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

Arabidopsis thaliana gene expression upon exposure to nanoparticles (NPs), biotic and abiotic stresses, or NPs plus ABA phytohormone, PART 1

ABSTRACT: Here we provide a set of 16 comparable transcriptome measures to monitor early changes in gene expression upon NP exposure. We evaluated A. thaliana response to 8 different types of NPs (metallic, carbonaceous and ranging from 10 to 80 nm) in comparison to biotic and abiotic stress inducers that represent most common environmental challenges for plants. Biotic stress was induced by infection with a necrotizing fungus (Alternaria brassicicola) or a hemibiotrophic bacterium (Pseudomonas syringae). Abiotic stresses induced by hypersaline conditions, drought and mechanical wounding were assayed in our plant growth model. The effect of abscisic acid (ABA), the most studied stress-responsive phytohormone which mediates stomatal closure and other reponses to drought and osmotic stress (ref), was also tested in the gene expression and phenotypes of NP-exposed plants. PART 1: Alternaria brassicicola (Abr), Pseudomonas syringae (Pst), saline stress (NaC), drought (drou), wounding (wou), 10nm TiO2 NPs (TiO2 10), 10nm AgNPs (Ag 10), bulk TiO2 (TiO), bulk AgNO3 (NO), Carbon Nanotubes NPs plus ABA (CNTs+). susana.garcias@ehu.esadditional contact details for submitter

INSTRUMENT(S): G2565CA DNA microarray scanner (Agilent Technologies)

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Susana Garcia-Sanchez

PROVIDER: E-MTAB-3331 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA sequencing analysis shows that titanium dioxide nanoparticles induce endoplasmic reticulum stress, which has a central role in mediating plasma glucose in mice

Project description:Titanium dioxide nanoparticles (TiO2 NPs) constitute the top five NPs in use today. A recent study determined that oral administration of TiO2 NPs increases plasma glucose in mice. In the current study, RNA sequencing (RNA-seq) technology was used to investigate genome-wide effects of TiO2 NPs. Clustering analysis of the RNA-seq data showed the most significantly enriched gene ontology terms and KEGG pathways related to the endoplasmic reticulum (ER) and ER stress. Molecular biology verification showed that TiO2 NPs activated a xenobiotic biodegradation response and increased expression of cytochrome P450 family genes in mouse livers, thus inducing ER stress in mice. ER stress activated MAPK and NF-B pathways and induced an inflammation response, resulting in phosphorylation of the insulin receptor substrate 1 and, consequently, insulin resistance. This was the main mechanism by which TiO2 NPs increased plasma glucose in mice. Meanwhile, ER stress disturbed the monooxygenase system, and thus generated reactive oxygen species (ROS). Relief of ER stress with 4-phenylbutyric acid inhibited all the above effects of TiO2 NPs, including the generation of ROS. Therefore, TiO2 NP-induced ER stress was a decisive factor with a central role in plasma glucose disturbance in mice.

2019-11-14 | GSE107084 | GEO

Arabidopsis thaliana SWATH-MS - Overexpression of a Monocot Acyl-CoA-Binding Protein Confers Broad-Spectrum Pathogen Protection in a Dicot

Project description:Plants are continuously infected by various pathogens throughout their lifecycle. Previous studies have reported that the expression of Class III acyl-CoA-binding proteins (ACBPs) such as the Arabidopsis ACBP3 and rice ACBP5 were induced by pathogen infection. Transgenic Arabidopsis AtACBP3-overexpressors (AtACBP3-OEs) displayed enhanced protection against the bacterial biotroph, Pseudomonas syringae, although they became susceptible to the fungal necrotroph Botrytis cinerea. A Class III ACBP from a monocot, rice (Oryza sativa) OsACBP5 was overexpressed in the dicot Arabidopsis. The resultant transgenic Arabidopsis lines conferred resistance not only to the bacterial biotroph P. syringae but to fungal necrotrophs (Rhizoctonia solani, B. cinerea, Alternaria brassicicola) and a hemibiotroph, (Colletotrichum siamense). Changes in protein expression in R. solani-infected Arabidopsis OsACBP5-overexpressors (OsACBP5-OEs) were demonstrated using proteomic analysis. Biotic stress-related proteins including cell wall-related proteins such as FASCILIN-LIKE ARABINOGALACTAN-PROTEIN10, LEUCINE-RICH REPEAT EXTENSIN-LIKE PROTEINS, XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE PROTEIN4 and PECTINESTERASE INHIBITOR18; proteins associated with glucosinolate degradation including GDSL-LIKE LIPASE23, EPITHIOSPECIFIER MODIFIER1, MYROSINASE1, MYROSINASE2 and NITRILASE1; as well as a protein involved in jasmonate biosynthesis, ALLENE OXIDE CYCLASE2, were induced in OsACBP5-OEs upon R. solani infection. These results indicated that upregulation of these proteins in OsACBP5-OEs conferred protection against various plant pathogens.

