GEO DataSets

(Submitter supplied) Long oligonucleotide microarrays were used for the study of expression profile changes during seedling photomorphogenesis in rice and in Arabidopsis. Different light quality treatments were applied to seedlings. To dissect organ-specific light effects, we further profiled shoot and root organs in both species. Keywords = rice Keywords = Arabidopsis Keywords = photomorphogenesis Keywords: ordered

Organism:

Oryza sativa; Arabidopsis thaliana

Type:

Expression profiling by array

Platforms:

GPL1077 GPL1829

36 Samples

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(Submitter supplied) An expression profiling assay comparing dark-grown soybean seedlings with seedlings treated with 1 h far-red light using different organs including cotyledons, hook, and hypocotyl with the soybean cDNA 18kA and 18kB microarrays.

Organism:

Glycine max

Type:

Expression profiling by array

Platforms:

GPL13822 GPL13823

24 Samples

Download data: GPR

(Submitter supplied) Plant diurnal oscillation is a 24-hour period based variation. The correlation between diurnal genes and biological pathways was widely revealed by microarray analysis in different species. Rice (Oryza sativa) is the major food staple for about half of the world's population. The rice flag leaf is essential in providing photosynthates to the grain filling. However, there is still no comprehensive view about the diurnal transcriptome for rice leaves. more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

40 Samples

Download data: CEL

(Submitter supplied) Transcriptional programs are important for the development of complex eukaryotic organisms. Suites of genes expressed with temporal and spatial controls by regulatory networks in response to environmental cues are the cornerstone for achieving the specification of morphology and physiology of the tissue or organ systems. Thus, an important issue of developmental biology is to define the subsets of expressed genes and their expression patterns that are related to the organ or tissue system. more...

Organism:

Oryza sativa; Oryza sativa Indica Group

Type:

Expression profiling by array

Platform:

GPL2025

190 Samples

Download data: CEL

(Submitter supplied) In angiosperms, stigma provides initial nutrients and guidance cues for pollen grain germination and tube growth. However, little is known about genes that regulate these processes in rice. Here we generate rice stigma-specific gene expression profiles through comparing genome-wide expression patterns of hand dissected unpollinated stigma at anthesis with seven tissues including seedling shoot, seedling root, mature anther, ovary at anthesis, seeds of five days after pollination, 10-day-old embryo, 10-day-old endosperm as well as suspension cultured cells by using 57K Affymetrix rice whole genome array. more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

13 Samples

Download data: CEL

(Submitter supplied) Pollen development from the microspore involves a series of coordinated cellular events, and the resultant mature pollen is specialized in function that it can quickly germinate and produces a polar-growth pollen tube derived from the vegetative cell to deliver two sperms for fertilization. Understanding the molecular program underlying pollen development and germination still remains a major challenge for plant biology. more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

24 Samples

Download data: CEL

(Submitter supplied) As a species mostly planted in tropical and subtropical regions, rice is sensitive to chilling temperature, especially at reproductive stage. However, the effect of low temperature on seed development has not been well characterized. The transcriptome of two rice cultivars Zhonghua11 and Hanfeng were analyzed to characterize the gene regulatory networks of rice seed during low temperature treatment.

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

16 Samples

Download data: CEL

(Submitter supplied) Light initiates the seedling deetiolation transition by promoting major changes in gene expression mainly regulated by phytochrome (phy) photoreceptors. During the initial dark-to-light transition, phy photoactivation induces rapid changes in gene expression that eventually lead to the photomorphogenic development. Recent reports indicate that this process is achieved by phy-induced degradation of Phy-Interacting bHLH transcription Factors (PIFs) PIF1, PIF3 PIF4 and PIF5, which are partly redundant constitutive repressors of photomorphogenesis that accumulate in darkness. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

30 Samples

Download data: CEL, CHP

(Submitter supplied) We generated genome-wide high-resolution maps of H4K16ac and H3K23ac in Arabidopsis thaliana and Oryza sativa.

Organism:

Oryza sativa; Arabidopsis thaliana

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13222 GPL13160

5 Samples

Download data: BW

(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) 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) Rice is highly sensitive to drought, and the effect of drought may vary with the different genotypes and development stages. Genome-wide gene expression profiling was used as the initial point to dissect molecular genetic mechanism of this complex trait and provide valuable information for the improvement of drought tolerance in rice. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice exposed to drought stress. more...

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

36 Samples

Download data: CEL

(Submitter supplied) Etiolated seedling response to one hour of continuous red light. Four-day-old dark-grown wild-type RLD and phyA101, phyB1 and phyAphyB mutant seedlings were transferred to Rc (680 nm, 8 mol m-2 s-1) for 1 h or retained in darkness as controls. Three different biological replicates of each treatment were grown separately and extracted, processed, and analyzed independently.RNA was extracted and subjected to expression analysis by using the Affymetrix ATH1 microarray containing approximately 22,000 Arabidopsis genes .

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

24 Samples

Download data

(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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(Submitter supplied) Rice transgenic plants of the bZIP encoding gene, OsbZIP48, in the Pusa Basmati 1 (PB1) variety have been found to display differences in the total height. In order to elucidate changes at the transcriptome level, microarray of the 10-day-old seedlings of over-expresseion (OE) and knock-down (KD) lines along with vector control (VC) were carried out.

Organism:

Oryza sativa Indica Group; Oryza sativa

Type:

Expression profiling by array

Platform:

GPL2025

10 Samples

Download data: CEL

(Submitter supplied) We analyzed the transcriptional activity of rice chromosom 4 using a tiling path microarray based on PCR-generated genomic DNA fragments. Five organ samples from various developmental stages and cultured cells were examined. Keywords: ordered

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL1722

15 Samples

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(Submitter supplied) The array represents a minimal tilling-path covering rice chromosome 4. This tilling-path was assembled using 15,141 BAC subclone fragments. All subclone fragments were PCR amplified using universal primers and plasmids containing the genomic DNA fragment as the template. DNA gel electrophoresis was performed for all fragments and poor amplifications were not included here. This tiling array covers 33.8 Mb or 96% of rice Nipponbare chromosome 4. more...

Organism:

Oryza sativa

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(Submitter supplied) The proper accumulation of BBX22 mediated by COP1 is crucial for plants to maintain better growth fitness when growing in the dark environment as well as responding to seasonal changes in day-length. The constitutive-photomorphogenic development of the cop1 mutant is enhanced in cop1BBX22-GFPox plants, which show a short hypocotyl, high anthocyanin accumulation and expression of light-responsive genes. more...

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

9 Samples

Download data: CEL

(Submitter supplied) Three rice major tissues, namely flag leaf, shoot and panicle, were involved in this study. Each tissue had two kinds stress treatment, drought and high salinity, in 3 different time courses. For drought treated samples, an additional water recovery was applied. Each experiment had three replicates. Keywords: Comparison of gene expression in three tissues with stress treatment and without treatment

Organism:

Oryza sativa

Type:

Expression profiling by array

Platform:

GPL1829

21 Samples

Download data: GPR