Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Leaf transcriptomes of Arabidopsis thaliana colonized by representative phyllosphere commensals alone and in combination with the pathogen Pseudomonas syringae DC3000

ABSTRACT: Plants are colonized by a variety of microorganisms, the plant microbiota. In the phyllosphere, the above-ground parts of plants, bacteria are the most abundant inhabitants. Most of these microorganisms are not pathogenic and the plant responses to commensals or to pathogen infection in the presence of commensals are not well understood. We report the Arabidopsis leaf transcriptome after 3 to 4 weeks of colonization by Methylobacterium extorquens PA1 and Sphingomonas melonis Fr1, representatives of two abundant genera in the phyllosphere, compared to axenic plants. In addition, we also sequenced the transcriptome of Arabidopsis 2 and 7 days after spray-infection with a low dose of P. syringae DC3000 and in combination with the commensals.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Christine Vogel

PROVIDER: E-MTAB-4683 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Response to salt stress treatment over time in Oryza sativa L. Japonica Nipponbare, RNA-seq dataset

Project description:Oryza sativa L. Japonica nipponbare seedlings were treated with 300mM NaCl or water, and then samples were taken after one hour, five hours and 24 hours, to assess which genes are differentially expressed over time during salt stress treatment. The results from this dataset are also compared with those from the same samples assayed using RNA-seq.

2015-08-25 | E-MTAB-1625 | biostudies-arrayexpress

Salt stress in salt sensitive Oryza sativa Indica group Pokkali (salt sensitive)

Project description:Oryza sativa Indica group Pokkali (salt sensitive) seedlings were subjected to salt stress or control conditions and sampled at five time points over the course of 4 hours. RNA samples extracted were assayed using the Illumina HiSeq 2000 platform.

2020-01-01 | E-MTAB-1914 | biostudies-arrayexpress

Salt stress in salt sensitive Oryza sativa Indica group IR29

Project description:Oryza sativa Indica group IR29 (salt sensitive) seedlings were subjected to salt stress or control conditions and sampled at five time points over the course of 24 hours. RNA samples extracted were assayed using the Illumina HiSeq 2000 platform.

2017-10-02 | E-MTAB-1913 | biostudies-arrayexpress

iiTRAQ protein profiles of petunia seedlings in response to cold stress

Project description:iTRAQ-based quantitative proteomic analysis of petunia seedlings exposed to low temperature.

2016-02-23 | PXD002189 | Pride

Proteomic Analysis Reveals the Association between the Path-ways of Glutathione and α-Linolenic Acid Metabolism and Lanthanum Accumulation in Tea Plants

Project description:Tieguanyin (TGY) and Shuixian (SX) cultivars of Camellia sinensis were selected to explore the mechanism underlying the accumulation of the rare earth element lanthanum through proteomics. Roots and fresh leaves of TGY and SX with low- and high-accumulation potential for lanthanum, respectively, were studied; 845 differentially expressed proteins (DEPs) were identified. Gene ontology analysis showed that the DEPs are involved in redox processes and related to molecular functions, such as defense and oxidative stress reactions, catalytic activity, and metal ion binding. Kyoto Encyclopedia of Genes and Genomes metabolic pathway analysis showed that DEPs were associated with glutathione (GSH) and α-linolenic acid metabolism, plant pathogen interaction, and oxidative phosphorylation. Thirty-seven proteins in the GSH metabolism pathway showed significant differences, of which 18 GSH S-transferases show differential expression patterns in the root system.The expression multiples of GST (TEA004130.1) and GST (TEA032216.1) in T1L and T0L were 6.84 and 4.06, respectively, which were significantly higher than those in S1L and S0L. The lanthanum-induced activation of the GSH-related antioxidant defense system may cause the difference in TGY and SX. The LOX2.1 (TEA011765.1) and LOX2.1 (TEA011776.1 expression ratios) in the α-linolenic acid metabolic pathway were 2.44 and 6.43 in T1R and T0R, respectively, which were significantly higher than those in S1R snd S0R. The other differential proteins were also sig-nificantly upregulated in TGY leaves.The synthesis of specific substances induces lantha-num-associated defense responses in TGY, which is of great significance for the stability of its yield.

