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

Identification of Direct Targets of RPX a NAC transcription factor of Arabidopsis thaliana

ABSTRACT: To determine the role of RPX on cell proliferation and organ development, we performed microarray experiments in search of RPX target genes by using an estradiol-inducible RPX protein. Estradiol-treatment allows for the nuclear translocation of the constitutively expressed chimeric transcription factor XVE and subsequent expression of RPX from the LexA promoter. Stable transgenic T3 seedlings were either treated with 10 uM estradiol or ethanol (mock) for 2 hours. Three mock and three estradiol treated samples were used for RNA isolation and hybridization.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Jos Schippers

PROVIDER: E-GEOD-34837 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Inducible overexpression analysis of KUODA1 in Arabidopsis seedlings

Project description:To identify potenital target genes of the transcription factor KUODA1 (AT5G47390), we performed expression profiling using an estradiol inducible overexpression system. Estradiol-treatment allows for the nuclear translocation of the constitutively expressed chimeric transcription factor XVE and subsequent expression of KUA1 from the LexA promoter. Stable trangenic T3 seedlings were grown for 14 days and either treated with 15 M-BM-5M estradiol or ethanol (mock) for 4 hours. Two mock and two estradiol treated samples were used for RNA isolation and hybridization.

2013-12-31 | E-GEOD-50520 | biostudies-arrayexpress

Transcription factor ATAF1 integrates carbon starvation responses with trehalose metabolism

Project description:Global transcriptome patterns were obtained from ATAF1-IOE seedlings at 1 h, 2 h and 5 h after estradiol induction or mock treatment, and from mature ATAF1-IOE leaves at 5 h after estradiol induction or mock treatment. To identify genes rapidly responding to elevated ATAF1 expression estradiol induction experiments were performed on ATAF1-IOE seedlings after 1 h, 2 h and 5 h of ATAF1 induction. In addition, expression profiles were obtained from mature leaves after 5 h of ATAF1 induction.

2014-08-30 | E-GEOD-54676 | biostudies-arrayexpress

Genome wide expression analysis of EST-induced EBE-XVE using Affymetrix ATH1 array

Project description:Global transcriptome patterns were determined in XVE-14 and wild-type seedlings induced for 45 min b-estradiol in order to identify the genes early regulated by EBE transcription factor. We used microarrays to identify genes differentially expressed in EST-inducible EBE over-expression line #14 compared to wild-type plants, 45 min after 2µM EST induction. Three independent biological replications were performed. In order to identify potential direct/early target genes of EBE transcription factor, estradiol inducible overexpression system was used. Three week old Arabidopsis EBE-XVE (line 14) and WT seedlings were treated with ß-estradiol (2µM) for 45 min. RNA was isolated from shoot and subjected to hybridization on Affymetrix microarrays. Experiment was performed in 3 biological replications and genes differentially expressed between estradiol treated EBE-XVE and WT plants were identified as potential early targets of EBE.

2013-03-30 | E-GEOD-27855 | biostudies-arrayexpress

Genome wide identification of SHYG early target genes

Project description:Global transcriptome patterns were performed using SHYG-IOE-5h (5h after Estradiol and Mock treatment) To identify genes more rapidly responding to elevated SHYG , we perfromed gene expression profiling (Affymetrix) upon 5h Est treatment of SHYG-IOE plants.

2013-12-29 | E-GEOD-38721 | biostudies-arrayexpress

Identification of ORB1 target genes using inducible overexpression system

Project description:The aim was to identify genes associated to the down-regulation TARGET OF RAPAMYCIN (TOR) pathway in Arabidopsis. For this purpose, three independent amiR-tor lines (amiR-tor9, amiR-tor17 and amiR-tor 20) and EV lines 3 and 6 days after EST- or non-induction were used for expression profile analysis using Affymetrix microarray. Two weeks-old transgenic seedlings were transferred to MS plate with 20ÂµM estradiol to induce the overexpression of amiR-tor (consequently, repression of AtTOR levels) under the control of an estradiol-(EST) inducible promoter. Identically treated wild-type Col-0 and pER8 empty-vector (EV) transformed seedlings were served as controls. Seedlings were harvested after 3 and 6 (amiR-tor lines) days. genetic modification

