GEO DataSets

(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; Oryza sativa Japonica Group

Type:

Expression profiling by array

Platform:

GPL2025

10 Samples

Download data: CEL

(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) 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) 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:

Arabidopsis thaliana; Oryza sativa

Type:

Expression profiling by array

Platforms:

GPL198 GPL2025

16 Samples

Download data: CEL

(Submitter supplied) Overexpression of OsMYB103L leads to leaf rolling in transgenic rice plants. To explore the possible molecular mechanism of OsMYB103L’s effects on rice leaf development, we examined the expression profiles of OsMYB103L overexpression transgenic rice plants and wild type leaf blades using Digital Gene Expression (DGE) profiling analysis.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13160

2 Samples

Download data: TXT

(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) Phosphate (Pi) deficiency severely affects crop yield. Modern high yielding rice genotypes are sensitive to Pi deficiency whereas traditional rice cultivars are naturally compatible to low Pi ecosystems. However, the underlying molecular mechanisms for low Pi tolerance in traditional genotypes remain largely elusive. To delineate the molecular mechanisms for low Pi tolerance, two contrasting rice genotypes - Dular (low Pi tolerant) and PB1 (low Pi sensitive) - have been selected. more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

24 Samples

Download data: CEL

(Submitter supplied) We first compared the transcriptomes of the roots of WT seedlings grown under P+ and P- conditions. Using a 2-fold change and a FDR (false discovery rate) of <0.05 as the cut-off for selecting the differentially expressed transcripts, we found that the expression of 581 genes was induced and that the expression of 120 genes was repressed by Pi starvation. We then compared the expression levels of these 581 PSI genes in the WT and phl2. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17639

6 Samples

Download data: TXT

(Submitter supplied) Low phosphate concentrations are frequently a constraint for maize growth and development, and therefore, enormous quantities of phosphate fertilizer are expended in maize cultivation, which increases the cost of planting. Low phosphate stress not only increases root biomass but can also cause significant changes in root morphology. Low phosphate availability has been found to favor lateral root growth over primary root growth by dramatically reducing primary root length and increasing lateral root elongation and lateral root density in Arabdopsis. more...

Organism:

Zea mays

Type:

Expression profiling by array

Platform:

GPL6438

9 Samples

Download data: GPR

(Submitter supplied) We sequenced the poly(A)+ and poly(A)- samples of the roots and shoots from 10-day-old WT seedlings grown under P+ and P- condition. The WT plant refers to Columbia ecotype Arabidopsis seedlings. Each condition has two replicates. After total RNA extraction, ribosomal RNAs were removed using RiboMinus™ Plant Kit repeated two times. The poly(A)+ and poly(A)- constituent were separated with oligo(dT) magnetic beads (Oligotex mRNA Mini Kit, QIAGEN). more...

Organism:

Arabidopsis thaliana

Type:

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

Platforms:

GPL13222 GPL17639

16 Samples

Download data: XLSX

(Submitter supplied) We examined the transcriptional data in rice leaves of TOP6A3 overexpressed line (TOP6A3-OE1) with WT (K3) plants under normal growth.

Organism:

Oryza sativa

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19290

4 Samples

Download data: XLSX

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

Type:

Genome variation profiling by array

Platform:

GPL198

20 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

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(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:

GPL5740 GPL5739

44 Samples

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(Submitter supplied) Oligoarray analysis was used to identify genes differentially expressed in 2 mm sections of the basal stem region of wild type T89, PtAIL1 over-expressing or PtAIL1 RNAi lines of P. tremula x Populus tremuloides 24h and 72h after adventitious rooting induction.

Organism:

Populus trichocarpa; Populus tremula x Populus tremuloides

Type:

Expression profiling by array

Platform:

GPL13485

27 Samples

Download data: PAIR

(Submitter supplied) Stem cuttings of P. trichocarpa (clone 101-74) were rooted in liquid medium without growth regulators (basal medium). The first emerging roots were observed on cuttings 6 days after the start of culture. The highest average root number per cutting (10 ± 2 roots/cutting) was obtained after 14 days. The first macroscopic evidence of root initiation was the appearance of root primordia, as lateral bulges observed at the stem surface 3 to 4 days after transfer to basal medium. more...

Organism:

Populus trichocarpa

Type:

Expression profiling by array

Platform:

GPL2699

9 Samples

Download data: PAIR

(Submitter supplied) [Oryza sativa Genome Oligo Set Version 1.0 was designed by Beijing Genomics Institute (BGI) and contain 60,727 70mer oligos representing both indica and japonica genomes. All oligos were designed from cDNAs, expreseed sequence tag (EST) sequences, predicted genes of BGI rice genome build and other public resources. Mapping to TIGR rice genome pseudommolecues release 2 is based on the BLAST results, if a oligo has greater than 97% identity to a gene sequence from TIGR pseudomolecules, the oligo represents that gene. more...

Organism:

Oryza sativa Indica Group; Oryza sativa

Type:

Expression profiling by array

Platforms:

GPL1774 GPL1773

30 Samples

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