GEO DataSets

(Submitter supplied) Several metals are essential nutrients for plants but metals are toxic in excess, deleteriously affecting crop yield and quality. Various kinds of genes involved in metal homeostasis have been investigated in detail over the past few decades and the mechanisms of how metals are absorbed from soil and distributed in plants have been elucidated. However, numerous genes related to metal homeostasis remain to be investigated and a comprehensive analysis of the expressions of these genes is required. more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL6864

39 Samples

Download data: TXT

(Submitter supplied) Detailed analysis of genome-wide transcriptome profiling in rice root is reported here, following Cr-plant interaction. Such studies are important for the identification of genes responsible for tolerance, accumulation and defense response in plants with respect to Cr stress. Rice root metabolome analysis was also carried out to relate differential transcriptome data to biological processes affected by Cr (VI) stress in rice. more...

Organism:

Oryza sativa; Oryza sativa Indica Group

Type:

Expression profiling by array

Platform:

GPL2025

15 Samples

Download data: CEL, CHP

(Submitter supplied) Dongxiang wild rice (Oryza rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.) and is well known for its superior level of tolerance against cold, drought and diseases. To date, however, little is known about the salt-tolerant character of Dongxiang wild rice. To elucidate the molecular genetic mechanisms of salt-stress tolerance in Dongxiang wild rice, the Illumina HiSeq 2000 platform was used to analyze the transcriptome profiles of the leaves and roots at the seedling stage under salt stress compared with those under normal conditions. more...

Organism:

Oryza rufipogon

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15800

4 Samples

Download data: TXT

(Submitter supplied) Iron (Fe) toxicity is a major challenge for plant cultivation in acidic water-logged soil environments, where lowland rice is a major staple food crop. Only few studies addressed the molecular characterization of excess Fe tolerance in rice, and these highlight different mechanisms for Fe tolerance in the studied varieties. Here, we screened 16 lowland rice varieties for excess Fe stress growth responses to identify contrasting lines, Fe-tolerant Lachit and -susceptible Hacha. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13160

23 Samples

Download data: TSV, XLSX

(Submitter supplied) The root system is a crucial determinant of plant growth potential because of its important functions, e.g., acquisition of water and nutrients, structural support, and interaction with symbiotic organisms. Elucidating the molecular mechanisms of root development and functions is therefore necessary for improving plant productivity, particularly for crop plants including rice. As an initial step towards developing a comprehensive understanding of the root system, we performed a large-scale transcriptome analysis of the rice root via a combined laser microdissection and microarray analysis approach.

Organism:

Oryza sativa Japonica Group; Oryza sativa

Type:

Expression profiling by array

Platform:

GPL6864

38 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) Higher plants have developed sophisticated mechanisms to efficiently acquire and use micronutrients such as copper and iron. In the present work, we studied effects produced by the presence of a wide copper range in growth media and altered copper transport on iron homeostasis in Oryza sativa plants. The global analysis of gene expression in the rice seedlings grown under copper deficiency versus excess in the medium showed an increased expression of the genes involved in iron homeostasis. more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL8756

8 Samples

Download data: GPR

(Submitter supplied) transcriptomic study of the impact of iron toxicity on rice plant (Oryza sativa L.; cv ‘I Kong Pao’ ) after short term (3 days) or long term (3 weeks) exposure to ferrous iron (125 ppm). Twenty five days old rice seedlings were exposed to 0 or 125 mg/L ferrous iron for 3 days and 3 weeks in hydroponic culture. Comparison between control and iron stressed plants were done at the shoot and the root levels. more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL15304

8 Samples

Download data: TXT

(Submitter supplied) Autotoxicity plays an important mechanism in regulating plant productivity. Ferulic acid (FA) is phytotoxic and was identified in extracts and residues of rice plants as a candidate for rice allelochemicals. To help characterize the autotoxicity mechanism of rice, we present the first large-scale, transcriptomic analysis of rice root responses to ferulic acid.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL8852

6 Samples

Download data: TXT

(Submitter supplied) Fe deficiency stimulates a coordinated response involving reduction, transport and redistribution of Fe in the roots. The expression of genes regulated by Fe deficiency in the two contrasting Arabidopsis thaliana ecotypes, Tsu-1 and Kas-1, shows that different ecotypes can respond in diverse ways, with different Fe regulated overrepresented categories. We use microarrays to analyze the Fe deficiency responses of contrasting Arabidopsis thaliana ecotypes (Tsu-1 and Kas-1).

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

18 Samples

Download data: CEL

(Submitter supplied) A DNA microarray analysis detected large-scale changes of gene expression in response to Cd stress with a substantial difference between the two barley genotypes differing in Cd tolerance and accumulation. Cd stress led to higher expression of genes involved in transport, carbohydrate metabolism and signal transduction in the low-grain-Cd-accumulating genotype. Novel transporter genes such as zinc transporter genes were identified as being associated with low Cd accumulation. more...

