E-MTAB-1582
Ontology highlight
ABSTRACT:
PROVIDER: E-MTAB-1582 | ExpressionAtlas | 2015-11-26
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-MTAB-1582-analysis-methods.tsv | Tabular | |||
| E-MTAB-1582-atlasExperimentSummary.Rdata | Rdata | |||
| E-MTAB-1582-configuration.xml | Xml | |||
| E-MTAB-1582-percentile-ranks.tsv | Tabular | |||
| E-MTAB-1582.condensed-sdrf.tsv | Tabular |
Items per page: 5 1 - 5 of 50 |
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE30091: Expression analysis of the effect of protoplasting and sorting in roots exposed to low pH GSE30095: Expression analysis of root cell types after treatment with low pH GSE30096: Expression analysis of developmental stages of Arabidopsis roots exposed to low pH GSE30097: Time-course expression analysis of the low pH (pH 4.6) response in Arabidopsis whole roots GSE30098: Expression analysis time-course of Arabidopsis roots to sulfur deficiency GSE30099: Expression analysis of root cell types after treatment with sulfur deficient media GSE30100: Expression analysis of developmental stages of Arabidopsis roots exposed to sulfur deficient media GSE30104: Genome-wide identification of SCARECROW (SCR) direct targets using a custom Agilent promoter array Refer to individual Series
2011-11-23 | E-GEOD-30166 | biostudies-arrayexpress
Project description:Genome wide transcriptome profiling of pericycle cells from roots exposed to auxin, cytokinin and both hormones simultaneously. Lateral root organogenesis in Arabidopsis is governed by a complex network of hormonal regulations. Plant hormones auxin and cytokinin were demonstrated to be the key regulators of this lateral root organogenesis and their mode of interaction is antagonistic. The aim of the project is to understand the role of the auxin - cytokinin signalling pathways in lateral root organogenesis.
2020-03-13 | GSE146778 | GEO
Project description:To gain further insights into a larger number of processes potentially altered by high nickel (Ni), we performed a transcriptional profiling of whole roots of Arabidopsis thaliana accession Columbia-0 (Col-0) exposed to 100 µM nickel, a concentration that induces slight chlorosis and intermediate inhibition of root and shoot growth.
2019-10-16 | GSE138859 | GEO
Project description:In this work we show that root illumination influences Pi starvation response, enhancing the root and shoot growth arrest and limiting the root/shoot ratio as well as root hair elongation. A transcriptomic study in dark-grown roots (DGR) roots identifies several genes that respond to Pi deficiency that were not previously reported. Hormone profiling revealed that Pi starvation reduces the level of trans-Zeatin (tZ) but significantly increases the amount of cis-Zeatin (cZ) and cis-Zeatin Riboside (cZR). We have analyzed the transcriptomic response of Arabidopsis roots to phosphate starvation combined with cis- or trans-zeatin treatments for 8 hours.
2019-11-01 | GSE131056 | GEO
Project description:In this study, we undertook a comprehensive quantitative proteomic profiling of Arabidopsis roots from plants grown on Mn-deplete media, aiming at dissecting and cataloging the responses of Arabidopsis roots to Mn deficiency. We used LC-Q Exactive Orbitrap mass spectrometer to compile a near complete inventory of the Arabidopsis root proteome. We identified several novel components of cellular Mn homeostasis and show that many putatively important changes in response to Mn deficiency are only evident at one of the omics levels under investigation.
2018-10-26 | PXD003309 | Pride
Project description:Transcriptional profiling of Arabidopsis thalina seedlings in response to high (140 µM) and low (20 µM) concentrations of chromate (K2CrO4). Low concentrations of chromate (e.g. 40 µM) promoted primary root growth, while high concentrations (e.g. 140 µM) repressed growth and increased formation of root hairs, lateral roots and adventitious roots.
2013-02-21 | GSE44324 | GEO
Project description:Muraro2014 - Vascular patterning in Arabidopsis roots
Using a multicellular model, maintanence of vascular patterning in Arabidopsis roots has been studied. The model that is provided here is the single-cell version of the model. The two-cell and multicellular models described in the paper can be downloaded as python scripts (follow the curation tab to get these files).
This model is described in the article:
Integration of hormonal signaling networks and mobile microRNAs is required for vascular patterning in Arabidopsis roots.
Muraro D, Mellor N, Pound MP, Help H, Lucas M, Chopard J, Byrne HM, Godin C, Hodgman TC, King JR, Pridmore TP, Helariutta Y, Bennett MJ, Bishopp A.
Proc Natl Acad Sci U S A. 2014 Jan 14;111(2):857-62.
