Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Arabidopsis thaliana

ABSTRACT: ChIP-seq of GNL/GATA22 of Arabidopsis thaliana (35S::GNL:YFP:HA:GR gnc gnl, after treatment 4 hours with 10 μM Dexamethasone and Mock)

PROVIDER: PRJNA291959 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR2145280.fastq.gz	Fastqsanger.gz
	SRR2145281.fastq.gz	Fastqsanger.gz
	SRR2145282.fastq.gz	Fastqsanger.gz
	SRR2145283.fastq.gz	Fastqsanger.gz
	SRR2145284.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

cuc2-identification-Dynamic and specificity of CUP-SHAPED COTYLEDON transcription factors during leaf development

Project description:ngs2014_39_leafnet2-cuc2-identification-Identification of CUC2 targets-10-days old 35S::CUC2-GR Arabidopsis transgenic line grown in liquid culture have been treated for 6 hours with DEXAMETHASONE 10µM or Mock.

2022-05-18 | GSE184530 | GEO

Arabidopsis Forever Young Flower (FYF): 35S::FYF+GR

Project description:Transcriptional profiling of 35S::FYF+GR transgenic plant's floral buds(DEX treat) compared to 35S::FYF+GR transgenic plant's floral buds(mock treat). DEX : Dexamethasone

2015-06-01 | GSE69411 | GEO

Ath_Agilent_v2_Riechmann array expression profile AP1-GR ap1cal inflorescences - chx experiment

Project description:This experiment describes gene expression after the activation of APETALA1-GR, to study and identify AP1 target genes. We used a 35S:AP1-GR ap1 cal line to induce a synchronized response activating the AP1-GR fusion protein in ap1 cal inflorescence-like meristems through dexamethasone or dexamethasone+cycloheximide treatment. Tissue samples were collected at 3hrs after the treatment. The expression profiles of the individual samples were then analyzed by gene expression profiling using whole-genome oligonucleotide arrays (Agilent, custom-commercial). We treated inflorescences of 35S:AP1-GR ap1-1 cal-1 plants with a dexamethasone-containing or a mock solution, or with identical solutions that contained in addition 10 M-NM-<M cycloheximide. Tissue was collected 3 hours after the treatment. Samples from each of the four biological replicates resulted in a set of four hybridization pairs: Mock vs. Dex, Mock vs. Chx, Mock vs. Dex+Chx, and Chx vs. Dex+Chx. Dye polarities were switched between biological replicates.

2011-01-01 | E-GEOD-20175 | biostudies-arrayexpress

Microarray designed to find PIN polarity regulators downstream of TIR1/AFB

Project description:Roots of 5-day-old 35S::WRKY23-GR were treated for 6 hours with 10 μM DEX or DMSO, respectively. Wt Col-0 and 35S::WRKY23-SRDX plants were treated with 10 μM NAA or DMSO for 6 hours. Roots were subsequently collected for RNA isolation. All replicates were sampled in three independent experiments. Total RNA (200 μg per array) was hybridized to ATH1 Affymetrix Arabidopsis arrays in accordance with the standard procedures at the VIB Nucleomics Core. Data files containing probe level intensities (.cel files) were used for background correction and normalization was done in R (http://www.r-project.org) using the Bioconductor package affylmGUI (http://bioinf.wehi.edu.au/affylmGUI/) using the log2 scale RMA procedure. Genes with the same or contrasting WRKY23 expression profiles were selected by Pavlidis template matching in TMeV 4.0 (TIGR) (28). Finally, genes with a significant p value (< 0.001), denoting expression above background with minimum 2-fold change compared to the respective control, were retained for further analysis. First, by comparing 35S::WRKY23-GR roots with and without induction by dexamethasone, we obtained a set of 110 genes as potential WRKY23 targets, which were up-regulated in dexamethasone-treated seedlings. Next, we identified 950 genes, which were auxin-inducible in Col-0 wild type (Wt), but lost this auxin responsiveness in dominant-negative 35S::WRKY23-SRDX roots. The overlap between the two datasets yielded a list of 61 genes (Fig. S1B). Because WRKY23 acts downstream of the SLR/IAA14 transcriptional repressor, this genelist was compared with previously published microarray data on auxin-treated solitary root1 (slr-1) mutant seedlings

