Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

10 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of Arabidopsis 14 day-old seedlings expressing either mCherry-RAX1-GR or mCherry-GR with 4h mock vs. dexamethasone treatment

ABSTRACT: In order to identify relevant target genes of RAX1 (AT5G23000) involved in meristem initiation in Arabidopsis we generated dexamethasone inducible lines expressing either a mCherry-RAX1-GR or a mCherry-GR (mock construct) fusion protein. We analysed differential gene regulation after 4 hours of dexamethasone or mock treatment in 14 day-old seedlings. Paired-end sequencing was performed using 3 biological replicate for each genotype and differentially expressed genes were identified for the interaction of genotype and treatment.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Parcy Francois

PROVIDER: E-MTAB-7050 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq of Arabidopsis 14 day-old seedlings expressing either mCherry-RAX1-GR or mCherry-GR with 4h mock vs. dexamethasone treatment

Project description:RNA-seq of Arabidopsis 14 day-old seedlings expressing either mCherry-RAX1-GR or mCherry-GR with 4h mock vs. dexamethasone treatment

| PRJEB27846 | ENA

Transcription profiling of rice plants overexpressing OsNAC6-GR after DEX treatment

Project description:Transcription profiling of the rice plants overexpression OsNAC6-GR after the DEX treatment.

2008-04-02 | E-MEXP-1066 | biostudies-arrayexpress

ChIP-MS for GR in liver from wild type and E47 mutant mice

Project description:Glucocorticoids (GCs) are widely prescribed effective drugs, but their clinical use is compromised by severe side effects including hyperglycemia, hyperlipidemia and obesity. They bind to the Glucocorticoid Receptor (GR), which acts as a ligand-gated transcription factor. The transcriptional activation of metabolic genes by GR is thought to underlie these undesired adverse effects. Using mouse genetics, ChIP-Seq, RNA-Seq and ChIP-MS, we found that the bHLH transcription factor E47 is required for the regulation of hepatic glucose and lipid metabolism by GR in vivo, and that loss of E47 prevents the development of hyperglycemia and hepatic steatosis in response to GCs. Here we show that E47 and GR co-occupy metabolic promoters and enhancers. E47 is needed for the efficient binding of GR to chromatin and for the adequate recruitment of coregulators such as Mediator. Taken together, our results illustrate how GR and E47 regulate hepatic metabolism, and how inhibition of E47 might provide an entry point for novel GC therapies with reduced side effect profiles. These ChIP-MS data sets show IPs for GR in both wildtype and E47 mutant mouse livers treated with the synthetic glucocorticoid Dexamethasone.

2018-11-22 | PXD010157 | Pride

The organoid generated from murine small intestine: mCherry-positive vs. mCherry-negative

Project description:The organoids heterogenously expressed mCherry by the lentivirus transduction were dissociated into single cells. A single mCherry- positive and -negative cell were collected and grown up to the organoids, respectivery. The difference of the gene expression profile between mCherry- positive and -negative organoids was assessd by maicroarray.

2014-07-16 | GSE59425 | GEO

Characterization of Glucocorticoid Receptor (GR) in Mouse Liver

Project description:We proposed an experiment that determines liver gene regulation profiles in GRLKO. By comparison to the wide type C57BL/6 mouse, we determined the contribution of GR on liver gene expression either at basal level or after Dexamethasone (DEX) injection. WT and GR knockout mice were divided into two groups, one with dexamethasone treatment and one with out. Each group has four replicates.

2015-12-11 | E-GEOD-75682 | biostudies-arrayexpress

Transcription profiling by array of Arabidopsis overexpressing LBD16 and LBD18 to investigate downstream genes

Project description:Pro35SLBD16:GR or Pro35SLBD18:GR transgenic seedlings that overexpress LBD16 or LBD18 fused to glucocorticoidsteroid hormone binding domain(GR) under CaMV35S promoter were grown for 12 days under long-day conditions (16h light/ 8h dark).

