Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

51 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Arabidopsis thaliana roots at 7DAG; Col-0, scl3 (LOF) and SCL3 OE (GOF)

ABSTRACT: Transcriptional profiling of root part comparing wild type with scl3 mutant and SCL3 OE. We used Affymetrix ATH1 microarrays to determine the effect of GRAS transcription factor SCL3 on growth and development of Arabidopsis root system by global transcriptome analysis and to identify new regulators in the regulatory pathway. Three-condition experiments, Col-0, scl3 and SCL3 OE. Biological triplicates: 3 WT, 3 scl3 and 3 SCL3 OE

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Eun Kyung Yoon

PROVIDER: E-GEOD-41544 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Arabidopsis thaliana roots at 7DAG; ga1, ga1 scl3 (LOF) and ga1 SCL3 OE (GOF)

Project description:Transcriptional profiling in the root between ga1, ga1 scl3 and ga1 SCL3 OE. We used Affymetrix ATH1 microarrays to determine the effect of GRAS transcription factor SCL3 and gibberellin on the growth and development of the Arabidopsis root system by global transcriptome analysis and to identify new regulators in the regulatory pathway. Three-condition experiments, ga1, ga1 scl3 and ga1 SCL3 OE. Biological triplicates: 3 ga1-3 , 3 ga1-3 scl3 and 3 ga1-3 SCL3 OE

2014-09-05 | E-GEOD-61104 | biostudies-arrayexpress

Arabidopsis thaliana roots at 7DAG; Col-0, scl3 (LOF) and SCL3 OE (GOF)

Project description:Transcriptional profiling of root part comparing wild type with scl3 mutant and SCL3 OE. We used Affymetrix ATH1 microarrays to determine the effect of GRAS transcription factor SCL3 on growth and development of Arabidopsis root system by global transcriptome analysis and to identify new regulators in the regulatory pathway.

2012-10-13 | GSE41544 | GEO

Arabidopsis thaliana roots at 7DAG; ga1, ga1 scl3 (LOF) and ga1 SCL3 OE (GOF)

2014-09-05 | GSE61104 | GEO

IMA1 OE #7-4 line compared to EYFP OE line (control)

Project description:RNAseq transcriptome of IRON MAN1 OE line. IMA1 OE plants accumulate Fe in their tissue and exhibit a constitutive induction of their root Fe uptake system.

2016-10-08 | GSE87745 | GEO

Chip-chip from mouse olfactory epithelium (OE) and liver with antibodies against H3K9me3 and H4K20me3

Project description:The Olfactory Receptor (OR) genes are specifically expressed in the MOE in a monogenic and monoallelic fashion. Only 1 out of 2800 alleles is expressed in each olfactory sensory neuron in mice. ChIP-chip from mouse olfactory epithelium (OE) and liver for H3K9me3 and H4K20me3 revealed that the ORs are highly enriched for these modifications in OE but not in liver. 24 samples were analyzed (20 from OE and 4 from liver) with matching inputs as controls. For the OE samples, there were 2-3 replicates for each array.

2011-05-03 | E-GEOD-24420 | biostudies-arrayexpress

Expression data from MeGRX232-OE and MeGRX360-OE Arabidopsis

Project description:MeGRX232 and MeGRX360 are drought-inducible CC-type glutaredoxins in cassava. Overexpression of them in Arabidopsis caused different effects on plant growth. We used microarray to identified the different expression genes in MeGRX232-OE and MeGRX360-OE Arabidopsis

2016-05-06 | GSE81136 | GEO

Skeletal muscle myoblasts: GATA4-Wt, -KO, -OE; day 0, 3

Project description:Gene expression in satellite cell-derived primary myoblasts islolated from Gata4-loxP mice. Myoblasts were infected with nLacZ for control (Wt), Cre recombinase to knockout GATA4 (KO), or GATA4 expression vector to overexpress GATA4 (OE). Infected myoblasts were cultured in growth medium (day 0) then differentiated into myotubes in differentiation medium for 3 days (day 3). Total 18 samples. Three replicates in each myoblast; GATA4-Wt, -KO, and -OE myoblasts at day 0 and day 3.

