Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome analysis of ROP10 GTPase-mediated abscisic acid (ABA) signaling in Arabidopsis

ABSTRACT: In this study, we have identified genes that are respectively activated and repressed by the low concentration of ABA and show that ROP10 gates a specific subset of genes that are responsive only to a low ABA concentration. Keywords: Whole seedlings of wild-type (Ws) and the mutant (rop10-1) treated with or without ABA 12 Arabidopsis ATH1 chips were purchased from Affymetrix. Total RNA was extracted and purified from 1µM ABA-treated or non-treated Ws and rop10-1. Each genotype/treatment has three biological replicates. Probe labeling, array hybridization and scanning were done by the University of California-Irvine DNA Microarray Facility.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Zhi-Liang Zheng

PROVIDER: E-GEOD-3454 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Transcriptome analysis reveals specific modulation of abscisic acid signaling by ROP10 small GTPase in Arabidopsis.

Xin Zeyu Z Zhao Yihong Y Zheng Zhi-Liang ZL

Plant physiology 20051028 3

Abscisic acid (ABA) is a hormone that modulates a variety of agronomically important growth and developmental processes and various stresses responses, but its signal transduction pathways remain poorly understood. ROP10, a member of ROP small GTPases in Arabidopsis (Arabidopsis thaliana), is a plasma membrane-associated protein specifically involved in negative regulation of ABA responses. To dissect the ROP10-mediated ABA signaling, we carried out transcriptome analysis using the Arabidopsis f ...[more]

PMID: 16258012

Similar Datasets

Transcriptome analysis of ROP10 GTPase-mediated abscisic acid (ABA) signaling in Arabidopsis

Project description:In this study, we have identified genes that are respectively activated and repressed by the low concentration of ABA and show that ROP10 gates a specific subset of genes that are responsive only to a low ABA concentration. Keywords: Whole seedlings of wild-type (Ws) and the mutant (rop10-1) treated with or without ABA

2005-11-14 | GSE3454 | GEO

Grape skin transcriptome in the berries cultured in vitro treated with exogenous abscisic acid

Project description:The softened green berries of Cabernet Sauvignon were cultured in a Petri dish. 0.3M sucrose solution with (±)-abscisic acid (ABA) and without (±)-ABA (control) were applied to the Petri dishes. The berry skins were sampled at 3 and 10 days after the application. PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Kazuya Koyama. The equivalent experiment is VV17 at PLEXdb. ABA treated - time: 3 days(2-replications); ABA treated - time: 10 days(2-replications); Non-treated (control) - time: 3 days(2-replications); Non-treated (control) - time: 10 days(2-replications)

2011-08-25 | E-GEOD-31662 | biostudies-arrayexpress

Genes regulated by GRF1 and GRF3 in Arabidopsis roots

Project description:Arabidopsis Affymetrix ATH1 GeneChips were used to compare the mRNA profiles of root tissues of the grf1/grf2/grf3 triple mutant and transgenic plants overexpressing miR396-resistant variants of GRF1 (P35S:rGRF1) or GRF3 (P35S:rGRF3) with those of the corresponding wild-type (Col-0 or WS). Wild-type (Arabidopsis thaliana ecotypes Col-0 and Ws), the triple mutant grf1/grf2/grf3, and transgenic plants overexpressing rGRF1 or rGRF3 were grown in vertical culture dishes on modified KnopM-bM-^@M-^Ys medium for 2 weeks and then root tissues were collected for RNA extraction. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Tarek Hewezi. The equivalent experiment is AT109 at PLEXdb.] genotype: Arabidopsis thaliana ecotypes Col-0(3-replications); genotype: Arabidopsis thaliana ecotypes WS(3-replications); genotype: Triple mutant grf1/grf2/grf3(3-replications); genotype: P35S:rGRF1 overexpression(3-replications); genotype: P35S:rGRF3 overexpression(3-replications)

2012-03-13 | E-GEOD-31593 | biostudies-arrayexpress

Grape skin transcriptome in the berries grown on the vine treated with exogenous abscisic acid

Project description:The experiment was conducted using grapevines of Cabernet Sauvignon grown in a field. At veraison, the clusters in the vines were sprayed with a 400 mgl-1(+)-abscisic acid (ABA) solution. The ABA treated berries and non-treated berries (control) were harvested at 14 and 28 days after veraison and peeled. PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Kazuya Koyama. The equivalent experiment is VV16 at PLEXdb. ABA treated - developmental stage name: 14 days after veraison(3-replications); ABA treated - developmental stage name: 28 days after veraison(3-replications); untreated (control) - developmental stage name: 14 days after veraison(3-replications); untreated (control) - developmental stage name: 28 days after veraison(3-replications)

2011-08-26 | E-GEOD-31664 | biostudies-arrayexpress

atmyc2_cop1_mutant_light_ABA_treatment

Project description:Although many regulatory components of light signaling have been functionally characterized, only a few of them have been reported to cross talk with other signaling cascades. In this study, we have analyzed the expression profiles of Arabidopsis genes in wild-type, atmyc2 mutant, cop1-6 mutant, and atmyc2 cop1-6 double mutant seedlings grown under constant dark, constant blue-light, and constant blue-light along with abscisic acid (ABA) to illustrate the interplay of negative regulators, AtMYC2 and COP1, in light and ABA signaling Keywords: Light and abscisic acid treatment Expression data for wild-type, atmyc2, cop1-6, and atmyc2 cop1-6 seedlings under constant dark, blue-light and blue-light along with abscisic acid Ten-day-old Arabidopsis (wild-type, atmyc2 mutant, cop1-6 mutant, and atmyc2 cop1-6 double mutant) seedlings grown under constant dark, constant blue-light (35 µmol/sec/m2), and constant blue-light along with ABA (0.5 µm) were used for RNA extraction and hybridization on Affymetrix microarrays. Two biological replicates of each sample were used for microarray analysis.