2023-03-11 | PXD039195 | Pride

Application of data-independent acquisition approach to study the proteome dynamics of plant pathogenesis responses

Project description:Plants and pathogens are entangled in a continual arms race. The plants are evolved to have a dynamic defense and immune mechanisms to resist the infection and enhance the immunity for the second wave attacks from the same or different type of pathogenic species. Not only in the evolutionally or physiologically, the plant-pathogen interaction is also highly dynamic in the molecular level. Recently, the emerging quantitative mass spectrometry-based proteomics approach, data-independent acquisition (DIA), was developed for the analysis of proteome in a high throughput fashion. In this study, the DIA approach was applied to quantitatively trace the change of the plant proteome from the early to late stage of pathogenesis progression. This study revealed that the early stage of the pathogenesis response, the proteins directly related to the chaperon for the defense proteins. In the later stage, not only the defense proteins but also a set of the pathogen associate molecular pattern triggered immunity (PTI), effector triggered immunity (ETI) related proteins were highly induced. Our finding showed the dynamics of the regulation in protein level and demonstrated that the potential of using DIA approach for tracing the dynamics of the plant proteome during pathogenesis responses.

2019-02-18 | PXD012226 | Pride

A proteomics approach to study the role of lipid droplets in plant defense

Project description:Lipid Droplets (LDs), classically viewed as lipid storage particles, are recently emerging as dynamic organelles associated with stress responses and development; however, their involvement in plant immunity has been little investigated. Here we studied LDs in Arabidopsis thaliana leaves that respond to Pseudomonas syringae pv. tomato DC3000 avrRpm1 by inducing a hypersensitive defense reaction (HR), as well as during senescence. We established a protocol to reproducibly isolate LDs from a limited amount of tissue and performed a proteomic analysis of LDs from Pseudomonas-infected (for 24 h and 72 h) and senescent leaves. The proteomes defined shared ~50% similarity, with an enrichment of proteins associated with the Gene Ontology terms “transport” and “responses to stress”. As validation, we confirmed LD localization of glycerol-3-phosphate-acetyltransferase 8 (GPAT8) and GPAT4, enzymes required for e.g., cutin biosynthesis, by transient expression of GFP fusions in HR-induced leaves of Nicotiana benthamiana. Similarly, we proved the localization to LDs of aldehyde dehydrogenase 3F1 (ALDH3F1), α-dioxygenase1 (α-DOX1) and caleosin3 (CLO3), all involved in the synthesis of fatty acid derivatives. Moreover, we found that PAD3 (phytoalexin deficient 3) was distributed in patches along the ER and plasma membrane, and in LDs near dead cells. The nature of these proteins and of the additional components characterized in the LDs, together with the phenotypic examination of selected mutants, established a functional link between LDs and plant immunity. Our data suggest that these organelles participate in protein trafficking and in lipid changes that affect the interaction of plants with invading pathogens.

2022-02-23 | PXD011499 | Pride

RNA-seq data of four Lupinus angustifolius lines profiled for anthracnose resistance, based on leaves RNA isolates from inoculated and control (mock-inoculated) plants

Project description:Resistant lines (Mandelup, carrying the AnMan allele and 83A:476 carrying the Lanr1 allele), the line which is putative novel donor of resistance (Boregine) and a susceptible line (Population 22660) were used in this study. 4 weeks after sowing, when the plants reached 4-6 leaf stage, plants were inoculated with Colletotrichum lupini or mock-inoculated (control plants) and then kept for 24 hours in darkness under ~100% humidity and temperature of 25°C. Leaves were sampled at 6, 12, 24, 36, and 48 hours post inoculation.

2022-11-02 | E-MTAB-11164 | biostudies-arrayexpress

Response to salt stress treatment over time in Oryza sativa L. Japonica Nipponbare, microarray dataset

2015-12-04 | E-MTAB-1624 | biostudies-arrayexpress

tps1-2_apices

Project description:To monitor gene expression changes pre floral transition and during early flower development col-0 and tps1-2 GVG::TPS1 (von Dijken, 2004) plants were grown under SD (8 hr light, 16 hr dark) for 21 days. Plants were then shifted to LD (16 hr light, 8 hr dark) conditions to induce flowering. RNA was isolated from micro-dissected apical tissue harvested 0 and 5 days after the shift to LD and double-stranded cDNA was synthesized. Biotinylated cRNA probes were prepared and hybridized to the Affymetrix ATH1 array in duplicate (biological replicates).

2013-02-15 | E-MEXP-3727 | 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