Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

45 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcription profiling of Medicago truncatula after innoculation with Phymatotrichopsis omnivora

ABSTRACT: To identify host signaling pathways triggered by P. omnivora
infection, we used microarrays to monitor the expression profiles
and the molecular process associated with initial entry at 3 days post-inoculation and colonization at 5 days post-inoculation

ORGANISM(S): Medicago truncatula

SUBMITTER: Yuhong Tang

PROVIDER: E-MEXP-1994 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Medicago truncatula and Macrophomina phaseolina interaction

Project description:This experiment was designed to study the interactions between Medicago truncatula and the charcoal rot pathogen Macrophomina phaeolina. Two-week-old plants grown in Magenta boxes supplied with 1/2 MS salt and 1% sucrose were inoculated with M. phaseolina covered wheat seeds, and roots were harvested at 24, 36 and 48 hours after inoculation. Control plants were mock inoculated with a sterile wheat seed, and roots were harvest 24 hours later. Pooled RNAs were used in the array experiment using Affymetrix GeneChip(r) Medicago Genome Array.

2012-05-15 | E-MEXP-3580 | biostudies-arrayexpress

Medicago truncatula wild-type and mutant plantlet roots treated with symbiotic lipochitooligosaccharides

Project description:This SuperSeries is composed of the following subset Series: GSE33636: Gene expression data from Medicago truncatula plantlet roots treated with symbiotic lipochitooligosaccharides (LCOs). GSE33637: Gene expression data from Medicago truncatula mutant plantlet roots treated with Myc-LCOs. Refer to individual Series

2012-05-30 | E-GEOD-33638 | biostudies-arrayexpress

myc cell types

Project description:cortical cell of non-mycorrhizal roots (cor), arbuscule-containing cells (arb) and non-arbuscule-containing cells (nac) of M. truncatula roots colonized with Glomus intraradices were collected by laser capture microdissection (LCM) and used for RNA extraction and Medicago microarray hybridisation

2011-10-05 | E-MEXP-3385 | biostudies-arrayexpress

Gene expression data from Medicago truncatula mutant plantlet roots treated with Myc-LCOs.

Project description:Legumes interact with soil fungi, leading to the development of arbuscular mycorrhizal (AM) roots. Diffusible AM fungal signals were identified as sulphated and non-sulphated LCOs (sMyc-LCOs and nsMyc-LCOs). Applying Myc-LCOs on roots of symbiotic mutants, we used GeneChips to detail the global programme of gene expression in these mutants in response to the external application of Myc-LCOs. To harvest tissues for transcriptome profiling, three biological replicates consisting of 10 plantlets per treatment were selected. After 6 h of incubation in the climate chamber, 10 plantlets per batch were removed from the treatment (Myc-LCOs) or control solutions and harvested. During harvest, one mm of the root tip of each plantlet was removed and discarded. The remaining 2 to 2.5 cm of the distal root region were cut off and directly frozen in liquid nitrogen.

2012-05-30 | E-GEOD-33637 | biostudies-arrayexpress

Gene expression data from Medicago truncatula plantlet roots treated with symbiotic lipochitooligosaccharides (LCOs).

Project description:Legumes interact with soil microbes, leading to the development of nitrogen-fixing root nodules and arbuscular mycorrhizal (AM) roots. While nodule initiation by diffusible lipochitooligosaccharide (LCO) Nod-factors of bacterial origin (Nod-LCOs) is well characterized, diffusible AM fungal signals were only recently identified as sulphated and non-sulphated LCOs (sMyc-LCOs and nsMyc-LCOs). Applying Myc-LCOs in parallel to Nod-LCOs, we used GeneChips to detail the global programme of gene expression in response to the external application of symbiotic LCOs. To harvest tissues for transcriptome profiling, three biological replicates consisting of 20 plantlets per treatment were selected. After 6 h of incubation in the climate chamber, 10 plantlets per batch were removed from the treatment (Myc-LCOs or Nod-LCOs) or control solutions and harvested, while the other 10 remained in the respective solutions for a total of 24 h. During harvest, one mm of the root tip of each plantlet was removed and discarded. The remaining 2 to 2.5 cm of the distal root region were cut off and directly frozen in liquid nitrogen.

