Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

21 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Plant Systems Biology data submission

PROVIDER: E-MTAB-12690 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Transcription profiling of Arabidopsis thaliana leaves as reaction to caterpillar (Trichoplusia ni) feeding and fungi (Laccaria bicolor) infection of the roots

Project description:Arabidopsis thaliana plants were grown from seeds. Roots of 9 day old plants were inoculated with L. bicolor. After 4 weeks, two T. ni larvae per plant fed for 24 h. Leaves were subsequently harvested, shock frozen in liquid nitrogen and prepared for RNA extraction

2020-06-01 | E-MTAB-8523 | biostudies-arrayexpress

Transcription profiling of Arabdiposis plants with rhizobacteria-induced systemic resistance after exposure to Spodoptera exigua or Pieris rapae herbivory

Project description:Role of rhizobacteria-induced systemic resistance in Arabidopsis on the response to Spodoptera exigua or Pieris rapae herbivory

2008-06-10 | E-MEXP-1485 | biostudies-arrayexpress

Proteomic Analysis of Canola Inoculated with Bacteria under Salt Stress

Project description:In order to understand the salt response-mechanisms and ability of plant growth promoting bacteria to moderate harmful effect of salt, two Canola cultivars, salt-tolerant Hyola308, and salt-sensitive Sarigol, were treated with Inoculation with plant growth promoting bacteria, Pseudomonas fluorescens, and salt. For this quantitative proteomics technique was used.

2016-06-24 | PXD001580 | Pride

arcole / pgpr-Nitrogenous nutrition efficiency of canola in spring : identification of targets for plant breeding

Project description:pc_arcole - arcole / pgpr - What are the genes implicated in the efficiency of nitrogenous nutrition when A.thaliana is inoculated with a PGPR (Plant Growth Promoting Rhizobacteria)? - A.thaliana seeds germinated and grew during ten days until they were transfered in 6 different media: 0,5 mM nitrate with PGPR (Plant Growth Promoting Rhizobacteria), 0,5mM nitrate without PGPR, 2mM nitrate with PGPR, 2mM nitrate without PGPR, 20 mM nitrate with PGPR, 20 mM nitrate without PGPR. Young plantlets grew 7 days in these new mediums. Shoots are collected in eppendorf. 6 dye-swap - dose response,organ comparison,treated vs untreated comparison

2012-05-31 | E-GEOD-36730 | biostudies-arrayexpress

The effect of γ-butyrolactone (MB3) treatment on the transcript response after wounding of Arabidopsis thaliana roots

Project description:In a previous study, we found that wound-induced transcriptional expression is strongly correlated with an increase of the level of acetylation of the N-tails of histone 3. To investigate if the increase in histone acetylation is a prerequisite for the induction of wound-induced gene expression, we performed transcriptional profiling of wounded roots with and without treatment with γ-butyrolactone (MB3), a chemical inhibitor of GNAT-MYST family of histone acetyltransferase .

2019-11-29 | E-MTAB-7612 | biostudies-arrayexpress

Volatiles of two growth-inhibiting rhizobacteria commonly enroll AtWRKY18 function

Project description:Volatiles of certain rhizobacteria can cause growth inhibitory effects on plants/ Arabidopsis thaliana. How these effects are initiated and which mechanisms are enrolled is not yet understood. Obviously the plant can survive/live with the bacteria in the soil, which suggest the existance of a regulatory mechanism/network that provide the possibility for coexistance with the bacteria. To shed light on this regulatory mechanism/network we performed a microarray anlaysis of Arabidopsis thaliana co-cultivated with two different rhizobacteria strains. In this study we used the ATH1 GeneChip microarray to investigate the transcriptional response of 4 to 5 days old Arabidopsis thaliana seedlings at 6 h, 12 h and 24 h exposure to volatiles of the rhizobacteria Serratia plymuthica HRO-C48 or Stenotrophomonas maltophilia R3089. Seedlings from Arabidopsis thaliana were harvested at different time points at exposure to volatiles of two different strains of bacteria. Samples were taken at the start of the experiment (T0) and after 6, 12 and 24 hours (T6, T12, T24 respectively). Two biological replicates from pooled seedlings (from 5 plates, from the respective time points) were used for RNA extraction and hybridization on Affymetrix microarrays (ATH1 GeneChip; GEO accsession GPL198).

2012-01-25 | E-GEOD-35325 | biostudies-arrayexpress

Transcriptome profiling of banana in response to growth-promoting rhizobacteria

Project description:We report the banana transcriptome profile in response to two distinct growth-promoting rhizobacteria, Bacillus amyloliquefaciens and Pseudomonas fluorescens. The goal of our study is to identify plant genes differentially regulated by rhizobacteria-plant interaction along time. At the same time, we show that despite these two rhizobacteria regulate distinct sets of genes, the same functional categories has been over-represented, such as transcription factor activity, response to stress and metabolic processes.

2016-04-21 | GSE80495 | GEO

Quantitative proteome, phosphoproteome and acetylome analysis of Arabidopsis thaliana root responses to persistent osmotic and salinity stress.

Project description:Environmental conditions contributing to abiotic stresses such as drought and salinity result in large annual economic losses around the world. As sessile organisms, plants cannot escape the environmental stresses they encounter, but instead must adapt to survive. Previous studies investigating osmotic and/or salt responses have largely focused on understanding short-term responses (0-1h) at the transcriptomic, proteomic and phosphoproteomic level; however, our understanding of intermediate to longer-term adaptation (24h - days) is relatively limited. In addition to protein abundance and phosphorylation changes, recent evidence suggests reversible protein acetylation may be important for abiotic stress responses. Therefore, to characterize the effects of osmotic and salt stress, we undertook a label-free proteomic and PTMomic analysis of Arabidopsis roots exposed to 300mM Mannitol and 150mM NaCl for 24 h. We quantitatively assessed protein abundance, phosphorylation and acetylation.

2022-05-04 | PXD019139 | Pride

The bacterial cell-cycle regulator GcrA is a Ï70 co-factor that drives gene expression from a subset of methylated promoters.

Project description:Cell cycle progression in most organisms requires tightly regulated programs of gene expression. The transcription factors involved typically stimulate gene expression by binding specific DNA sequences in promoters and recruiting RNA polymerase. Here, we find that the essential cell cycle regulator GcrA in Caulobacter crescentus activates the transcription of target genes in a fundamentally different manner. GcrA forms a stable complex with RNA polymerase and localizes to almost all active Ï70-dependent promoters in vivo, but activates transcription primarily at promoters harboring certain DNA methylation sites. Whereas most transcription factors that contact Ï70 interact with domain 4, GcrA interfaces with domain 2, the region that binds the -10 element during strand separation. Using kinetic analyses and a reconstituted in vitro transcription assay, we demonstrate that GcrA can stabilize RNA polymerase binding and directly stimulate open complex formation to activate transcription. Guided by these studies, we identify a regulon of ~200 genes, providing new insight into the essential functions of GcrA. Collectively, our work reveals a new mechanism for transcriptional regulation, and we discuss the potential benefits of activating transcription by promoting RNA polymerase isomerization rather than exclusively recruitment. Examination of GcrA, RNAP, Sigma70 ChIP in PYE and in PYE + rifampicin-treated for 30 min; sigma32 and sigma54 in PYE + rifampicin-treated for 30 min

2015-11-10 | E-GEOD-73925 | biostudies-arrayexpress

arcole / pgpr-Nitrogenous nutrition efficiency of canola in spring : identification of targets for plant breeding

2012-06-01 | GSE36730 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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