GEO DataSets

(Submitter supplied) The WRKY gene family has a very ancient origin but has faced extensive duplication only in the plant kingdom so much that Arabidopsis (Arabidopsis thaliana) has 74 copies of WRKY genes encoding transcription factors while 109 can be found in Rice (Oryza sativa L.). Several studies in the last decade has pointed their involvement in an heterogeneous number of biological processes, from development to hormone signalling, dormancy and senescence, but a wide number of WRKY genes are transcriptionally regulated during biotic or abiotic stresses. more...

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by array

Platform:

GPL4315

40 Samples

Download data: GPR

(Submitter supplied) In this study, we used a cross-species network approach to uncover nitrogen (N)-regulated network modules conserved across a model and a crop species. By translating gene network knowledge from the data-rich model Arabidopsis (Arabidopsis thaliana, ecotype Columbia-0) to a crop, rice (Oryza sativa spp. japonica (Nipponbare)), we identified evolutionarily conserved N-regulatory modules as targets for translational studies to improve N use efficiency in transgenic plants.

Organism:

Oryza sativa; Arabidopsis thaliana

Type:

Expression profiling by array

Platforms:

GPL198 GPL2025

16 Samples

Download data: CEL

(Submitter supplied) Drought, salinity and sub-optimal temperatures are stresses that cause adverse effects on the growth of plants and the productivity of crops. In this study, we have analyzed the expression profiles of rice genes under control and abiotic stress conditions using microarray technology to identify the genes differentially expressed during various abiotic stresses. Keywords: Stress treatment

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

12 Samples

Download data: CEL

(Submitter supplied) Plants initially undergo a period of vegetative development, in which it produces leaves from shoot apical meristem (SAM) and roots from the root apical meristem. Later in development, the SAM undergoes a change in fate and enters reproductive development called as floral transition, producing flowers and seeds. Our understanding of the molecular and genetic mechanisms that underlie reproductive development in plants has increased tremendously in the past decade, essentially through the work on Arabidopsis. more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

45 Samples

Download data: CEL

(Submitter supplied) Accumulating information indicates that plant disease resistance signaling pathway frequently interact with other pathways regulating developmental processes or abiotic stress responses. However, the molecular mechanisms of these types of crosstalk remain poorly understood in most cases. Here we report that OsWRKY13, an activator of rice resistance to both bacterial and fungal pathogens, functions as a convergent point of the crosstalk between pathogen-induced salicylate-dependent defense pathway and at least five other physiological pathways. more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

9 Samples

Download data: CEL, CHP, EXP

(Submitter supplied) In response to bacterial infection, early transcriptional re-programming occurs in the host plant. We used microarrays to analyse the global transcriptomic response to Xoo. infection in a resistant rice cultivar (IR24). This was analysed in parallel with microarrays examining Xoo infection in a susceptible rice cultivar (IRBB21) as well as in response to Xoc [GSE19239], viral [GSE11025], parasite [GSE10373] and fungal [GSE7256, GSE18361] infections in rice, in order to identify common and distinct responses to biotic stress.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

24 Samples

Download data: CEL

(Submitter supplied) Purpose: To understand the dynamic salt-sress response in Arabidopsis and Marchantia

Organism:

Oryza sativa Japonica Group; Marchantia polymorpha; Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

5 related Platforms

80 Samples

Download data: BW, XLSX

(Submitter supplied) To identify genes that co-express with rice cellulose synthase genes involved in rice secondary cell wall formation, transcriptome analyses was performed using rice internodesbefore and after the heading stage, where secondary cell wall formation extensively occur.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL6864

59 Samples

Download data: TXT

(Submitter supplied) We have implemented an integrated Systems Biology approach to analyze overall transcriptomic reprogramming and systems level defense responses in the model plant Arabidopsis thaliana during an insect (Brevicoryne brassicae) and a bacterial (Pseudomonas syringae pv. tomato strain DC3000) attack. The main aim of this study was to identify the attacker-specific and general defense response signatures in the model plant Arabidopsis thaliana while attacked by phloem feeding aphids or pathogenic bacteria. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL15699

4 Samples

Download data: GPR

(Submitter supplied) We have implemented an integrated Systems Biology approach to analyze overall transcriptomic reprogramming and systems level defense responses in the model plant Arabidopsis thaliana during an insect (Brevicoryne brassicae) and a bacterial (Pseudomonas syringae pv. tomato strain DC3000) attack. The main aim of this study was to identify the attacker-specific and general defense response signatures in the model plant Arabidopsis thaliana while attacked by phloem feeding aphids or pathogenic bacteria. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL15699

4 Samples

Download data: GPR

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platform:

