E-GEOD-47812
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ABSTRACT:
PROVIDER: E-GEOD-47812 | ExpressionAtlas | 2015-06-15
REPOSITORIES: ExpressionAtlas
Similar Datasets
Project description:Os02g31890 encodes a dehydration-responsive transcription factor (named ´ARID´) from rice (Oryza sativa, cv. Dongjin). Expression profiling was performed 90 min after the start of dehydration stress in roots of Oryza sativa wild-type plants (cv. Dongjin) and a knock-out (i.e. arid) mutant.
2013-11-30 | GSE42683 | GEO
Project description:Gene expression data for rice grain (Oryza sativa L.) aroma performed using bulk pools of aromatic and non-aromatic RILs derived from a cross between Pusa 1121 and Pusa 1342
| PRJNA207973 | ENA
Project description:Information about protein expression in rice grain across both pigmented and non-pigmented rice varieties is still relatively scarce. The data provided here represent proteomic data obtained from selected 6 Malaysian local rice varieties with varying pigmentations (black, red and white). The selected pigmented rice varieties such as black (BALI and Pulut hitam 9) and red rice (MRQ100 and MRM16) have shown high antioxidant activities and non-pigmented rice (MRQ76 and MR297) contain amino acid and micronutrient contents. This project aimed to obtain global protein expression profile as well as differential protein expression between the selected pigmented and non-pigmented rice varieties particularly proteins with their functions responsible for nutritional (i.e. antioxidant, folate and low glycaemic index) and quality (i.e. aromatic) traits. Integration of this proteomics dataset with other available in-house omics data could facilitate the identification of significant functional markers related to nutritional and quality traits. Total proteins were prepared from dehusked matured seeds harvested from three different rice plants of each variety (3 protein samples per variety). The proteins were trypsin digested before subjected to SWATH-MS proteomics analysis. Proteins were identified by matching tandem mass (MS/MS) spectra from both 1D and 2D IDA to Oryza sativa japonica and indica rice databases available at UniProt by using ProteinPilot software (v4.2) (AB Sciex). Quantification of proteins was carried out by determining protein peak areas extracted from SWATH analysis data sets using PeakView (v2.1) (AB Sciex) software. Differentially expressed protein between varieties were identified using T-test analysis with a set threshold for fold change ± 1.5 and p‐value < 0.05.
2020-04-27 | PXD018338 | Pride
Project description:Microarray data of contrasting genotypes were performed between control and stress conditions. Please cite the following work, if you are using the data Sujitha, D., Kumar, H.G.J., Thapliayal, G. et al. Transcription factors controlling the expression of oxidative stress associated genes in rice (Oryza sativa L.). Plant Biotechnol Rep (2023). https://doi.org/10.1007/s11816-023-00819-8
2023-02-13 | GSE181763 | GEO
Project description:Purpose: Transcriptional profiling of Oryza sativa japonica Nipponbare roots after one, three and seven days post inoculation with Azoarcus olearius BH72 (vs. non-inoculated controls) to understand the changes in transcriptomic response of rice roots to colonization by bacterial endophyte at initial stages of interaction; Additional set-up was included in which bacterial growth was boosted (through increasing 20-times carbon source - malic acid in the plant's hydroponic medium) to study rice roots transcriptome during enhanced colonization by the endophyte after three days post inoculation. Methods: Rice root mRNA profiles after one day, three days (including additional set-ups for boosted colonization), and seven days post inoculation with Azoarcus olearius BH72 and corresponding non-inoculated controls were generated by RNA sequencing, in triplicates, using Illumina NextSeq 500. Raw reads were then filtered, trimmed (PHRED > 33) and mapped onto IRGSP-1 version of Oryza sativa ssp. japonica cv. Nipponbare genome using CLC Genomics Workbench 8.5.1 (Qiagen, Germany). Expression of 17 selected genes was confirmed via RT-qPCR. Results: Using the RNA-Seq technology we obtained transcriptomic data from 24 sequencing libraries, with an average 46,181,160 clean reads per library, of which 87% or more were mapped onto the Oryza sativa ssp. japonica cv. Nipponbare IRGSP-1.0 genome (Fig. S3). We considered genes as differentially regulated (DEG) that exhibited at least 1.5-fold-change in expression level between Azo-colonized and non-colonized roots and FDR<0.05. Conclusions: Bacteria appeared to short-circuit the initial root defense responses for a compatible interaction during endophytic establishment, involving previously unknown putative rice candidate genes.
