Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Expression data from OsSIK2-overexpression and mutant rice seedlings

ABSTRACT: Receptor-like kinases (RLKs) play important roles in plant development and defense responses; however, their functions in other processes remain unclear. Here, we report that OsSIK2, an S-domain RLK from rice, is involved in abiotic stress and senescence process, integrating stress signals into developmental program for adaptive growth. We used microarrays to detail the gene expression in OsSIK2-overexpression and mutant lines from 14-day-old rice seedlings and identified distinct regulated genes. We sought to obtain distinct regulated genes by OsSIK2. To that end,the aerial parts of different rice seedlings,including OsSIK2-overexpression lines, mutant and respective controls, were harveted for total RNA extraction and hybridization on Affymetrix microarrays.

ORGANISM(S): Oryza sativa

SUBMITTER: Xiang Lu

PROVIDER: E-GEOD-51151 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Expression data from rice embryo and endosperm development

Project description:The receptor-like kinases (RLKs) plays critical roles in signal transduction through sensing the extracellular signals and activating the downstream signal transduction by phosphorylating their targets. Up to now, there are only a few RLKs have been functionally identified. In this study, we systemically analyzed the expression pattern of rice genes, especially the RLK coding genes during embryo and endosperm development. Rice Ovary and three development stages of embryo and endosperm (embryo 3, 9, 12 DAF; Endosperm 3, 9, 16 DAF) were analyzed, all of them were biologically repeated two times.

2012-02-01 | E-GEOD-27856 | biostudies-arrayexpress

Global expression profiling of low temperature induced genes in chilling tolerant japonica rice

Project description:Three week old seedlings of rice cultivar Jumli Marshi (spp. Japonica) was exposed to cold (+4C) temperatures for varying time periods. Tissue samples were collected in replicates. Microarray data analysis was then performed on the extracted totalRNA from the samples.

2013-05-01 | E-MEXP-3718 | biostudies-arrayexpress

Transcriptomic profiling of rice (Oryza sativa) cv. Sijung and Jumli Marshi during early chilling stress

Project description:The aim of this study was to conduct global gene expression profiling and comparative analysis of two chilling tolerant rice varieties, Jumli Marshi and Sijung (spp. Japonica), during early chilling stress (24h, 10C). Leaf tissue from cv. Jumli Marshi and cv. Sijung plants grown under chilling stress conditions were harvested after 4 and 24 h. Control plants (0 h) were harvested at the beginning of the experiment, i.e., at mid-day. Three biological replicates were profiled for each time point and variety. In order to readily detect highly (saturated) as well as weakly (near background signal) expressed genes, scanning was done twice on the microarrays: at the PMT sensitivity level 100% (pmt100) and 10% (pmt10).

2014-11-30 | E-MTAB-3121 | biostudies-arrayexpress

Comparative Proteome Profiling of Susceptible anComparative Proteome Profiling of Susceptible and Resistant Rice Cultivars Identified an Arginase Involved in Rice Defense Against Xanthomonas oryzae pv. oryzae d Resistant Rice Cultivars Identified an Arginase Involved in Rice Defense Against Xanthomonas oryzae pv. oryzae

Project description:Xanthomonas oryzae pv. oryzae (Xoo), the causative agent of bacterial blight disease, is one of the major threats to rice productivity. Yet, the molecular mechanism of rice-Xoo interaction is elusive. Here, we report comparative proteome profiles of Xoo susceptible (Dongjin) and resistant (Hwayeong) cultivars of rice in response to two-time points (3 and 6 days) of Xoo infection. Low-abundance proteins were enriched using a protamine sulfate (PS) precipitation method and isolated proteins were quantified by a label-free quantitative analysis, leading to the identification of 3846 protein groups. Of these, 1128 proteins were significantly changed between mock and Xoo infected plants of Dongjin and Hwayeong cultivars. Based on the abundance pattern and functions of the identified proteins, a total of 23 candidate proteins were shortlisted that potentially participate in plant defense against Xoo in the resistant cultivar. Of these candidate proteins, a mitochondrial arginase-1 showed Hwayeong specific abundance and was significantly accumulated following Xoo inoculation. Overexpression of arginase-1 in susceptible rice cultivar (Dongjin) resulted in enhanced tolerance against Xoo as compared to the wild-type (WT). In addition, expression analysis of defense-related genes encoding PR1, glucanase I, and chitinase II by qRT-PCR showed their enhanced expression in the overexpression lines as compared to WT. Mitochondrial localization of the selected arginase was further confirmed by fluorescent microscopy using GFP-tagged arginase. Taken together, our results uncover the proteome changes in the rice cultivars and highlight the functions of arginase in plant defense against Xoo.

