Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Responses of fully proliferating Arabidopsis leaves to short-term osmotic stress

ABSTRACT: Drought is an important environmental factor affecting plant growth and biomass production. Despite this importance little is known on the molecular mechanisms regulating plant growth under water limiting conditions. The main goal of this work was to investigate, using a combination of growth and molecular profiling techniques, how stress arrests CELl proliferation in Arabidopsis thaliana leaves upon osmotic stress imposition. Plants were grown on nylon meshes overlaying control 0.5MS media. At 9 DAS when third leaf is fully proliferating seedlings were transfered to either mannitol (25mM) or control plates, and proliferating leaves were micro-dissected at 1.5h, 3h, 12h and 24h after stress imposition and using RNAlater solution (25mM). Samples were from three independent biological experiments. Each sample was pooled from multiple plants and multiple plates in one experiment. RNA samples were submitted to ATH1 array hybridization.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: aleksandra skirycz

PROVIDER: E-GEOD-22107 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

The expression profiles of 31 transcription factors in wild-type Col-0 plants upon mild osmotic stress, including 10 time points and different leaf tissues

Project description:The expression level of the 31 genes (ERF-1 (AT4G17500), ERF2 (AT5G47220), ERF5 (AT5G47230), ERF6 (AT4G17490), ERF11 (AT1G28370), ERF8 (AT1G53170), ERF9 (AT5G44210), ERF59 (AT1G06160), ERF98 (AT3G23230), MYB51 (AT1G18570), STZ (AT1G27730), WRKY28 (AT4G18170), WRKY33 (AT2G38470), WRKY15 (AT2G23320), ZAT6 (AT5G04340), WRKY48 (AT5G49520), RAP2.6L (AT5G13330), K11J9.4 (AT5G61590), bHLH (AT2G43140), GATA3 (AT4G34680), GA2OX6 (AT1G02400), GA3OX1 (AT1G15550), GA2OX4 (AT1G47990), GA20OX1 (AT4G25420), EXLB3 (AT2G18660), MPK3 (AT3G45640), RAP2.2 (AT3G14230)) was measured upon mild osmotic stress (25mM mannitol) in the third leaf of wild-type plants during the proliferating (9 days after stratification (DAS)), expanding (15 DAS) and mature (22 DAS) developmental stage. The expanding third leaf (15 DAS) was harvested at a high temporal resolution (20 min, 40 min, 1 h, 2 h, 4 h, 8 h, 12 h, 16 h, 24 h and 48 h), whereas the proliferating and mature leaf tissues were harvested 24h after transfer to control or 25 mM mannitol-containing medium. A detailed expression pattern over time for each gene was generated with the nCounter Nanostring® technology.

2017-11-28 | E-MTAB-6205 | biostudies-arrayexpress

Transcriptome study of Caulobacter RHG1 and Bacillus sp. treated Arabidopsis thaliana roots at 12 and 48 hours after treatment

Project description:Arabidopsis thaliana 4-day-old seedlings were treated with the plant growth promoting rhizobacteria Caulobacter RHG1 or the neutral bacteria Bacillus sp. At 12 and 48 hours after treatment, roots were harvested, RNA was extracted and RNA-Seq data were generated. The goal of this experiment was to detect changes at the transcript level that were specific for the plant growth promoting rhizobacteria RHG1.

2023-03-11 | E-MTAB-12690 | biostudies-arrayexpress

PARP_inhibition_transfer

Project description:Arabidopsis plants grown in vitro on control media on a nylon mesh; transfered after 7days either to control or 0.2mM 3-Methoxybenzamide (3MB) containing media were sampled after 24, 48, 96 and 168h to obtain data if/how PARP inhibition changes transcription of plants in respect to the observed growth enhancement

2014-01-24 | E-MTAB-1466 | biostudies-arrayexpress

Quantitative N-terminome of N-end rule mutant in Arabidopsis

Project description:According to the /N-end rule pathway, proteins with basic N-termini are targeted for degradation by the Arabidopsis thaliana E3 ligase, PROTEOLYSIS6 (PRT6). Here, we undertook a quantitative proteomics study of N-end rule mutant prt6, to investigate the impact of this pathway on the etiolated seedling. Isolation of N-terminal peptides using terminal amine isotope labelling of samples (TAILS) combined with Tandem mass tag (TMT) identified over 3000 unique N-termini. Trypsin and GluC have advantage of identification of Acetylated or neo-peptides respectively. Seed storage proteins and Cysteine proteins actives are differentially regulated in abundance in the prt6 mutants, which are represent downstream targets of transcription factors known to be N-end rule substrates.

2017-10-27 | PXD006450 | Pride

Genome-wide transcriptome analysis bZIP29 dominant negative repressor line in root tips of Arabidopsis

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

Transfer of 5d old Col-0 and WEE1 KO seedlings to control medium for 0h-5h-24h

Project description:Col-0 and WEE1KO (wee1-1 and wee1-2) were germinated on control medium on a nylon mesh and transferred 5 days after germination to control medium. Samples were harvested at three different time points after transfer: 0 h, 5 h, and 24 h. All sampling points were performed in four independent experiments for Col-0, two independent experiments for wee1-1 and two independent experiments for wee1-2. For each time point in each experiment ﾱ50 root tips were collected and frozen in liquid nitrogen. RNA was extracted from root tissue with TriZol reagent (Invitrogen) and purified with RNneasy kit (Qiagen). The RNA of two independent experiments for Col-0 and WEE1KO were subsequently pooled and used for microarray analysis.

2011-07-24 | E-MEXP-3048 | biostudies-arrayexpress

Transcription profiling by array of wild type and arr1,10,12 mutant Arabidopsis seedlings treated with the cytokinin benzyladenine

Project description:Effect of the cytokinin BA on wt and arr1,10,12 mutant seedlings

2008-06-01 | E-MEXP-1573 | biostudies-arrayexpress

Transcription profiling of Arabidopsis early gibberellin responses

Project description:The aim is to identify early gibberellin responsive genes in a gibberellin deficient strain such as ga1-3. Such genes are likely regulated by DELLA proteins which are master gibberellin repressors. DELLA proteins are rapidly degraded after gibberellin treatment, but their direct target genes still need to be elucidated. Experiment Overall Design: A set of 4 biological replicates was generated for each treament. Arabidopsis seedlings were treated with water or 2 uM GA4 and whole shoots collected after 1h. A comparison of water vs. GA4 treated samples should render a list of early gibberellin responsive genes.

2008-06-16 | E-GEOD-8739 | biostudies-arrayexpress

A Kinetic Analysis of Auxin-mediated Changes in Transcript Abundance in Arabidopsis Reveals New Mediators of Root Growth and Development

Project description:Auxin-dependent transcript abundance was assayed by transferring 6 day old Arabidopsis grown on a a nylon mesh to IAA-containing or control media Seedling roots were harvested 0, 0.5, 1, 2, 4, 8, 12, or 24 hours after treatment and the resultant RNA was used for microarray analysis to determine the kinetic profiles of auxin-responsive gene expression. 8 timepoints after control or IAA treatment done in triplicate

2013-09-01 | E-GEOD-42007 | biostudies-arrayexpress

Cell type-specific auxin responses in the Arabidopsis thaliana root

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

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