Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

14 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Interaction between the light environment and the Arabidopsis wound response

ABSTRACT: We have previously identified a significant increase in chloroplast reactive oxygen species in wounded leaves of Arabidopsis and other plants, which is light-dependent (Flor-Henry et al. (2004) BMC Plant Biology 4:19). The aims of this study were to (i) examine the early response to mechanical wounding in Arabidopsis leaves, (ii) test the hypothesis that light-dependent chloroplast ROS may play a role in signalling for changes in gene expression in wounded leaves, and (iii) examine the broader impact of the light environment on the wound response in Arabidopsis. Keywords: Stress response The experiment was a two-by-two factorial design, with wounding and light as the two variables. In each replicate, there are 4 treatments: unwounded/light, unwounded/dark, wounded/light, wounded/dark. Three independent biological replicate experiments were performed, with one array hybridisation performed per treatment.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Krishna Morker

PROVIDER: E-GEOD-13803 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Plasmodiophora brassicae infection of Arabidopsis thaliana

Project description:Arabipdosis thaliana (ecotype Col-0) was infected with the root pathogen Plasmodiophora brassicae. Gene expression of the host plant has been analyzed at two time points after inoculation (10 and 23 days after inoculation) compared to the correspondend control plants.

2005-02-25 | E-MEXP-254 | biostudies-arrayexpress

Identification of genes related to agarwood formation: transcriptome analysis of healthy and wounded tissues of Aquilaria sinensis

Project description:Agarwood is an expensive resinous heartwood derived from the wounded Aquilaria plants. To identify the primary genes that maybe related to agarwood formation, we sequenced 2 cDNA libraries generated from healthy and wounded A. sinensis (Lour.) Gilg. A total of 89,137 unigenes with an average length of 678.65 bp were obtained, and they were annotated in detail at bioinformatics levels. Of those associated with agarwood formation, 30 putatively encoded enzymes in the sesquiterpene biosynthesis pathway, a handful of transcription factors, and protein kinases related to wound signal transduction. Three full-length cDNAs of sesquiterpene synthases (ASS1-3) were cloned and expressed in Escherichia coli, and enzyme assays revealed that they are active enzymes, with the major products being M-NM-4-guaiene. A methyl jasmonate (MJ) induction experiment revealed that the expression of ASS was significantly induced by MJ, and the production of sesquiterpenes was elevated accordingly. The expression of some transcription factors and protein kinases, especially MYB4, WRKY4, MPKK2 and MAPK2, was also induced by MJ and coordinated with ASS expression, suggesting they maybe positive regulators of ASS. This study provides extensive transcriptome information for Aquilaria spp. and valuable clues for elucidating the mechanism of wound-induced agarwood sesquiterpenes biosynthesis and their regulation. healthy and wounded stems of three-year-old A. sinensis trees

2013-12-31 | E-GEOD-42246 | biostudies-arrayexpress

Effect of TIF on gene expression under inductive and non-inductive photoperiods

Project description:The primary objective of this project is to determine the physiological and developmental differences between photoperiod and root induced tuberization responses in potato using genomic techniques. These experiments will establish baseline genomic and proteomic response associated with a partially characterized root-produced compound (TIF) that either substitutes for, or over-rides, the primary leaf perceived photoperiod induction signal in potato. The proposed work will answer the following questions. Are photoperiod and root induced tuberization responses the same? Do photoperiod and root induced tuberization trigger the same developmental processes in the stolon? How are photoperiod and root induced signals expressed in the genome of the leaf, stolon and roots? The data from the proposed experiments will prove invaluable in identifying key pathways in specific tissues to target in subsequent experiments in order to determine identify of, and establish the mode of action of the TIF compound. Keywords: Direct comparison 35 hybs total

2007-09-01 | E-GEOD-8280 | biostudies-arrayexpress

wt and opr3 control and systemic wounding

Project description:wt plants (ws) and opr3 mutant plants were wounded Half of the rosette leaves of 6 weeks old plants were wounded by clamping a tweezers across the midvein. RNA was extracted from control and systemic leaves 2 h after wounding, and was subject to affymetrix ATH1 chip. one repeat: wt control, wt systemic wounding, opr3 control, opr3 systemic wounding

2010-12-01 | E-GEOD-14332 | biostudies-arrayexpress

Expression data from Arabidopsis leavs 10 min after wounding.

