Expression data from rice embryo,endosperm,root,leaf and seedling
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE11966 | GEO | 2009/02/02
SECONDARY ACCESSION(S): PRJNA105837
REPOSITORIES: GEO
Similar Datasets
Project description:Expression profiles of protein coding genes were characterized using Affymetrix rice genome array to compare with expression profiles of miRNAs. Experiment Overall Design: Five tissues (embryo, endosperm, leaf and root of 7-day-old seedlings, 10-day-old seedling) were analyzed, each has two biological repeats.
2009-02-08 | E-GEOD-11966 | biostudies-arrayexpress
Project description:Immatured rice seeds 7-8 days after pollination were used for expression analysis and matured rice leaf was used as control. Targets from biological replicates of both were generated and the expression were determined using Affymetrix Rice Genome arrays.
2011-12-06 | GSE26840 | GEO
Project description:Upper and lower parts (flanks) of rice (Oryza sativa sp. japonica) shoot bases at 0.5 h and 6 h after gravistimulation was used for expression analysis in control and gravistimulated samples.Targets from biological replicates of both control and gravistimulated samples were generated and expression profiles were determined Affymetrix Rice Genome arrays.
2011-09-02 | GSE31834 | GEO
Project description:We report the application of methylacytosine immunoprecipetation combined with Illumina sequencing (MeDIP-seq) for high-throughput profiling of DNA methylation in rice embryo 3, 6, 9 DAP and endosperm 2, 3, 6, 9 DAP. A total number of 12-14 million of 2×49 bp paired-end reads was generated for each sample, and BOWTIE2 was used for read mapping. We generated genome-wide DNA methylation profiles of rice embryo and endosperm. This study provides a framework to systemically characterize the effect of DNA methylation in developing seeds and will help to illustrate the epigenetic regulation of rice seed development.
2015-09-01 | GSE57706 | GEO
Project description:Rice grains are rich in starch but are deficient in proteins containing essential amino acids such as lysine and threonine. Therefore, efforts have been made to improve the nutritional value of rice by overexpressing the genes involved in lysine biosynthesis and/or suppression of lysine catabolism that led to the increased protein content in rice grains. Despite the economic and nutritional benefits rice, the protein accumulation mechanisms are largely elusive. Therefore, to explore the comprehensive proteome profiles, three different parts of rice grains including embryo, endosperm, bran were harvested from weedy rice cultivars (cv. Dharial) and its EMS mutant (DM) having 9.3 and 14.8% of protein content in rice grains, respectively. Here, we utilized a label-free quantitative proteomic analysis and this approach led to the identification of total 5,821 proteins. Of these, 322, 723, and 550 proteins revealed significant differences in their abundance in rice embryo, endosperm, and bran, respectively. Functional classification of identified proteins revealed that enrichment of proteins associated with nitrogen compound biosynthesis and transport, intracellular transport, localization, protein/amino acid synthesis, and photosynthesis, among others were observed in endosperm and bran of high protein mutant rice cultivar. Taken together, the current study uncovers the proteome changes and highlight the various functions of metabolic pathways associated with protein accumulation in rice.
2023-09-21 | PXD036806 | Pride
Project description:Indica rice seedlings of IR64 variety were grown hydroponically for 7-days in a culture room with a daily photoperiodic cycle of 14h light and 10h dark. Seedlings were incubated in 0.1% dimethyl sulfoxide (control) or 50 micromolar solutions of indole-3-acetic acid (IAA treatment) and benzyl aminopurine (BAP treatment) for 1h and 3h. Equal amounts of 1h and 3h samoles were pooled for each treatment before RNA isolation. The 5 micrograms of each total RNA sample was processed for microarray analysis according to Affymetrix protocol. Keywords: Rice, seedling, IAA, BAP, hormone response
2009-06-08 | GSE5167 | GEO
Project description:BACKGROUND:Water deficiency is one of the most serious worldwide problems for agriculture. Recently, it has become more serious and outspread, which urgently requires the production of drought-tolerant plants. Microarray experiments using mRNA from air-dried leaves and roots of rice were performed in an attempt to study genes involved in acute dehydration response. RESULTS:Set of 10,537 rice genes was significantly up- or down-regulated in leaves or roots under the treatment. Gene Ontology analysis highlighted gene expression during acute dehydration response depending on organ types and the duration of stress. Rice responded by down-regulating many processes which are mainly involved in inhibiting growth and development. On the other hand, phytohormones (ABA, cytokinin, brassinosteroid) and protective molecules were induced to answer to multiple stresses. Leaves induced more genes than roots but those genes were scattered in various processes, most significantly were productions of osmoprotectants and precursors for important pathways in roots. Roots up-regulated fewer genes and focused on inducing antioxidants and enhancing photosynthesis. Myb, zf-C3HC4, and NAM were most strongly affected transcription factors with the dominance of leaf over root. CONCLUSIONS:Leaf and root tissues shared some common gene expression during stress, with the purpose of enhancing protective systems. However, these two tissues appeared to act differently in response to the different level of dehydration they experience. Besides, they can affect each other via the signaling and transportation system.
| S-EPMC3878681 | biostudies-literature
Project description:Immatured rice seeds 7-8 days after pollination were used for expression analysis and matured rice leaf was used as control. Targets from biological replicates of both were generated and the expression were determined using Affymetrix Rice Genome arrays. Rice immatured seed after 7-8 days pollination were selected of early development for RNA extraction and hybridization on Affymetrix microarrays. Matured rice leaf was set as control. Each with 3 replicates were analyzed.
2011-12-06 | E-GEOD-26840 | biostudies-arrayexpress
Project description:During the pathogenesis of virus disease, lots of changes occur in plant hosts including the altered gene expression profiles. Rice stripe virus (RSV) is the type member of Tenuivirus, transmitted by Laodelphax striatellus in a circulative propagative man To investigate the molecular differences in two japonica rice genotypes WuYun3 and KT95-418 in response to RSV infection, Affymetrix rice genome array were used to analyze and compare their transcriptional profiles. Keywords: disease state analysis
2009-04-02 | GSE11025 | GEO
Project description:The receptor-like kinases (RLKs) plays critical roles in signal transduction through sensing the extracellular signals and activating the downstream signal transduction by phosphorylating their targets. Up to now, there are only a few RLKs have been functionally identified. In this study, we systemically analyzed the expression pattern of rice genes, especially the RLK coding genes during embryo and endosperm development.
2012-02-01 | GSE27856 | GEO