Oryza sativa Japonica Group
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA185783 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The plant volatile linalool plays important roles in the regulation of defense responses in rice. To clarify the response to linalool in rice at gene expression level, we performed a microarray analysis using the Agilent Rice Oligo Microarray (44k, custom-made; Agilent Technologies, Redwood City, CA, USA). As a result, many defense-related genes including pathogenesis-related (PR) genes were upregulated in the linalool synthase-overexpressing transgenic rice.
2013-04-01 | GSE43383 | GEO
Project description:Phosphate starvation/sufficient rice seedling, root or shoot Pi-starvation or Pi-sufficient stresses responsible rice genes, including previously unannotated genes were identified by Illumina mRNA-seq technology. 53 million reads from Pi-starvation or Pi-sufficient root or shoot tissues were uniquely mapped to the rice genome, and these included 40574 RAP3 transcripts in root and 39748 RAP3 transcripts in shoot. We compared our mRNA-seq expression data with that from Rice 44K oligomicroarray, and about 95.5% (root) and 95.4% (shoot) transcripts supported by the array were confirmed expression both by the array and by mRNA-seq, Moreover, 11888 (root) and 11098 (shoot) RAP genes which were not supported by array, were evidenced expression with mRNA-seq. Furthermore, we discovered 8590 (root) and 8193 (shoot) previously unannotated transcripts upon Pi-starvation and/or Pi-sufficient.
2012-01-06 | E-MTAB-4302 | biostudies-arrayexpress
Project description:OsMYC2-responsive genes in OsMYC2-overexpressing transgenic rice
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Project description:Global gene expression in Abp57-overexpressing transgenic rice
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Project description:The plant volatile linalool plays important roles in the regulation of defense responses in rice. To clarify the response to linalool in rice at gene expression level, we performed a microarray analysis using the Agilent Rice Oligo Microarray (44k, custom-made; Agilent Technologies, Redwood City, CA, USA). As a result, many defense-related genes including pathogenesis-related (PR) genes were upregulated in the linalool synthase-overexpressing transgenic rice. An Agilent Rice Oligo Microarray (44k, custom-made; Agilent Technologies, Redwood City, CA, USA) was used for the microarray analysis. Total RNA was extracted from leaf blades of four-leaf stage rice plants. Line 13 was used as the linalool synthase-overexpressing transgenic rice plant. For each biological replicate, material from at least three rice plants was pooled to provide a single sample for RNA extraction. We performed 3 biological replicates for each treatment. All microarray procedures and data analyses were performed according to the manufacturerM-bM-^@M-^Ys instructions. RNA integrity was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Redwood City, CA, USA). Total RNA (100 ng) was labeled with Cy-3 using an Agilent Low Input Quick Amp Labeling Kit, One-Color (Agilent Technologies). Fluorescently labeled targets were hybridized to Agilent Rice Oligo Microarrays for 17 h at 65M-BM-0C. After hybridization, following wash processes were performed according to the manufacturerM-bM-^@M-^Ys instructions, and hybridized microarrays were scanned using an Agilent Microarray Scanner (G2565CA; Agilent Technologies). Feature extraction software (Agilent Feature Extraction; Agilent Technologies) was used to delineate and measure the signal intensity of each spot in the array, and to normalize intensities. The background was measured around each spot as local background, calculated by the Feature Extraction software. Statistical data extraction processes were performed according to the manufacturerM-bM-^@M-^Ys instructions.
2013-04-01 | E-GEOD-43383 | biostudies-arrayexpress
Project description:Expression data from OsRP1L1-overexpressing plant leaf in japonica rice (cv. Ishikari-shiroge (I-S))
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Project description:Transcriptional profiling of MIT knockdown plants. MIT is a mitochondrial Fe transporter essential for rice growth and development. The goal was to determine the effects of MIT on global rice gene expression.
2011-04-07 | GSE28428 | GEO
Project description:Expression data from leaf of plant overexpressing OsXa5 in japonica rice (cv. Ishikari-shiroge (I-S))
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Project description:In this study, we examined the transcriptome dynamics within the matured fully expanded rice leaf and used strand-specific RNA sequencing to generate a comprehensive transcriptome dataset for the mature rice leaf. The rice Nipponbare (Oryza sativa l. japonica) seedlings were grown in the greenhouse. About 20 days after planting, the fully opened 4th leaves was cut it into seven 3-cm segments, from bottom to tip and labeled as sections 1 to 7, respectively. The tissues were immediately frozen in liquid nitrogen for total RNA extraction. Two biological replicates were collected for each section. Note: All samples in SRA were assigned the same sample accession (SRS685294). This is incorrect as there are different samples, hence âSource Nameâ was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.
2015-08-16 | E-MTAB-4372 | biostudies-arrayexpress
Project description:Methionine sulfoxide reductases catalyze the reduction of MetSO back to the correct Met residue. Previously, the gene of Capsicum annuum methionine sulfoxide reductase B2 was isolated and CaMSRB2-overexpressing tomato shows enhanced growth, which may trigger increased resistance to the pathogens. To assess the role of this enzyme in rice, we generated transgenic lines under the control of the rice Rab21 (responsive to ABA protein 21) promoter with/without Bar marker gene. Several physiological tests such as MV and Fv/Fm, indicators of an oxidative stress-inducing agent and a potential maximal PSII quantum yield, respectively strongly suggested CaMSRB2 confers drought tolerance to rice. Using 3′-tiling microarray covering the whole rice genes, we carried out genome-wide expression analyses with CaMsrB2-transformed rice (Oryza sativa L. cv. ILMI). Rice was grown in port for six weeks and treated with drought by water withholding for two days.
2013-04-01 | GSE41204 | GEO