Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

57 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of Arabidopsis seedlings exposed to ANep1 Treatment

ABSTRACT: In order to study the Nep1 responsive genes in Arabidopsis, experiments were performed with the Affymetrix GeneChip Arabidopsis ATH1 Genome Array (Santa Clara, CA; Cat # 900385). Experiment Overall Design: Seven-day old Arabidopsis seedlings were exposed to Nep1 (10 ug/mL) treatment or using sterilized, deionized H2O as a control for 30 min. Two independent biological replications were conducted using two independent samples and two microarrays.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Hanhong Bae

PROVIDER: E-GEOD-4638 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Necrosis- and ethylene-inducing peptide from Fusarium oxysporum induces a complex cascade of transcripts associated with signal transduction and cell death in Arabidopsis.

Bae Hanhong H Kim Moon S MS Sicher Richard C RC Bae Hyeun-Jong HJ Bailey Bryan A BA

Plant physiology 20060512 3

Treatment of Arabidopsis (Arabidopsis thaliana) with a necrosis- and ethylene-inducing peptide (Nep1) from Fusarium oxysporum inhibited both root and cotyledon growth and triggered cell death, thereby generating necrotic spots. Nep1-like proteins are produced by divergent microbes, many of which are plant pathogens. Nep1 in the plant was localized to the cell wall and cytosol based on immunolocalization results. The ratio of chlorophyll a fluorescence (F685 nm/F730 nm) significantly decreased af ...[more]

PMID: 16698904

Similar Datasets

Identification of genes expressed during ROL barrier formation in rice root

Project description:Potential components of the barrier to radial oxygen loss (ROL) are suberin and/or lignin, which accumulate at the cell wall in the cells of peripheral cell layers of the root. Chemical composition of the apoplastic barrier in rice roots was characterized and it was suggested that ROL can be restricted by the formation of a suberized exodermis and/or lignified sclerenchyma in the outer part of the root. To characterize reorganization of primary carbon metabolism in rice roots during the ROL barrier formation, we obtained the profiles of polar metabolites and the profiles of fatty acids of different zones of rice roots from plants growing in stagnant (anaerobic) and in well aerated medium. Biochemical data are combined with the results of microarray analysis. Nine days after germination, the seedlings were transferred to well aerated nutrient solution or stagnant deoxygenated nutrient solution. Stagnant solution contained 0.1% (w/v) dissolved agar and was deoxygenated (dissolved oxygen, <0.5 mg lM-bM-^@M-^S1) prior to use by flushing with N2 gas. After 14 d (23 d old), adventitious roots, 100-150 mm long, were harvested from rice plants grown either in aerated or stagnant conditions and RNA was extracted from 10 mm segments from the regions 0-10 mm, 10-20 mm and 20-30 mm from the root apex have been cut with sterile razor blade and collected and processed separately. Total RNAs were labeled with a Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturerM-bM-^@M-^Ys instructions. Aliquots of Cy5-labeled and Cy3-labeled cRNA (825 ng each) were used for hybridization in a rice 44K oligo-DNA microarray.

2014-02-18 | E-GEOD-52128 | 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

Auxin-independent NAC pathway regulates cell wall metabolism in response to explant-specific wounding during regeneration in Arabidopsis

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-12-31 | E-GEOD-74587 | biostudies-arrayexpress

Arabidopsis thaliana: safranal-treated seedlings versus control seedlings

Project description:Transcriptional profiling of Arabidopsis thaliana seedlings treated with safranal, highlighting to the physiological function of plant volatile chemicals by observing early response of gene expressions in Arabidopsis seedlings. Two-condition experiment, safranal-treated seedlings vs. control seedlings. Biological replicates:2 control replicates, 2 safranal-treated.

2016-01-13 | E-GEOD-76787 | biostudies-arrayexpress

Auxin-independent NAC pathway regulates cell wall metabolism in response to explant-specific wounding during regeneration in Arabidopsis I

Project description:In this study, through a genome-wide transcriptome analysis of wounding in the leaf explant, we identified NAC1 (petunia NAM and Arabidopsis ATAF1, ATAF2, and CUC2) family transcription factor gene that acts in response to wounding and functions in regulation of cell wall metabolism. RNA-Seq analysis of the genes up-regulated by NAC1

2015-12-31 | E-GEOD-74584 | biostudies-arrayexpress

Transcription profiling time series of Arabidopsis seedlings treated with the cytokinin benzyladenine or DMSO

Project description:10 day old seedlings were treated with 5uM of the cytokinin Benzyladenine(BA)or DMSO at 15min, 45min, 120min, 480min and 1440min

2006-08-24 | E-MEXP-749 | biostudies-arrayexpress

Auxin-independent NAC pathway regulates cell wall metabolism in response to explant-specific wounding during regeneration in Arabidopsis II

2015-12-31 | E-GEOD-74585 | biostudies-arrayexpress

Zhang-arabidopsis-auxin vs NPA

Project description:transcription profiling of different development stage and different treatment

2012-02-22 | E-MEXP-3127 | biostudies-arrayexpress

Transcription profiling of Arabidopsis sav mutants

Project description:Plants grown at high densities perceive a decrease in the red to far-red (R:FR) ratio of incoming light, resulting from absorption of red light by canopy leaves and reflection of far-red light from neighboring plants. These changes in light quality trigger a series of responses known collectively as the shade avoidance syndrome. During shade avoidance, stems elongate at the expense of leaf and storage organ expansion, there is reduced branching, and flowering is accelerated. We identified several loci in Arabidopsis, mutations in which lead to plants defective in multiple shade avoidance outputs. Here we describe SAV3, an aminotransferase, and show that SAV3 catalyzes the formation of indole-3-pyruvic acid (IPA) from L-tryptophan (L-Trp), the first step in a previously proposed, but uncharacterized, auxin biosynthetic pathway. This pathway can be rapidly deployed to biosynthesize auxin at the high levels required to initiate the multiple changes in body plan associated with shade avoidance. Experiment Overall Design: Wild type Col-0, sav3-2 and sav1-1 seedlings were used here. They were treated with or without 1hr of low R:FR light (R:FR ratio=0.7). Three independent biological replicates were used.

2008-06-16 | E-GEOD-9816 | biostudies-arrayexpress

Early transcriptomic responses of rice leaves to herbivory by Spodoptera frugiperda

Project description:In this experiment we aimed to decipher the transcription response of rice to the different cues of an herbivory attack from the chewing caterpillar Spodoptera frugiperda. We performed a herbivory mimic procedure on seedlings and applied mechanical wounding (WOS), application of herbivore oral secretions (OS) after wounding (WOS+) and dysbiotic OS (WOS-) on rice leaves. RNA was extracted from control and treated leaves after two hours. 5 biological replicates corresponding to 5 pooled leaves were performed for each of the four condition

2023-08-31 | E-MTAB-13227 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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