GPL17639

28 Samples

Download data: TXT

(Submitter supplied) During microbe-associated molecular pattern (MAMP)-triggered immunity (MTI) more than 5000 Arabidopsis genes are significantly altered in their expression and the question arises, how such an enormous reprogramming of the transcriptome can be regulated in a safe and robust manner? For the WRKY transcription factors, which are important regulators not only of this defense response, it appears that they act in a complex regulatory sub-network rather than in a linear fashion, which is much more vulnerable to gene function loss either by pathogen-derived effectors or by mutations. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

12 Samples

Download data: TXT

(Submitter supplied) During microbe-associated molecular pattern (MAMP)-triggered immunity (MTI) more than 5000 Arabidopsis genes are significantly altered in their expression and the question arises, how such an enormous reprogramming of the transcriptome can be regulated in a safe and robust manner? For the WRKY transcription factors, which are important regulators not only of this defense response, it appears that they act in a complex regulatory sub-network rather than in a linear fashion, which is much more vulnerable to gene function loss either by pathogen-derived effectors or by mutations. more...

Organism:

Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL17639

16 Samples

Download data: TXT

(Submitter supplied) Benzothiadiazole (BTH) is a so-called ‘plant activator’ and protects plants from diseases by activating the salicylic-acid (SA) signaling pathway. We identified BTH-responsive genes in rice leaves 24 h after treatment using rice 44K microarray. Keywords: response to chemical treatment

Organism:

Oryza sativa

Type:

Expression profiling by array

Dataset:

GDS3070

Platform:

GPL5101

8 Samples

Download data: TXT

Analysis of leaves of Oryza sativa plants treated with benzothiadiazole (BTH). BTH is a functional analog of salicylic acid and enhances the resistance of rice to the fungal pathogen Rhizoctonia solani. Results provide insight into the molecular mechanisms underlying BTH-induced disease resistance.

Organism:

Oryza sativa

Type:

Expression profiling by array, transformed count, 2 agent sets

Platform:

GPL5101

Series:

GSE7567

8 Samples

Download data: TXT

(Submitter supplied) Potassium (K+) is one of the most important nutrient ions in plant cells and play crucial roles in many plant physiological and developmental processes. K+ deficiency is the common abiotic stress in natural environment, which inhibits plant growth and reduces production of crops. We used microarrays to analyse the transcriptomic changes in rice roots after suffering K+ starvation at different times. more...

Organism:

Oryza sativa; Oryza sativa Japonica Group

Type:

Expression profiling by array

Platform:

GPL2025

18 Samples

Download data: CEL

(Submitter supplied) Regulation of gene expression by reactive oxygen species (ROS) is an important component of abiotic stress signal transduction mechanisms. Previous genome-wide analysis of chilling-induced changes in gene expression suggested a potential role of H2O2 and other ROS as key signals in the induction of early response genes in japonica rice (cv. Nipponbare). Candidate regulators including bZIP-, Myb- or WRKY-types of transcription factors that were responsive to both chilling (10oC) and exogenous H2O2, and their probable target clusters (as1/ocs/TGA1-like, MybR-like element containing genes) were inferred by integrative analysis of qPCR expression profiles and ab initio promoter motif data. more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platforms:

GPL6338 GPL6339

20 Samples

Download data

(Submitter supplied) The central role of transcriptional regulation in integrating various low temperature response mechanisms has been established in Arabidopsis, where the CBF/DREB regulon plays a prominent role during acclimation. Rice is sensitive to chilling but many japonica cultivars can survive continuous exposure to as low as 10oC for up to 7 days during the most critical stage of seedling establishment better than most indica cultivars. more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platforms:

GPL5739 GPL5740

44 Samples

Download data

(Submitter supplied) 'Systems-wide' approaches such as microarray RNA-profiling are ideally suited to the study of the complex, overlapping responses of plants to biotic and abiotic stresses. However, commercial microarrays are only available for a limited number of plant species and development costs are so substantial as to be prohibitive for most research groups. Here, we evaluate the use of cross-hybridisation to Affymetrix oligonucleotide GeneChip microarrays to profile the response of the banana (Musa sp.) leaf transcriptome to drought stress using a genomic DNA (gDNA)-based probe-selection strategy to improve the efficiency of detection of differentially expressed Musa transcripts.

Organism:

Oryza sativa; Musa sp.; Arabidopsis thaliana

Type:

Expression profiling by array; Other

Platforms:

GPL2025 GPL198

4 Samples

Download data: CEL, CHP

(Submitter supplied) Complete submergence represses photosynthesis and aerobic respiration causing rapid mortality in most terrestrial plants, but some species have evolved traits allowing them to survive prolonged flooding. Here, we studied the response to submergence of two species and their F1 hybrid in the genus Rorippa, which is related to the model Arabidopsis. We showed that these species have high tolerance to complete, deep submergence, but R. more...

Organism:

Rorippa amphibia; Arabidopsis thaliana; Rorippa sylvestris; Rorippa amphibia x Rorippa sylvestris

Type:

Genome variation profiling by array

Platform:

GPL198

20 Samples

Download data: CEL