2022-01-06 | PXD027569 | Pride

A global profiling of gene expression in chilling stress in rice

Project description:RNA-Seq was performed to study the change of gene expression before and after chilling treatment in rice. Different change patterns were identified. We have provided a complete view of transcriptome under cold stress condition, which will deepen our understanding of gene expression regulation in cold stress response as well as cold stress response mechanism for monocot plants. The mRNA profiles of 15-day-old rice seedlings with and without chilling treatment (4 Â°C for 33 h) were generated by deep sequencing using Illumina Hiseq 2000 platform.

2016-04-13 | E-GEOD-67373 | biostudies-arrayexpress

Expression data from rice roots treated with Gln

Project description:We used GeneChip Rice Genome Array (Affymetrix, Santa Clara, CA, USA) to identify genes that were rapidly induced by glutamine in rice roots. Transcriptomic analysis of rice roots revealed that the expression of at least 35 genes involved in metabolism, transport, signal transduction, and stress responses was rapidly induced by glutamine within 30 minutes. Total RNA from –N and Gln-treated roots (2.5 mM Gln, 30 min) was extracted using a phenol extraction protocol. RNA samples from two biological repeats were sent to the Affymetrix Gene Expression Service Lab at Academia Sinica, Taipei, Taiwan (http://ipmb.sinica.edu.tw/affy/) for target preparation, and hybridization to the GeneChip Rice Genome Array.

2015-06-30 | E-GEOD-56770 | biostudies-arrayexpress

Rice stem at early stage growth: Control vs.Chromosome segment substitution lines (SLs) from a cross the Koshihikari (japonica) and Habataki (indica)

Project description:By performing QTL mapping using 82 backcross inbred lines (BILs) of the Koshihikari (japonica) and Habataki (indica) cultivars for the rice initial growth, we identified two QTLs, qEPD1 and qEPD2, responsible for modulating plant height and/or leaf sheath length. To narrow down the number of candidate genes of each QTL, we conducted transcriptional profiling using RNAs isolated from the vegetative stem of Koshihikari and its two substituted lines (SL) with the Habataki qEPD1 or qEPD2 allele. Expression profiling with the rice 44K-Agilent microarray (Agilent-028517) was conducted using RNAs extracted from the 30-day-old vegetative stem of the corresponding lines. Each dataset was obtained from three biological replicates.

2012-03-31 | E-GEOD-35762 | biostudies-arrayexpress

Transcriptomes of Rice internode before and after heading

Project description:To identify genes that co-express with rice cellulose synthase genes involved in rice secondary cell wall formation, transcriptome analyses was performed using rice internodesbefore and after the heading stage, where secondary cell wall formation extensively occur. Transcriptomes of rice third or the fourth internodes were analyzed at 17, 8, and 1 day before, and 6, 13, and 35 days after heading Please note that the current data were normalized together with additional 143 sample data available in GEO and the list of the sample accessions is provided in Series supplementary file [normalized_together_GSMs.txt].

2013-10-01 | E-GEOD-51289 | biostudies-arrayexpress

Probing the Existence of an Alternative Gibberellin Receptor(s) in Rice Aleurone Cells

Project description:Many years after the discovery of GID1 as the GA receptor, the belief in the existence of GA-binding protein (GBP) in aleurone cells still persists. Actually, some recent reviews and textbooks still contain information about the possibility of an alternative GA perception mechanism mediated by GBPs. Thus, to finally clarify this issue, we examined the expression of GA-regulated genes using rice embryoless half-seeds of four kinds of GA signaling mutants, each one independently carrying mutated GID1, DELLA, and GA-related F-box, which are all encoded by single genes in rice, allowing for convenient study of the GA perception system. The comprehensive microarray analysis using these rice mutants revealed that all genes tested to be responsive to GA in the wild-type (WT) aleurone cells consistently did not respond to GA in the gid1 or slr1 mutant. All microarray experiments were performed according to the manufacturerM-bM-^@M-^Ys manual. The Feature Extraction software (Agilent Technologies) was used to delineate and measure the Cy3 and Cy5 signal intensities of each spot in the array. The resulting data were normalized using the Variance-stabilizing normalization (VSN) algorithm.

2014-12-19 | E-GEOD-64290 | biostudies-arrayexpress

Gene expression profiling for early rice stamen

Project description:Plant organ formation, or organogenesis is the process in which the primordium derived from shoot apical meristem develops into an organ with a given shape and proper function, through a series of cell division and differentiation. To decipher the genetic program underling plant organ formation, we targeted early rice stamen development that covers most important events in male organ formation and germ cell initiation in plants. Totally, seven samples were used in this experiment. Stamens of stages 2-6 was collected through microdissection under microscope. And to ensure the stamen primordia collected are at corresponding stages, rice panicles were cut in half longitudinally, one half for paraffin sectioning to confirm developmental stages and the other half for preparing GEP samples. Samples of primordial and just-expanded third leaves were used as controls because leaf and stamen are homolog organs. RNA was extracted and amplified with Two-Cycle Eukaryotic Target Labeling Assay kit, and then hybridized to microarrays. Three biological replicates were applied for each sample.

2013-12-17 | E-GEOD-53347 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data