E-GEOD-34209
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRJNA149675
PROVIDER: E-GEOD-34209 | ExpressionAtlas | 2015-06-01
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-GEOD-34209-analysis-methods.tsv | Tabular | |||
| E-GEOD-34209-atlasExperimentSummary.Rdata | Rdata | |||
| E-GEOD-34209-configuration.xml | Xml | |||
| E-GEOD-34209-percentile-ranks.tsv | Tabular | |||
| E-GEOD-34209.condensed-sdrf.tsv | Tabular |
Items per page: 5 1 - 5 of 101 |
Similar Datasets
Project description:Transcriptome analysis of genes regulated by overexpression of LATERAL ORGAN BOUNDARIES (LOB) in Arabidopsis thaliana
| PRJNA149675 | ENA
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.
2011-12-07 | GSE34209 | GEO
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
Project description:This model is from the article:
The influence of cytokinin-auxin cross-regulation on cell-fate determination in Arabidopsis thaliana root development
Muraro D, Byrne H, King J, Voss U, Kieber J, Bennett M.
J Theor Biol.2011 Aug 21;283(1):152-67.
PMID: 21640126,
Abstract:
Root growth and development in Arabidopsis thaliana are sustained by a specialised zone termed the meristem, which contains a population of dividing and differentiating cells that are functionally analogous to a stem cell niche in animals. The hormones auxin and cytokinin control meristem size antagonistically. Local accumulation of auxin promotes cell division and the initiation of a lateral root primordium. By contrast, high cytokinin concentrations disrupt the regular pattern of divisions that characterises lateral root development, and promote differentiation. The way in which the hormones interact is controlled by a genetic regulatory network. In this paper, we propose a deterministic mathematical model to describe this network and present model simulations that reproduce the experimentally observed effects of cytokinin on the expression of auxin regulated genes. We show how auxin response genes and auxin efflux transporters may be affected by the presence of cytokinin. We also analyse and compare the responses of the hormones auxin and cytokinin to changes in their supply with the responses obtained by genetic mutations of SHY2, which encodes a protein that plays a key role in balancing cytokinin and auxin regulation of meristem size. We show that although shy2 mutations can qualitatively reproduce the effect of varying auxin and cytokinin supply on their response genes, some elements of the network respond differently to changes in hormonal supply and to genetic mutations, implying a different, general response of the network. We conclude that an analysis based on the ratio between these two hormones may be misleading and that a mathematical model can serve as a useful tool for stimulate further experimental work by predicting the response of the network to changes in hormone levels and to other genetic mutations.
2024-09-02 | BIOMD0000000416 | BioModels
Project description:The genome of Arabidopsis contains 122 ERF transcription factor genes, some of which play diverse roles in the development and stress responses. A previous transcriptome analysis of Arabidopsis revealed that gene expression under combinatory stress conditions is not predictable from the combination of individual stresses (GSE46760). Searching for commonly regulated genes verified that only 11 genes were regulated in all stress combinations . Among these 11 genes, Rap2.9 (AT4G06746) was down-regulated under all stress conditions. Transgenic Arabidopsis thaliana lines overexpressing Rap2.9 under CaMV 35S promotor were generated, and the microarray analysis revealed that overexpression of Rap2.9 in A. thaliana plants causes massive reprogramming of transcription resulting in the alteration of the hormonal homeostasis and imbalances in signalling cascades related to stress response. Further analysis also revealed that Rap2.9 played an crucial role in plant development and stress tolerance in Arabidopsis plants.
2018-07-31 | GSE102714 | GEO
Project description:To optimize access to nitrogen under limiting conditions, root systems must continuously sense and respond to local or temporal fluctuations in nitrogen availability. In Arabidopsis thaliana and several other species, external N levels that induce only mild deficiency stimulate the emergence of lateral roots and especially the elongation of primary and lateral roots. However, the identity of the genes involved in this coordination remains still largely elusive. In order to identify novel genes and mechanisms underlying nitrogen-dependent root morphological changes, we investigated time-dependent changes in the root transcriptome of Arabidopsis thaliana plants grown under sufficient nitrogen or under conditions that induced mild nitrogen deficiency.
