Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA381131 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5398240.fastq.gz | Fastqsanger.gz | |||
| SRR5398241.fastq.gz | Fastqsanger.gz | |||
| SRR5398242.fastq.gz | Fastqsanger.gz | |||
| SRR5398243.fastq.gz | Fastqsanger.gz | |||
| SRR5398244.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Auxin plays a pivotal role in virtually every aspect of plant morphogenesis. It simultaneously orchestrates a wide variety of processes, including cell wall biogenesis, transition through the cell cycle, and metabolism of a wide range of chemical substances, among others. The coordination principles for such complex regulation in a cell at a system level are poorly understood. Here, we apply a whole-genome approach to estimate the coherence of the auxin-regulated transcriptional response in gene groups, united by a certain biological process, molecular function or cell component, based on the fold change of the expression level. The corresponding analysis of RNA-Seq data for Arabidopsis roots treated with auxin for 6 h revealed that the intervals for the fold change of gene expression levels are quite narrow for many functional gene groups. The fold-specific manner of auxin response in most of these groups was confirmed using independent microarray data. To predict the mechanisms underlying such a coordinated expression, we performed motif enrichment analysis, which revealed TBX1-3, SBX, REG and TCP/site 2 as the candidates associated with fold-specific responses to auxin.
2017-06-01 | GSE97258 | GEO
Project description:We combined transcriptomic profiling of auxin related mutants with genetic and biochemical approaches and live-cell imaging techniques of Arabidopsis roots to understand the role of auxin-driven gibberellin level changes during root development, particularly root cell elongation. We show that auxin negatively regulates the level of gibberellin in root elongation zone. Auxin signalling steers the expression of gibberellin deactivating enzymes - GIBBERELLIN 2-OXIDASES (GA2OX) exclusively in root elongation zone. Interestingly, GA2OX8 expression is high in tissues with elevated auxin levels, such as vasculature or stem cell niche, fitting with the observed effect of auxin on gibberellin level. Here we show that GA2OX enzymes are negative regulators of root cell elongation. Gibberellin decrease caused by GA2OX8 overexpression inhibits root cell elongation. In contrast, roots missing GA2OX genes elongate faster. These findings indicate that GA2OX8 enzymes represent an integration core of auxin and gibberellin signalling pathway in root elongation zone, vascular development and regulation of stem cell niche. Our results enhance understanding of complex mechanisms controlling root cell elongation.
2024-12-31 | GSE282145 | GEO
Project description:Cell type-specific auxin responses in the Arabidopsis thaliana root
| PRJNA152235 | ENA
Project description:We performed an analysis of transcriptomic responses to auxin within four distinct tissues of the Arabidopsis thaliana root. This high-resolution dataset shows how different cell types are predisposed to react to auxin with discrete transcriptional responses. The sensitivity provided by the analysis lies in the ability to detect cell-type specific responses diluted in organ-level analyses. This dataset provides a novel resource to examine how auxin, a widespread signal in plant development, influences differentiation and patterning in the plant through tissue-specific transcriptional regulation. To analyze the effect of auxin in separate spatial domains of the root, early transcriptional changes in response to auxin treatment were assayed by means of fluorescence activated cell sorting (FACS) and microarray analysis in four tissues of the Arabidopsis root (wild type Col-0). The samples covered inner and outer as well as proximal and distal cell populations; including the stele (reporter line pWOL::GFP), xylem-pole (xp) pericycle (enhancer trap line E3754), epidermis/lateral root cap (reporter line pWER::GFP) and columella (enhancer trap line PET111). One-week-old seedlings of the individual lines were treated with auxin (two hours, 5µM indole-3-acetic acid [IAA]) or mock treated, after which roots were harvested and cells were dissociated by cell wall digestion (1 hour; including 5uM IAA) . GFP-positive cells were sorted and used for microarray transcriptome analysis (as in Bargmann and Birnbaum, Plant Phys. 2010). For comparison, transcriptional responses to auxin were also assayed in intact (undigested) roots.
2013-08-06 | E-GEOD-35580 | biostudies-arrayexpress
Project description:We performed an analysis of transcriptomic responses to auxin within four distinct tissues of the Arabidopsis thaliana root. This high-resolution dataset shows how different cell types are predisposed to react to auxin with discrete transcriptional responses. The sensitivity provided by the analysis lies in the ability to detect cell-type specific responses diluted in organ-level analyses. This dataset provides a novel resource to examine how auxin, a widespread signal in plant development, influences differentiation and patterning in the plant through tissue-specific transcriptional regulation.
2013-08-06 | GSE35580 | GEO
Project description:This study evaluates the effects of exogenous auxin on the Arabidopsis thaliana root proteome at 8, 12, and 24 hours post-treatment.
2017-07-18 | PXD001400 | Pride
Project description:We report differences in the transcriptional responses of the root and the shoot to either auxin or ABA in comparison to mock treatment in dark-grown Arabidopsis thaliana seedlings. By examining the auxin responsiveness in the shoot or the root of a dark-growh ABA biosynthesis mutant, we found that auxin relies on intact ABA biosynthesis in order to regulate aspects of transriptional output.
2022-03-21 | GSE169302 | GEO
Project description:The root-colonizing fungal endophyte Serendipita indica, formerly known as Piriformospora indica, is well known to promote plant biomass production and stress tolerance of its host plants. Moreover, previous studies highlighted an important impact of the fungus on auxin homeostasis during the infection of Arabidopsis thaliana plants. Auxin is a key determinant of plant growth, including the growth of the root system. Auxin overproducing mutants, like for instance YUC9oe (Hentrich et al., 2013 Plant J.), show a pronounced root phenotype that can be restored by the co-cultivation with S. indica. We here report the comparative analysis of the effect of a mock- and S. indica-infection on both wild-type Arabidopsis plants (Col-0) and YUC9 overexpressing mutants. Our data provide evidence for the induction of GRETCHEN HAGEN 3 (GH3) genes that are involved in conjugating active free indole-3-acetic acid with amino acids. The fungus triggered induction GH3s is suggested to be involved in affecting the cellular auxin homeostasis.
2023-08-30 | GSE240683 | GEO
Project description:Maintenance of the root-meristem is determined by polar auxin transport (PAT) and asymmetric cell division (ACD). We find that flavonoids scutellarin and scutellarein, which both have 6-hydroxyl group that differs in its structure from all known-flavonoid PAT inhibitors, promote PAT and ACD in Arabidopsis thaliana root tip, and increase root length. We used microarrays to detail the global programme of gene expression under scutellarin and mock (DMSO) treatment and identified distinct classes of genes regulated by scutellarin.
2020-12-31 | GSE127830 | GEO
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