2021-09-01 | GSE174616 | GEO
Project description: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. In this study, we applied rice microarray to monitor the rhythmically expressed genes in rice seedling and flag leaves. We developed a new computational analysis approach and identified 6,266 (10.96%) diurnal probe sets in seedling leaves, 13,773 (24.08%) diurnal probe sets in flag leaves. About 65% of overall transcription factors were identified as flag leaf preferred. In seedling leaves, the peak of phase distribution was from 2:00am to 4:00am, whereas in flag leaves, the peak was from 8:00pm to 2:00am. The diurnal phase distribution analysis of gene ontology (GO) and cis-element enrichment indicated that, some important processes were waken by the light, such as photosynthesis and abiotic stimulus, while some genes related to the nuclear and ribosome involved processes were active mostly during the switch time of light to dark. The starch and sucrose metabolism pathway genes also showed diurnal phase. We conducted comparison analysis between Arabidopsis and rice leaf transcriptome throughout the diurnal cycle. In summary, our analysis approach is feasible for relatively unbiased identification of diurnal transcripts, efficiently detecting some special periodic patterns with non-sinusoidal periodic patterns. Compared to the rice flag leaves, the gene transcription levels of seedling leaves were relatively limited to the diurnal rhythm. Our comprehensive microarray analysis of seedling and flag leaves of rice provided an overview of the rice diurnal transcriptome and indicated some diurnal regulated biological processes and key functional pathways in rice. we generate rice diurnal gene expression profiles of seedling leaves and flag leaves using 57K Affymetrix rice whole genome array. keywords: rice (Oryza sativa L.), seedling leaves, flag leaves, diurnal, molecular functions, microarray
2011-03-24 | E-GEOD-28124 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) and small interfering RNAs (siRNAs) regulate gene expression in eukaryotes. Plant miRNAs modulate their targets mainly via messenger RNA (mRNA) cleavage. Small RNA targets have been extensively investigated in Arabidopsis using computational prediction, experimental validation, and degradome sequencing. However, small RNA targets are largely unknown in rice (Oryza sativa). Here, we report global identification of small RNA targets using high throughput degradome sequencing in the rice indica cultivar 93-11 (Oryza sativa L. ssp. indica). 177 transcripts targeted by total of 87 unique miRNAs were identified. Of targets for the conserved miRNAs between Arabidopsis and rice, transcription factors comprise around 70% (58 in 82), indicating that these miRNAs act as masters of gene regulatory nodes in rice. In contrast, non-conserved miRNAs targeted diverse genes which provide more complex regulatory networks. In addition, 5 AUXIN RESPONSE FACTORS (ARF) cleaved by the TAS3 derived ta-siRNAs were also detected. A total of 40 sRNA targets were further validated via RNA ligase-mediated 5M-bM-^@M-^Y rapid amplification of cDNA ends (RLM 5M-bM-^@M-^Y-RACE). Our degradome results present a detailed sRNA-target interaction atlas, which provides a guide for the study of the roles of sRNAs and their targets in rice. The degradome sequence of Young inflorescences from Oryza sativa L. ssp. indica (93-11) was sequenced
2010-01-01 | E-GEOD-19050 | biostudies-arrayexpress
Project description:Os02g31890 encodes a dehydration-responsive transcription factor (named ´ARID´) from rice (Oryza sativa, cv. Dongjin). Expression profiling was performed 90 min after the start of dehydration stress in roots of Oryza sativa wild-type plants (cv. Dongjin) and a knock-out (i.e. arid) mutant. Wild-type rice plants and a line carrying a T-DNA insertion in the third exon of the transcription factor gene (arid mutant) were subjected to dehydration stress for 90 min. Well-watered wild-type and T-DNA insertion plants were used as controls. Total RNA was extracted from roots and subjected to expression profiling using rice Affymetrix microarrays.
2013-11-30 | E-GEOD-42683 | biostudies-arrayexpress
Project description:In rice (Oryza sativa L.), the number of panicles, spikelets per panicle and grain weight are important components of grain yield. These characteristics are controlled by quantitative trait loci (QTLs) and are derived from variation inherent in crops.The identification of different yield related QTLs facilitates an understanding of the mechanisms involved in cereal crop yield, and may have utility in improving grain yield in cereal crops. an understanding of the mechanisms involved in cereal crop yield, and may have utility in improving grain yield in cereal crops. In the present study, We cloned and characterized a large-panicle QTL, and confirmed that the newly identified gene OsEBS (enhancing biomass and spikelet number) increased plant height, leaf size and spikelet number per panicle, leading to an average of 37.62% increase in total grain yield per plant. trait loci (QTLs) and are derived from variation inherent in crops. OsEBS-transgenic rice B10201 and B10301 and control Guichao2
2013-05-04 | E-GEOD-46616 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE16140: Transcriptome analysis of rice (Oryza sativa cv.TW16) in relation to infection with rice tungro spherical virus (RTSV) GSE16141: Transcriptome analysis of rice (Oryza sativa cv. Taichung Native 1) in relation to infection with RTSV Refer to individual Series
2010-05-18 | E-GEOD-16142 | biostudies-arrayexpress