Abstract:
As multicellular organisms grow, positional information is continually needed to regulate the pattern in which cells are arranged. In the Arabidopsis root, most cell types are organized in a radially symmetric pattern; however, a symmetry-breaking event generates bisymmetric auxin and cytokinin signaling domains in the stele. Bidirectional cross-talk between the stele and the surrounding tissues involving a mobile transcription factor, SHORT ROOT (SHR), and mobile microRNA species also determines vascular pattern, but it is currently unclear how these signals integrate. We use a multicellular model to determine a minimal set of components necessary for maintaining a stable vascular pattern. Simulations perturbing the signaling network show that, in addition to the mutually inhibitory interaction between auxin and cytokinin, signaling through SHR, microRNA165/6, and PHABULOSA is required to maintain a stable bisymmetric pattern. We have verified this prediction by observing loss of bisymmetry in shr mutants. The model reveals the importance of several features of the network, namely the mutual degradation of microRNA165/6 and PHABULOSA and the existence of an additional negative regulator of cytokinin signaling. These components form a plausible mechanism capable of patterning vascular tissues in the absence of positional inputs provided by the transport of hormones from the shoot.
This model is hosted on BioModels Database
and identified
by: BIOMD0000000522
.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource
for published quantitative kinetic models
.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to the public
domain worldwide. Please refer to CC0 Public Domain
Dedication
for more information.
2024-09-02 | BIOMD0000000522 | BioModels
Project description:The Arabidopsis basic leucine zipper transcription factor bZIP29 of the bZIP group I TF family, expressed mainly in proliferative tissues, is functionally characterized in this study. In roots, bZIP29 is highly expressed in the quiescent centre and the columella cells of the root apical meristem. Mutant analyses demonstrate that bZIP29 regulates root meristem cell number and root gravitropic responses. RNA-seq transcriptome profiling of the root meristem shows that bZIP29 target genes are linked to cell wall organization, and that gene regulatory networks controlling proper root meristem organization are intensively rewired upon its perturbation.
2016-11-07 | E-MTAB-3755 | biostudies-arrayexpress
Project description:The root cap surrounds the root meristem, protecting it from harsh environments and facilitating root movement through soil. In Arabidopsis, new root cap cells produced in the meristem displace older cells toward the root periphery, where they undergo programmed cell death and are released from the root. This rapid cell turnover is a unique feature of the root cap and is modulated in part by the combined action of four NAC transcription factors, as well as cell wall modification enzymes. Here we show that the transcription factor NIN-LIKE PROTEIN 7 (NLP7) regulates root cap maturation in Arabidopsis by modulating expression of each of the NAC TFs as well as several cell wall modifying enzymes. NLP7 is a homolog of NIN, a transcription factor required for nodulation in Lotus japonicas, and is highly expressed in the columella root cap. Mutants have altered columella root cap development and decreased levels of homogalacturonan, a major component of pectin. Reverse genetic analysis of genes differentially expressed in nlp7 roots showed that two cell wall modifying enzymes, CELLULASE5 and XTH5, modulate root cap maturation likely downstream of NLP7. Plant cell wall modification is critical for nodulation, and we propose that this characteristic is also present in NLPs. We used microarrays to identify the differences in gene expression between whole roots of WT and nlp7-1 Arabidopsis plants Roots were cut at the root/hypocotyl junction and collected into RLT buffer in the RNeasy plant mini kit. Approximately 60 roots were collected per replicate, with two biological replicates. RNA was extracted using the RNeasy Micro Kit. Probes for array analysis were preparedfrom 1μg total RNA with the one-cycle amplification protocol by Affymetrix according to the manufacturer's instructions. Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Arabidopsis Whole Genome ATH1 Affymetrix GeneChips.
2016-07-31 | E-GEOD-63474 | biostudies-arrayexpress
Project description:The cotyledons of etiolated seedlings from terrestrial flowering plants must emerge from the soil surface, while roots must penetrate the soil to ensure plant survival. We show here that the soil emergence related transcription factor PHYTOCHROME-INTERACTING FACTOR 3 (PIF3) regulates root penetration via transducing external signals perceived by the receptor kinase FERONIA (FER) in Arabidopsis thaliana. The loss of FER function in the fer-4 mutant resulted in a severe defect in root penetration into hard soil or medium. Single-cell RNA-seq profiling of roots revealed a distinct cell clustering pattern, especially for root cap cells, and revealed PIF3 as a putative FER-regulated transcription factor. Biochemical, imaging, and genetic experiments confirmed that PIF3 is required for root soil penetration. Moreover, FER interacted with and stabilized PIF3, which then modulated the expression of mechanosensitive ion channels and the sloughing of outer cells in the root cap. We propose a novel mechanism of soil penetration by plant roots.
2023-12-31 | GSE225299 | GEO