2011-06-01 | E-MEXP-1400 | biostudies-arrayexpress

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

GR and ER co-activation alters the expression of differentiation genes and associates with improved ER+ breast cancer outcome

Project description:Analysis of MCF-7 cells treated for 4h with Ethanol, Estradiol (E2), Dexamethasone (Dex), or Estradiol + Dexamethasone (E2 + Dex) In estrogen receptor (ER)-negative breast cancer (BC), high tumor glucocorticoid receptor (GR) expression has been associated with a relatively poor outcome. In contrast, using a meta-analysis of several genomic datasets, here we find that tumor GR mRNA expression is associated with improved ER+ relapse-free survival (RFS) (independently of progesterone receptor (PR) expression). To understand the mechanism by which GR expression is associated with a better ER+ BC outcome, the global effect of GR-mediated transcriptional activation in ER+ BC cells was studied. Analysis of GR chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) in ER+/GR+ MCF-7 cells revealed that upon co-activation of GR and ER, GR chromatin association became enriched at proximal promoter regions. Furthermore, following ER activation, increased association of GR was observed at ER, FOXO, and AP1 response elements. In addition, it was determined that ER associated with GR response elements, suggesting that ER and GR interact in a complex. Co-activation of GR and ER resulted in increased expression (relative to ER activation alone) of transcripts that encode proteins promoting cellular differentiation (e.g. KDM4B, VDR) and inhibiting Wnt-signaling (IGFBP4). Finally, expression of these individual pro-differentiation genes was associated with significantly improved RFS in ER+ BC patients. Together, these data demonstrate that the co-expression and subsequent activity of tumor cell GR and ER contribute to the less aggressive natural history of early-stage BC by coordinating the altered expression of genes favoring differentiation. Four treatment samples (Vehicle V, Dex D, E2, or Dex+E2). Three biological replicate experiments per sample. Vehicle sample is Ethanol control.

2016-04-01 | E-GEOD-79761 | biostudies-arrayexpress

Expression profile pAP1-AP1-GR ap1cal inflorescences - time series (days)

Project description:This experiment describes gene expression after the activation of APETALA1-GR, to study and identify AP1 target genes. We used a pAP1:AP1-GR ap1 cal line to induce a synchronized response activating the AP1-GR fusion protein in ap1 cal inflorescence-like meristems through dexamethasone treatment. Tissue samples were collected immediately after the treatment, as well as subsequent timepoints. The expression profiles of the individual samples were then analyzed by gene expression profiling using whole-genome oligonucleotide arrays (Agilent, custom-commercial) Four sets of biologically independent tissue samples were collect before DEX-induction (day 0, 0d), as well as at 2 days, 4 days and 8 days after the treatment. Samples for each timepoint and biological replicate were co-hybridized as indicated; one sample was labeled with Cy3 and the other with Cy5. The dyes used for labeling RNA from a given timepoint were switched for two of the replicate experiments, to reduce dye-related artifacts. This experimental setup resulted in a total of 3 hybridizations per set (0days vs 2days, 2days vs 4days, and 4days vs 8days), and an even number (2) of hybridizations of each dye polarity per comparison.

2014-01-01 | E-GEOD-47981 | biostudies-arrayexpress

Transcriptome analysis of genes regulated by overexpression of LATERAL ORGAN BOUNDARIES (LOB) in Arabidopsis thaliana

Project description:The Arabidopsis thaliana transcription factor LATERAL ORGAN BOUNDARIES (LOB) is expressed in the boundary between the shoot apical meristem and initiating lateral organs. To identify genes regulated by LOB activity, we used an inducible 35S:LOB-GR line. This analysis identified genes that are differentially expressed in response to ectopic LOB activity. 35S:LOB-GR and Col wild-type seedlings were treated with dexamethasone (DEX) or mock-treated. Three biological replicates were conducted for each treatment.

2011-12-07 | E-GEOD-34209 | 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