2019-05-10 | PXD013031 | Pride

Alternaria brassicicola infection regulates miRNAs in Arabidopsis thaliana [mRNA]

Project description:Plant microRNAs (miRNAs) have been implicated in plant immunity. These mainly focusing Arabidopsis thaliana threatened by (hemi-)biotrophic pathogens such as the bacterial pathogen Pseudomonas syringae. Here, we show that the Arabidopsis miRNA pathway is important for defense responses against the necrotrophic fungus Alternaria brassicicola. The miRNA pathway mutant ago1 exhibits an exaggerated response when treated with A. brassicicola, proposing that AGO1 is positive regulator. We found a subset of Arabidopsis miRNAs that quickly change their expression and their abundance in AGO1 complexes in plants exposed to A. brassicicola. The miRNAs responding to pathogen treatment are mainly targeting genes encoding metabolic enzymes, proteins involved protein degradation or transposons. In case of miR163, A. brassicicola infection results in increased levels of miRNA precursors and preferential accumulation of an unspliced form of pri-miR163, suggesting that A. brassicicola infection changes the transcriptional and post-regulation of pri-miRNAs. miR163 acts as a negative regulator of plant defense because mir163 mutants are more resistant when treated with A. brassicicola. Taken together, our results reveal the existence of positively and negatively acting Arabidopsis miRNA modulating the defense responses against A. brassicicola and highlight the importance of host miRNAs in the interaction between plants and necrotrophic pathogens.

2019-06-17 | GSE83478 | GEO

Alternaria brassicicola infection regulates miRNAs in Arabidopsis thaliana [sRNA]

2019-06-17 | GSE83487 | GEO

Changes in gene expression in MKK2 and MKKKC5 mutants after Alternaria infection

Project description:The mkkkC5 mutant, a knockout line of MAPKKKC5, shows changes in growth and development, as well as an altered Alternaria sensitivity. It was shown by Brader and Djamei et al.(2007) that Alternaria brassicicola sensitivity is also influenced by MKK2-activity. Aim of this experiment is to access the transcriptional changes in the mkkkc5plants as well as in plants overexpressing a constitutively active MKK2-version (MKK2EE). The second part of the experiment addresses transcriptional changes in these plants after Alternaria brassicicola infection. au07-09_alternaria Keywords: treatment variations Alternaria brassicicola infection of 25 day old mkkkc5- , pGreen::MKK2EE-myc and WT Col-0 plants. Sampling after 0, 1 and 2 days. Comparison between mutants and WT at corresponding timepoints. Additionally comparison between WT-samples at different timepoints. 16 dye-swap - CATMA arrays

2009-02-15 | E-GEOD-14443 | biostudies-arrayexpress

Changes in gene expression in MKK2 and MKKKC5 mutants after Alternaria infection

2009-02-15 | GSE14443 | GEO

Changes in gene expression in MKK2 and MKKKC5 mutants

2009-02-15 | GSE14501 | GEO

Changes in gene expression in MKK2 and MKKKC5 mutants: wt vs mutant comparison

Project description:The mkkkC5 mutant, a knockout line of MAPKKKC5, shows changes in growth and development, as well as an altered Alternaria sensitivity. It was shown by Brader and Djamei et al.(2007) that Alternaria brassicicola sensitivity is also influenced by MKK2-activity. Aim of this experiment is to access the transcriptional changes in the mkkkc5plants as well as in plants overexpressing a constitutively active MKK2-version (MKK2EE). The second part of the experiment addresses transcriptional changes in these plants after Alternaria brassicicola infection. - au07-09_alternaria - mkk2ee and mkkkc5 mutants Keywords: wt vs mutant comparison

2009-02-15 | GSE14444 | GEO

Functional characterization of Taf4b in Arabidopsis thaliana

Project description:Expression analysis was performed with two TDNA insertion mutants of taf4b i.e; taf4bprm (TDNA insertion in promoter region) and taf4bint (TDNA insertion in intronic region), Taf4b overexpression lines, taf4bprmcpr5 double mutant lines (Double mutant was generated by crossing taf4bprm with cpr5) and Col-0 in normal condition as well as with taf4bprm mutant and Col-0 infected with fungi AB (Alternaria brassicicola) and bacteria ES4 (Pseudomonas syringae pv.maculicola ES4326 ) in different perspectives. Affymatrix expression analysis was executed to provide mechanistic details of regulation of genes by Taf4b in plants.

2016-12-01 | GSE45690 | GEO

Expression data from C. elegans treated with anatase TiO2 nanoparticles

Project description:The nematode C. elegans was exposed to TiO2 nanoparticles (NPs) to evaluate the ecotoxicity of TiO2 nanoparticles. We used the DNA microarray method to understand changes in gene expression after the exposure to TIO2 NPs. We identified various genes involved in metal detoxification as well as in regulating worm development.

2017-03-03 | GSE95603 | GEO

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