement. Hybrid rice has immense potential to increase yield over other rice varieties and hence is crucial in meeting increasing demand of rice globally. Moreover, the molecular basis of heterosis is still not fully understood and hence it becomes imperative to unravel its genetic and molecular basis. In this context, RNA sequencing technology (RNA-Seq) was employed to sequence transcriptomes of two rice hybrids, Ajay and Rajalaxmi, their parental lines, CRMS31A (sterile line, based on WA-CMS) and CRMS32A (sterile line based on Kalinga-CMS) respectively along with the common restorer line of both hybrids, IR-42266-29-3R at two critical rice developmental stages viz., panicle initiation (PI) and grain filling (GF). Identification of differentially expressed genes (DEGs) at PI and GF stages will further pave the way for understanding heterosis. In addition, such kind of study would help in better understanding of heterosis mechanism and genes up-regulated and down-regulated during the critical stages of rice development for higher yield.
2015-08-02 | E-MTAB-4291 | biostudies-arrayexpress
Project description:Characterizing the role of rice NRAMP5 in Manganese, Iron and Cadmium Transport
| PRJNA152307 | ENA
Project description:5 leaves old rice plantlets were infected with Magnaporthe grisea spores and zero, two hours and twenty four houres after infection samples were collected
2014-01-31 | GSE50454 | 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:LongSAGE library in this series are from 'Whole Genome Analysis of Pathogen-Host Recognition and Subsequent Responses in the Rice Blast Patho-System' project. This work is supported by NSF-PGRP #0115642. Keywords: other
2004-11-08 | GSE1924 | GEO