GEO DataSets

(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) Expression profiles of one-week-old rice seedlings exposed to Pi-deficient solution for 6, 24, 48, 72 hours were monitored by microarray that contains approximately 60,000 rice clones (Affymetrix GeneChip). The probes were prepared from RNAs isolated from rice seedlings exposed to Pi-deficient solution for 6, 24, 48, 72 hours, respectively, and those non-treated controls. For hybridization, two biological replicates were used to extract RNAs from different batches of plants.

Organism:

Oryza sativa Japonica Group; Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

10 Samples

Download data: CEL

(Submitter supplied) The present work describes the effects on iron homeostasis when copper transport was deregulated in Arabidopsis thaliana by overexpressing copper transporters (COPTOE). A genome-wide analysis conducted on COPT1OE plants, highlighted that iron homeostasis gene expression was affected, both under copper deficiency and excess. Among the inhibited genes were those encoding the iron uptake machinery and their transcriptional regulators. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL2508

7 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of rice genes analyzing the effect of knockdown of OsHRZ1 and OsHRZ2 in HRZ2i lines. NT and HRZ2i lines 1, 2 and 3 (2i-1, 2i-2 and 2i-3, respectively) were treated under iron sufficiency for 7 days (+Fe 7d) or under iron deficiency for 1 day (-Fe 1d) or 7 days (-Fe 7d) in hydroponic culture.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL6864

9 Samples

Download data: TXT

(Submitter supplied) The transition metal copper (Cu) is an essential element for all living organisms. In plants, Cu plays key roles in electron transport chains of chloroplasts and mitochondria, as well as in cell wall metabolism, ethylene perception, molybdenum cofactor synthesis and oxidative stress protection. Because of its physiological importance, suboptimal concentrations of Cu trigger a re-organization of metabolism to economize on Cu, and pronounced Cu deficiency causes severe growth reduction and defects in male fertility. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9302

8 Samples

Download data: TXT

(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) Four-day-old seedlings germinated in wet paper were transferred to solution culture with 0.1 mM Fe(III)-EDTA for five days. Then seedlings were transferred to solution culture without Fe or with 0.1 mM Fe(III)-EDTA for five days. Roots and shoots were separated and used for RNA extraction.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL8852

8 Samples

Download data: TXT

(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) When iron is withdrawn from the growth medium of plants, large changes in gene expression have been observed. A double mutant with T-DNA insertions in the Arabidopsis yellow stripe1-like1 (At4g24120) and yellow stripe3-like (At5g53550) genes shows strong iron-related phenotypes. This study is intended to uncover the gene expression changes that occur in leaves and roots of the double mutant compared to wild type plants.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

18 Samples

Download data: CEL

(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) Copper and iron are essential micronutrients for most living organisms because they participate as cofactors in biological processes including respiration, photosynthesis and oxidative stress protection. In many eukaryotic organisms, including yeast and mammals, copper and iron homeostases are highly interconnected; however such interdependence is not well established in higher plants. Here we propose that COPT2, a high-affinity copper transport protein, functions under copper and iron deficiencies in Arabidopsis thaliana. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL2508

12 Samples

Download data: GPR

(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) 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) Fourteen days plants growth under hydroponic +P condition (200 μM) were treated under –P (no phosphate) condition for another 7 days, shoot of plants from 3 biological repeats were sampled for Affymetrix microarray analysis. We used microarrays to detail the global programme of gene expression underlying -Pi condition among WT and mutants of phr1, phr3 and triple mutant of phr1phr2phr3.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

12 Samples

Download data: CEL

(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:

GPL13160 GPL15800

8 Samples

Download data: TSV

(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) To examine differential effect of the mutation of rice OsPIPT6 on the gene exoression in shoot and root tissues, we performed microarray analysis using shoot and root tissues of wild-type and ospipt6-KO mutant.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL6864

12 Samples

Download data: TXT

(Submitter supplied) We report the comparison of transcript expression in OsbZIP83 overexpression lines b83OX-13, 15 and 19 against non-transformants (NT) in Fe-sufficient roots and leaves by RNA-Seq.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24468

8 Samples

Download data: XLSX

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

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24468 GPL19290

19 Samples

Download data

(Submitter supplied) We report the comparison of transcript expression of Fe-sufficient roots of OsIMA overexpression lines IMA1OX-4, IMA2OX-1, OsIMA knockdown lines IMA1i-2, IMA2i-3, and corresponding NT, as well as Fe-deficient roots of NT, by RNA-Seq.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

9 Samples

Download data: TXT