2020-09-07 | E-MTAB-9563 | biostudies-arrayexpress

LEAFY-GR time-course experiment in callus

Project description:Callus derived from 35S:LFY-GR plants was treated with dexamethasone- or was mock-treated for 0,2,4,6,8,10,12, or 22 hours. Four biologically independent sets of samples were generated and RNA probes derived from these samples were co-hybridized to a cDNA array enriched for flower-specific transcripts. The data were analyzed with Rosetta Resolver as described in Wagner et al. (2004). Keywords: time-course

2004-07-02 | GSE1411 | GEO

Auxin responsive genes in the Arabidopsis stem

Project description:15-20 cm tall 35S::Myc-GR-bdl plants were dipped headfirst in 15 µM dexamethasone or mock solution and after three hours of incubation second internodes were harvested and snap frozen in liquid nitrogen. Frozen plant material was pulverized with pestle and mortar and RNA was isolated by phenol/chlorophorm extraction as described previously (Mallory & Vaucheret 2010, PlantCell) with the modification of two additional concluding 70% EtOH washes

2017-05-29 | GSE97446 | GEO

KANADI1-regulated genes in shade

Project description:RNA-Seq of Arabidopsis thaliana Col-0 and 35S::FLAG-GR-KAN1 plants grown in ambient light or shade. 8 samples (Col-0 wildtype, 35S::FLAG-GR-KAN1 each in shade or ambient light, each with mock or Dexamethasone treatment) with two technical replicates were sequenced.

2015-08-11 | E-GEOD-68684 | biostudies-arrayexpress

Transcription profiling by array of Arabidopsis thaliana shoots treated with either DEX or CHX to identify STM-regulated target genes

Project description:Global expression of the Arabidopsis transcriptional regulator SHOOT MERISTEMLESS (STM) in a 35S:STM-GR transgenic line was induced for 3 hours with dexamethasone (DEX) compared to mock-induced (DMSO) control. Additionally,to identify direct targets, plants were treated with the protein synthesis inhibitor cycloheximide (CHX) together with DEX, compared to CHX treatment alone.

2018-05-29 | E-MTAB-6786 | biostudies-arrayexpress

Identification of genes cooperatively regulated by cytokinin and HD-ZIP III transcription factors

Project description:In Arabidopsis thaliana, cytokinin responsive B-type ARR transcription factors and HD-ZIP III transcription factors such as REVOLUTA (REV), act cooperatively as master regulators of shoot regeneration. To identify the downstream targets of ARR-HD-ZIP III transcriptional complex, we used an inducible line of REV, 35S::FLAG-GR-rREV, in which FLAG-tagged miR165/6-non-targetable form of REV (rREV)-GR fusion protein was expressed from 35S promoter. DEX treatment induced activation of REV by translocation of FLAG-GR-rREV fusion protein from cytoplasm to the nucleus. We treated 35S::FLAG-GR-rREV seedlings with 6-benzylaminopurine (6-BA, a cytokinin), dexamethasone (DEX), or 6-BA+DEX for 2 hours. Total RNAs were extracted and subjected to Agilent Arabidopsis Gene Expression Microarray analyses. The differentially expressed genes (>1.5-fold, p<0.05) were identified. 10-day-old 35S::FLAG-GR-rREV plants were treated with 6-benzylaminopurine (6-BA), dexamethasone (DEX), or 6-BA+DEX for 2 hours. DEX treatment induced activation of REV by translocation of FLAG-GR-rREV fusion protein from cytoplasm to the nucleus. Total RNA was extracted with RNeasy Mini Kit and hybridized to Agilent Arabidopsis Gene Expression Microarray. Differentially expressed genes were defined by a 1.5-fold expression difference with a P value<0.05. Biological replicates were performed.

2014-01-29 | E-GEOD-54469 | biostudies-arrayexpress

High-thoughput Illumina RNA sequencing to identify downstream target genes of RABBIT EARS (RBE) in the flowers of Arabidopsis thaliana

Project description:In order to identify putative downstream target genes of RBE, we sequenced mRNA from dexamethasone (DEX) and mock treated transgenic Arabidopsis line 35S:GR-RBE (RBE coding region fused to a glucocorticoid receptor domain driven by the constitutive 35S promoter) floral tissues. We compared the results from DEX and mock treatments and focused on the 832 genes whose expression was significantly reduced (P < 0.025) by 2-fold or more in DEX as compared to mock-treated plants. In this analysis, we identified MIR164c (EEP1) as a candidate target of RBE, which was further confirmed by other molecular and genetic analyses. Regulation of MIR164c by RBE is important for normal floral organ formation in Arabidopsis.

2012-07-12 | GSE36469 | GEO

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