Project description:Rapid responses to biotic and abiotic insults are crucial for plant survival. We examined the very early (10 min) wound transcriptome in order to increase our understanding regarding this critical intial phase of the plant response to stress. Our analysis revealed a rapid induction of stress-related transcripts that was distinct from the long term events which are dominated by jasmonic pathway responses. The transcriptome showed high correlation between the early wound response and other early but not late responses to innate immune interactions and other abiotic stresses. In addition those early responses were correlated with transcriptomes of response to singlet oxygen as displayed in the flu mutant. Singlet oxygen appears to be a signaling intermediate in the plant response to multiple stresses. 6 samples were analysed in total with 2 replicates from each type of treatment; control (unwounded plants), local (woundedd plants) and systemic (unwounded leaves from wounded plants).

2013-07-11 | E-GEOD-48676 | biostudies-arrayexpress

Transcriptome Analysis of Wounding-Induced Root to Shoot Communication in Arabidopsis thaliana.

Project description:Comparison of gene expression between shoots of root-wounded seedlings and shoots of control seedlings in Arabidopsis. We identified wounding-induced early (30 min) and late (360 min) root to shoot responsive genes (RtS). Two-condition experiment, shoots of root-wounded seedlings vs. shoots of control seedlings. Biological replicates: 2 control replicates, 2 treated replicates. Technical replicate: Dyeswap

2010-12-31 | E-GEOD-26374 | biostudies-arrayexpress

Transcription profiling of Arabidopsis Col0 and tpc1 plants wounded for 3 hours

Project description:Arabidopsis Col0 and tpc1 plants were wounded for 3h. 1/4 of leaf was crushed with pliers

2008-07-01 | E-MEXP-1392 | biostudies-arrayexpress

Transcription profiling of Arabidopsis thaliana six days after infection with Agrobacterium tumefaciens

Project description:This study focuses on responses of the host plant to infection and transformation with Agrobacterium tumefaciens. Genome wide changes in gene expression were integrated with the alterations in metabolite levels six days after inoculation of agrobacteria. Plants were infected with the virulent strain C58, harboring a T-DNA, or with strain GV3101, containing a disarmed Ti-plasmid. This allows discrimination between signals which derive from the bacterial pathogen and the T-DNA encoded genes. Experiment Overall Design: The bases of Arabidopsis thaliana (WS-2) inflorescence stalks were wounded and immediately infected with Agrobacterium tumefaciens or mock-infected for six days. Stalks of intact plants were inoculated with the oncogenic strain C58 (C58 6dpi 1 to 3) or the non-virulent strain GV3101 (GV3101 6dpi 1 to 3) to provide conditions close to nature. The gene expression data of three independent experiments of infected material were compared with three non-infected samples (reference 6dpi 1 to 3). Differential gene expression was determined by applying the LIMMA package (Linear Models for Microarray Data; Smyth, G.K. (2004) Applic. Genet. Mol. Biol. 3, Article 3; http://www.bepress.com/sagmb/vol3/iss1/art3/).

2009-12-02 | E-GEOD-13930 | biostudies-arrayexpress

Transcription profiling by array of Arabidopsis after infection with different strains of Agrobacterium tumefaciens

Project description:This study focuses on responses of the host plant to infection with Agrobacterium tumefaciens. Genome wide changes in gene expression were integrated with the alterations in metabolite levels three hours after inoculation of agrobacteria. Plants were infected with the virulent strain C58, harboring a T-DNA, or with strain GV3101, containing a disarmed Ti-plasmid. This allows discrimination between signals which derive from the bacterial pathogen and the T-DNA encoded genes. Experiment Overall Design: The bases of Arabidopsis thaliana (WS-2) inflorescence stalks were wounded and immediately infected with Agrobacterium tumefaciens or mock-infected for three hours. Stalks of intact plants were inoculated with the oncogenic strain C58 (C58 3 hpi 1 to 6) or the non-virulent strain GV3101 (GV3101 3 hpi 1 to 3) to provide conditions close to nature. The gene expression data of three independent experiments of infected material were compared with six non-infected samples (reference 3 hpi 1 to 6). Differential gene expression was determined by applying the LIMMA package (Linear Models for Microarray Data; Smyth, G.K. (2004) Applic. Genet. Mol. Biol. 3, Article 3; http://www.bepress.com/sagmb/vol3/iss1/art3/).

2009-12-02 | E-GEOD-13929 | biostudies-arrayexpress

Current injection and distal wound response in Arabidopsis thaliana

Project description:These data represent two experiments, one on wounding leaves and one based on injecting current into leaves. We first analyzed transcript levels in leaf 13 when leaf 8 was wounded. Transcripts levels in leaf 8 were then analyzed after current injection. Sample handling and normalisations were identical between experiments. Leaf 8 was wounded with forceps. 1 h later, leaf 13 was harvested. Unwounded leaf 13 was used for controls. For current injected (40 ?A, 10 s) versus non-current injected leaves, samples were harvested 1h after current injection. Non-current injected leaves used as control. In each case leaf 8 was used.

2013-08-21 | E-GEOD-41779 | 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