2013-01-31 | E-GEOD-38878 | biostudies-arrayexpress

Genome wide identification of ORE1 early target genes

Project description:Global transcriptome patterns were performed using ORE1-IOE-2h (2h after Estradiol and Mock treatment) as well as transiently (6h) overexpressed Arabidopsis mesophyll cell protoplasts To identify genes more rapidly responding to elevated ORE1 expression we here repeated the previous experiment (Balazadeh et al., 2010), but shortened the EST induction time to 2 h (ORE1-IOE-2h dataset). Furthermore, to exclude potential misinterpretation due to EST treatment we also included an experiment where we transiently expressed a 35S::ORE1 construct in Arabidopsis mesophyll cell protoplasts and extracted RNA 6 h after the transfection (35S::ORE1-6h dataset);

2013-01-01 | E-GEOD-37536 | biostudies-arrayexpress

The PXC3 receptor-like kinase constitutively interacts with BAK1 and is involved in vascular development in Arabidopsis.

Project description:We designed an experiment to identify BAK1 interactors considering that it could be a coreceptor for the GOLVEN6 (GLV6) signaling peptide involved in lateral root organogenesis in Arabidopsis thaliana. A BAK1pro:BAK1-GFP/bak1-4 line crossed to an estradiol-inducible GLV6 overexpression line (BAK1pro:BAK1-GFP/bak1-4xiGLV6) was treated with mock or estradiol followed by affinity purification mass spectrometry (AP-MS) experiments using anti-GFP beads in microsomal-enriched fractions. Statistical analysis of estradiol-treated vs. mock seedlings did not reveal significant differences. Nevertheless, we remarked that regardless of the treatment, several LRR-RLKs co-eluted with BAK1-GFP, comprising known, as well as, unknown interactors. We confirmed interaction of BAK1 with these LRR-RLKs by BIFC and identified the PXC3 receptor as a BAK1 constitutive interactor, which was further verified by co-IP.

2022-02-17 | PXD026487 | Pride

TuxNet: A simple interface to process RNA sequencing data and infer gene regulatory networks [XVE:PAN]

Project description:We obtained transcriptional profiles of roots from an XVE:PAN transgenic line under the control of the β-estradiol-inducible promoter, at times 0, 6, and 24 hours after induction of PAN expression.

2019-12-06 | GSE112564 | GEO

RNA-seq GLV6 overexpression during lateral root initiation in Arabidopsis thaliana

Project description:The goal of this experiment was to identify the downstream targets of the GOLVEN6 peptide signaling pathway in Arabidopsis thaliana, specifically during lateral root initiation. Using an estradiol inducible GLV6 overexpression construct in wildtype and rgi1rgi5 double mutant (mutant in receptors for the GLV6 peptide) backgrounds, in combination with gravistimulation induced lateral root formation, the RGI receptor dependent transcriptional effects of GLV6 overexpression were characterized. An estradiol inducible GLV6 overexpression line in a wildtype (iGLV6) and in an rgi1rgi5 double receptor mutant background (rgi1rgi5/iGLV6) were used. 4-day old seedlings of both lines were gravistimulated (vertically grown seedlings were turned counterclockwise by 90°) to induce lateral root initiation in the resulting root bends. 8h after gravistimulation, seedlings of both lines were treated with 2µM of estradiol to induce GLV6 overexpression, or DMSO as a mock treatment. 3h and 6h after treatment, root bends were dissected and collected for RNA-sequencing. This yielded a total of 8 samples per replicate; 3h mock treated iGLV6 (IM3), 3h estradiol treated iGLV6 (IE3), 3h mock treated rgi1rgi5/iGLV6 (RM3), 3h estradiol treated rgi1rgi5/iGLV6 (RE3), 6h mock treated iGLV6 (IM6), 6h estradiol treated iGLV6 (IE6), 6h mock treated rgi1rgi5/iGLV6 (RM6), 6h estradiol treated rgi1rgi5/iGLV6 (RE6). For each sample, 4 replicates were obtained. This setup enabled the comparison of the GLV6 induced transcriptional effects between wildtype and rgi1rgi5 mutants at 2 time points after treatment, in samples that are strongly enriched for lateral root initiation events.

2022-02-13 | E-MTAB-10891 | biostudies-arrayexpress

Nanopore sequencing of estradiol and DMSO treated XVE:ROS1-YFP plants

Project description:Transgenic plants carrying an estradiol-inducible ROS1-YFP construct (XVE:ROS1-YFP) were subjected to long-read sequencing (Oxford Nanopore Technologies) to assess the global impacts of ROS1 activity on the methylome of Arabidopsis thaliana (ecotype Col-0).

2022-11-07 | GSE211295 | GEO

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