2012-05-30 | E-GEOD-33636 | biostudies-arrayexpress

The interaction between glucose and cytokinin signal transduction pathway in Arabidopsis thaliana

Project description:Columbia (Col) seeds were sown on half-strength Murashige and Skoog (MS) medium, supplemented with 1% sucrose and 0.8% agar and grown vertically in culture room conditions. The 5-d-old homogenous seedlings were washed five times with sterile water and lastly with liquid half strength MS medium without sugar to remove residual exogenous sugar. In order to deplete internal sugars seedlings were grown in sugar free liquid half strength MS medium for 24 h in dark. Thereafter, the seedlings were treated with half-strength MS medium containing 0% G, 0% G + 1 uM BAP, 3% G, and 3% G + 1 uM BAP for 3 h in dark. RNA was extracted and microarray analysis was performed. Please note: G stands for glucose and BAP stands for 6-Benzylaminopurine (cytokinin)

2014-02-07 | E-MEXP-3827 | biostudies-arrayexpress

Transcription profiling of Arabidopsis etiolated seedlings, light-treated seedlings, leaves and flowers hybridized to ATH1 and AGRONOMICS1 arrays

Project description:RNA from etiolated seedlings, light-treated seedlings, leaves and flowers was hybridized to ATH1 and AGRONOMICS1 arrays.

2010-01-01 | E-MEXP-2472 | biostudies-arrayexpress

Identification of WRKY22 direct targets under submergence in Arabidopsis with ChIP

Project description:To identify direct targets of WRKY22, we created a transgenic Arabidopsis line that expresses a c-myc epitope-tagged WRKY22 and used ChIP followed by microarray hybridization (ChIP-chip) to screen for candidates and validate the in vivo protein-DNA interactions with ChIP followed by quantitative PCR (ChIP-Q-PCR). The WRKY22 and c-myc epitope tag fusion construct was generated and transformed into wrky22-ko2 plants. The resulting transgenic lines should have better ChIP efficiency than the wild-type background, due to the reduced competition for WRKY22 binding sites from endogenous WRKY22. ChIP-enriched DNA fragments were identified using criteria of a window of +300 to M-oM-<M-1200 of a gene for a promoter, a width of 4 probes or more, and a false discovery rate (FDR) < 0.1. The ChIP-chip experiments were repeated six times, i.e., six biological replicas. Candidates were defined by the presence of the promoter in three out of six biological replicas. Candidates were then classified based on their hypoxic responsiveness with a positive response defined as gene expression levels exhibiting > 2 or < 0.5-fold induction in any time point under submergence treatments in expression array data. Comparison of c-myc tagged WRKY22 transgenic plants vs wild-type (Columbia) plants. Both materials were submergence treated for 3 hours.

2013-07-03 | E-GEOD-40138 | biostudies-arrayexpress

Insights into Transcriptional Regulatory Pathways on Systemic Communication under Flooding in Arabidopsis

Project description:We analyzed global transcriptional changes in both shoots and roots of root-flooded Arabidopsis seedlings by microarrays. We also interpreted the significance of the systemic communication between roots and shoots by functional classification of affected genes. We performed genetic analysis with an ethylene signaling mutant, ein2-5, to correlate systemic flooding responses with ethylene signaling. We identified a class of genes that were up- or downregulated in shoots, but not affected in roots, under hypoxic conditions. A comprehensive managing program of carbohydrate metabolism was observed, providing an example of how systemic communications might facilitate the survival of plants under flooding. A proportion of long-distance hypoxic regulation was altered in ein2-5. Time course experiments (0.5, 1, 3, 6, and 12h for Columbia; 0.5, 3, and 6h for ein2-5). Tissues from root-flooded seedlings vs. Tissues from un-flooded seedlings. Biological replicates: 4 replicates for each time point, independently grown, treated, and harvested. One replicate per array. 2 of 4 replicates are dye-swapped.

2011-10-20 | E-GEOD-28885 | biostudies-arrayexpress

Alternative RNA processing events in a double NSR mutant Arabidopsis

Project description:We analyze the effect of a double deletion mutant for alternative-splicing regulators nsra and nsrb (Nuclear Speckle RNA binding proteins), on the Arabidopsis thaliana transcriptome. RNA-seq experiments (polyA+ RNA) in triplicates for each condition WT and nsrab mutants.

2016-07-03 | E-GEOD-65717 | 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