Organism:

Hordeum vulgare

Type:

Expression profiling by array

Platform:

GPL1340

4 Samples

Download data: CEL, CHP, DAT, JPG, TXT

(Submitter supplied) Whole-genome transcriptional profiles of rice cell types, isolated by laser-capture microdissection. The first comprehensive multi-organ cell type transcriptome atlas from a plant, with 40 distinct cell types from several developmental stages of seeds, shoots and roots, reveals cell-specific promoter motifs, interaction partner candidates, hormone response centers, and other previously unrecognized cellular properties and patterns. more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL1829

220 Samples

Download data: GPR

(Submitter supplied) Arsenic (As) is a carcinogenic metalloid that is a contaminant widely polluting rice paddy soils around the world. In order to gain better insight into molecular mechanism of rice exposed to As(III) stress, we used next-generation sequencing technology to acquire global transcriptome alteration and miRNA regulation in rice upon As(III) treatments. Our results suggest time course and As(III)-dosing treatments were devised. more...

Organism:

Oryza sativa Japonica Group

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL15370

20 Samples

Download data: TXT

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

Organism:

Oryza sativa

Type:

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

Platforms:

GPL27660 GPL23013

124 Samples

Download data: BW, TSV

(Submitter supplied) Genomic diversity is a source of transcriptomic and phenotypic diversities. Although genomic variations in rice (Oryza sativa) accessions have been extensively analyzed, information of transcriptomic and phenotypic variations, especially for below-ground variations, are limited. Here, we report the diversities of above- and below-ground traits and transcriptomes in highly diversified 61 rice accessions grown in the upland-field. more...

Organism:

Oryza sativa

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23013

2 Samples

Download data: BW

(Submitter supplied) Genomic diversity is a source of transcriptomic and phenotypic diversities. Although genomic variations in rice (Oryza sativa) accessions have been extensively analyzed, information of transcriptomic and phenotypic variations, especially for below-ground variations, are limited. Here, we report the diversities of above- and below-ground traits and transcriptomes in highly diversified 61 rice accessions grown in the upland-field. more...

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27660

122 Samples

Download data: TSV

(Submitter supplied) Iron (Fe) is an essential micronutrient for almost all organisms. However, Fe is frequently inaccessible to plants. To acquire insoluble Fe from soil, rice (Oryza sativa L.) plants employ a Combined Strategy, which is composed by all features of Strategy II, common to all Poaceae species, and some features of the Strategy I from non-Poaceae. To understand the evolution of Fe uptake mechanisms, we analyzed the root transcriptomic response to Fe deficiency in two species from the Oryza genus: O. more...

Organism:

Oryza sativa; Oryza rufipogon

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL15800 GPL13160

8 Samples

Download data: TSV

(Submitter supplied) Thermococcus gammatolerans, the most radioresistant archaeon known to date, is an anaerobic and hyperthermophilic sulfur-reducing organism living in deep-sea hydrothermal vents. Knowledge of mechanisms underlying archaeal metal tolerance in such metal-rich ecosystem is still poorly documented. We showed that T. gammatolerans exhibits high resistance to cadmium (Cd), cobalt (Co) and zinc (Zn), a weaker tolerance to nickel (Ni), copper (Cu) and arsenate (AsO4) and that cells exposed to 1mM Cd exhibit a cellular Cd concentration of 67µM. more...

Organism:

Thermococcus gammatolerans

Type:

Expression profiling by array

Platform:

GPL6958

24 Samples

Download data: GPR

(Submitter supplied) Arsenic (As) is considered as the most common toxic metalloid, but its molecular mode of action is not well understood. In this study, we demonstrated that As(V) induced intracellular ROS production and Ca2+ accumulation in rice roots. To understand the molecular basis of plant cell responses to As better, we have undertaken a large-scale analysis of the rice transcriptome during As(V) stress. Up-regulated genes were enriched in transcripts involved in abiotic stress, chemical detoxification pathways, secondary metabolic process, transcription regulation and protein degradation while down-regulated genes were enriched in transcripts involved in secondary cell wall biogenesis, cell cycle and oligopeptide transporter. more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL8852

3 Samples

Download data: TXT

(Submitter supplied) In flowering plants, the male gametophyte, the pollen, develops in the anther. Complex patterns of gene expression in both the gametophytic and sporophytic tissues of the anther regulate this process. The gene expression profiles of the microspore/pollen and the sporophytic tapetum are of particular interest. In this study, a microarray technique combined with laser microdissection (44K LM-microarray) was developed and used to characterize separately the transcriptomes of the microspore/pollen and tapetum in rice. more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL6864

33 Samples

Download data: TXT