2023-09-12 | GSE216293 | GEO
Project description:The WOX1 transcription factor is a multifunctional regulator of lateral-organ development that acts as a transcriptional repressor. WOX1 promotes lamina growth, controls marginal tissue differentiation and is involved in establishment and maintenance of the adaxial-abaxial pattern from the middle domain of leaf primordia. To identify the WOX1 downstream genes, we performed a microarray analysis of shoot apices of transgenic Arabidopsis thaliana lines harboring 35S::WOX1:glucocorticoid receptor (GR) in which the WOX1 function was temporarily enhanced by dexamethasone (DEX).
2018-05-11 | GSE79647 | GEO
Project description:Secondary metabolites play a key role in coordinating ecology and defense strategies of plants. Diversity of these metabolites arise by conjugation of core structures with diverse chemical moieties, such as sugars in glycosylation. Active pools of phytohormones, including those involved in plant stress response are regulated by glycosylation. While, much is known about glycosylation enzymes, we know little about their regulation or coordination with other biological processes. We characterized the flavonoid pathway transcription factor, TRANSPARENT TESTA 8 (TT8) in Arabidopsis thaliana, using an integrative 'omics strategy to provide a systems level understanding of the cellular machinery used to generate metabolite diversity by glycosylation. Metabolomics analysis of loss-of-function and inducible overexpression lines of TT8 showed that it coordinates glycosylation of not only flavonoids, but also nucleotides, thus, implicating TT8 in regulating pools of activated sugars. Transcriptome and promoter network analyses revealed that TT8 regulome included sugar transporters, sugar binding and sequestration proteins, and carbohydrate active enzymes. Interestingly, TT8 also affects brassinosteroid and jasmonic acid biosynthesis by directly binding to the promoters of key genes of these two pathways. This combined effect on metabolites glycosylation and stress hormones by TT8 overexpression lead to significant increase in tolerance towards multiple abiotic and biotic stresses. Conversely, loss of TT8 leads to increased sensitivity to these stresses. Thus, TT8 is an integrator of secondary metabolism and stress response.
2016-10-03 | MTBLS129 | MetaboLights
Project description:It has been reported that a number of small coding genes (30–100 amino acids) tend to be lineage-specifically emerged in evolution but such de-novo genes tend to be missed in genomes. Plant mitochondrial genomes might be fostering sources of de-novo genes because of a high rearrangement rate. However, the functional role of de-novo genes derived from mitochondria is unclear. Here, in the best model species of plants (Arabidopsis thaliana), we showed that Arabidopsis-specifically emerged de-novo genes derived from mitochondrial genome contributed to phenotypic variation in a species. We previously identified 49 candidates of small coding genes inducing abnormal morphological changes on overexpression in the nuclear genome. Among them, we focused on a candidate (sORF2146) potentially encoding 66 amino acids in large-scale intergenic genomic transferring region from mitochondrial genome. Comparative genome analysis showed that sORF2146 had been appeared in Arabidopsis lineage. Mitochondrial sORF2146 is fixed among A. thaliana ecotypes but nucleus sORF2146 is not fixed in A. thaliana ecotypes. After showing evidence that nucleus sORF2146 was transcribed and translated as a coding gene, we performed transcriptome analysis in transgenic plant overexpressing sORF2146. Genes associated with flowering transition are highly regulated in the transgenic plant. We then examined phenotypic effects of overexpression and knockdown transgenic plant. Overexpression and knockdown transgenic plant induce late and early flowering, respectively. Taken together, we conclude that a nucleus de-novo gene derived from mitochondria contributes to the variation of floral timing in Arabidopsis population.
2021-09-24 | GSE184689 | GEO