2009-12-31 | E-GEOD-8955 | biostudies-arrayexpress

Gene expression in mature pollen and sperm cells versus young seedling as a vegetative sporophyte reference control

Project description:Sperm cells represent the male partner that fuses with the egg cell during fertilization in all multi-cellular eukaryotic organisms, and, in flowering plants, is a founder of both embryo and nutritive endosperm. We examined the transcriptome of Oryza sativa ssp. japonica using the Affymetrix 57K rice genome GeneChip to provide an overview of genes activated in the paternal gamete. We used microarrays to detail the global program of gene expression in mature pollen and sperm cells at anthesis, which constitutes the stage immediately preceding pollen germination and gamete deposition leading up to fertilization. This documents the condition of the male gametophytic cells prior to fertilization. Keywords: tissue expression profile, male gametophyte, sperm, pollen, seedling Male gametophytic cells consisting of isolated pollen and isolated sperm cells collected at anthesis were compared with seedlings containing leaf, stem, root and apical meristems as a vegetative sporophytic control; three separate biological replicates were used.

2012-04-29 | E-GEOD-17002 | biostudies-arrayexpress

Transcript profiling of auxin/cytokinin crosstalk in the Arabidopsis primary root apex

Project description:AtIPT8/pga22 seedlings (gain-of-function mutant in Ws background; Sun et al. 2003, Plant Physiology 131, pp167-176) were grown on vertical plates for 7 days in LD. The seedlings were then incubated directly on the plate with medium containing 5 uM 17-beta-estradiol (for induction of the IPT8 gene) or 5 uM trans-zeatin for 12 and 24 h. 5 mm primary root tips were harvested from the seedlings and pooled for microarray analysis. Total RNA was isolated from the samples with the RNeasy Plant Mini Kit from Qiagen. 14 samples were used in this experiment.

2010-04-28 | E-GEOD-20231 | biostudies-arrayexpress

Expression data from ARPE-19 cells treated with LDL or ox-LDL

Project description:LDL or Ox-LDL 200ug/ml, which showed no loss of viability after a 48 hour exposure, induced a physiological and pathological transcriptional response, respectively. LDL induced a downregulation of genes associated with cholesterol biosynthesis while ox-LDL induced transcriptional alterations in genes related to inflammation, matrix expansion, lipid metabolism and processing, and apoptosis. Pentraxin-3 was secreted into the culture medium after RPE cells were stimulated with ox-LDL, and immunohistochemically evident in Bruchs membrane of human macular samples with age-related macular degeneration. ARPE-19 cells exposed to 200ug/ml ox-LDL had a 38% apoptosis rate compared to less than 1% when exposed to LDL or untreated controls (p<0.0001). While LDL induced a physiologic response by RPE cells, a pathological phenotypic response was seen after treatment with oxidatively modified LDL. The transcriptional, biochemical, and functional data provide initial support of a role for the hypothesis that modified LDLs are one trigger for initiating events that contribute to the development of age-related macular degeneration. Keywords: treatment with non-treatment control Human ARPE-19 cells were exposed to LDL or oxidatively modified LDL (ox-LDL) for 48 hours for RNA extraction and hybridization on Affymetrix microarrays. We sought to determine whether retina, pigment epithelial cells develop a pathologic phenotype after exposure to low density lipoproteins (LDL) that are oxidatively modified.We have made two comparsions: LDL treatment versus non-treatment; ox-LDL treatment versus non-treatment.

2006-09-01 | E-GEOD-5741 | biostudies-arrayexpress

Expression comparasion of rice seedlings of Osabl1 mutant and WT under ABA treatment

Project description:Expression profiles of seedling roots of rice mutant Osabl1 and wild-type under ABA treatment Mutant and wild-type expression profiling were compared and each has two biological repeats.

2011-10-12 | E-GEOD-18529 | biostudies-arrayexpress

Genome-wide transcriptome analysis of two maize inbred lines under drought stress during the seedling stage

Project description:To understand the transcriptome changes during drought tolerance in maize, the drought-tolerant line Han21 and drought-sensitive line Ye478, which show substantial differences in drought tolerance at the seedling stage, were selected for this study. Using the GeneChip Maize Genome Arrays, we applied genome-wide gene expression analysis to the two genotypes under gradual drought stress and re-watering. We identified 2172 common regulated transcripts in both lines under drought stress, with 1084 common up-regulated transcripts and 1088 common down-regulated transcripts. Among the 2172 transcripts, 58 potential protein kinases and 117 potential transcription factors were identified. The potential components of the ABA signaling pathway were identified from the common regulated transcripts. We also identified 940 differentially regulated transcripts between the two lines. Among the 940 transcripts, the differential expression levels of 29 transporters and 15 cell wall-related transcripts may contribute to the different tolerances of the two lines. Additionally, we found that the drought-responsive genes in the tolerant Han21 line recovered more quickly when the seedlings were re-watered, and 311 transcripts in the tolerant Han21 line were exclusively up-regulated at the re-watering stage compared to the control and stress conditions. Our study provides a global characterization of two maize inbred lines during drought stress and re-watering and will be valuable for further study of the molecular mechanisms of drought tolerance in maize. In two independent experiments, we generate maize gene expression profiles during drought stress and re-watering through comparing genome-wide expression patterns of drought stress treatment and re-watering treatment by using 17,555 Affymetrix maize whole genome array.

2010-06-16 | E-GEOD-16567 | 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