2015-02-18 | E-GEOD-66016 | biostudies-arrayexpress

Klf5 OE ES

Project description:Klf5 OE ES

| PRJNA1026845 | ENA

RNAseq transcriptome profiling of Brachypodium distachyon wildtype; GNRF-OE and gnrf mutants; and SWAM4-OE, SWAM4-DR and swam4 mutants.

Project description:Plant cell walls are complex structures that contain a matrix of cellulose, lignin and hemicellulose. The regulation of the biosynthesis of these components has been well-studied in the eudicot plant Arabidopsis thaliana, and a transcriptional network has been elucidated. Several NAC and MYB family transcription factors are key regulators of secondary cell wall biosynthesis, and their functional characterization provides significant insight into the complex underlying transcriptional network. Genetic and structural evidence suggests that genes controlling this process might be different between eudicots and monocots. Here, the model grass Brachypodium distachyon has been selected to characterize the function of GNRF (GRASS NAC REPRESSOR OF FLOWERING), SWAM1 (SECONDARY WALL ASSOCIATED MYB1), and SWAM4 in the regulation of secondary cell wall biosynthesis. Functional characterization was performed by using the overexpression plants GNRF-OE and SWAM4-OE; sodium azide mutant plants from a TILLING (Targeting Induced Local Lesion IN Genome) collection for gnrf-1, gnrf-2, gnrf-3, gnrf-4, gnrf-5, swam4-1, and swam4-2; a T-DNA insertional mutant plant, gnrf-6; and a dominant repressor plant, SWAM4-DR. GNRF-OE plants remained at juvenile stage and exhibited persistent vegetative growth, and some gnrf mutant plants were late flowering. SWAM4-DR plants were severely dwarfed. Stems of all genotypes mentioned above were subjected to RNA-seq analysis.

2019-08-02 | E-MTAB-8172 | biostudies-arrayexpress

High REDOX RESONSIVE TRANSCRIPTION FACTOR1 levels result in accumulation of reactive oxygen species in Arabidopsis thaliana shoots and roots [mature leaves]

Project description:Redox Responsive Transcription Factor1 (RRTF1) in Arabidopsis is rapidly and transiently upregulated by H202, as well as biotic and abiotic induced redox signals. Inactivation of RRTF1 restricts and overexpression promotes reactive oxygen species (ROS) accumulation in response to stress. Overexpressor (oe) lines are impaired in root and shoot development, light sensitive and susceptible to Alternaria brassicae infection. These symptoms are diminished by the beneficial root endophyte Piriformospora indica which reduces ROS accumulation locally in roots and systemically in shoots, and by antioxidants and ROS inhibitors which scavenge ROS. More than 850 stress-, redox-, ROS regulated-, ROS scavenging-, defense-, cell death- and senescence-related genes are regulated by RRTF1, ~ 30% of them have ROS related functions. Bioinformatic analyses and in vitro DNA binding assays demonstrate that RRTF1 binds to GCC-box and GCC-box like sequences in the promoter of RRTF1-responsive genes. Upregulation of RRTF1 by stress stimuli as well as H2O2 requires WRKY18/40/60. RRTF1 is co-regulated with the phylogenetically related RAP2.6, which contains GCC-box like sequene in its promoter, but RAP2.6 oe lines do not accumulate higher ROS levels. RRTF1 stimulates systemic ROS accumulation in distal non-stressed leaves. We conclude that the highly conserved RRTF1 rapidly, transiently and systemically induce ROS accumulation in response to ROS and ROS-producing abiotic and biotic stress signals. Necrotrophs stimulate RRTF1 expression, while symbiotic interactions of Arabidopsis with (hemi)-biotrophs and P. indica do not affect or repress RRTF1 expression. Mature leaves of 5 weeks-old Col-0 wild type and RRTF1-overexpressor Arabidopsis (called oe18), which were grown on soil under short-day condition at 20˚C, were subjected to RNA extraction and Affymetrix microarray analysis. Three biological independent experiments for both Col-0 and oe18 were performed.

2015-04-23 | E-GEOD-64853 | 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