Differentially expressed genes under different stress conditions in rice
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa Oryza sativa Japonica Group
PROVIDER: GSE7532 | GEO | 2008/04/01
SECONDARY ACCESSION(S): PRJNA99405
REPOSITORIES: GEO
Similar Datasets
Project description:Rice is one of important crop and, the genome has been already completely sequenced. Moreover we collected more than 30K rice FL-cDNA clones as transcriptome resources. However, the cDNA collection did not reveal the transcription activity and specificity of expression. So, we designed 60-mer oligo array based on the array system of Agilent Technologies (GPL477) as custom array. For validation of the array, we tested the reproducibility of labeling and hybridization. After this validation, 22K rice oligo array was supplied from Agilent Technologies (GPL892). 2: reproducibility of hybridization-1: We made a dye-swap experiment to validate dye-effect and data reproducibility between arrays. We hybridized shoot (as control) and other developmental stage tissues. This data also indicated the diversity of gene expression profile among developmental stages. Keywords: variety among tissues
2008-04-01 | GSE7531 | GEO
Project description:Rice is one of important crop and, the genome has been already completely sequenced. Moreover we collected more than 30K rice FL-cDNA clones as transcriptome resources. However, the cDNA collection did not reveal the transcription activity and specificity of expression. So, we designed 60-mer oligo array based on the array system of Agilent Technologies (GPL477) as custom array. For validation of the array, we tested the reproducibility of labeling and hybridization. After this validation, 22K rice oligo array was supplied from Agilent Technologies (GPL892). 1: reproducibility of labeling: mRNA of shoot sample was amplified and labeled more than 10 times with Cy3 and Cy5, and both Cy3- and Cy5-labeled cRNA was hybridized on a slide (self-hybridization), and validate the reproducibility of labeling. In addition, we also amplified and labeled mRNA of other samples with Cy3 and Cy5, and made a self-hybridization. The intensity data of these array was also indicated transcription activity of genes in these samples. Keywords: variety among tissues
2008-04-01 | GSE7530 | GEO
Project description:Rice is one of important crop and, the genome has been already completely sequenced. Moreover we collected more than 30K rice FL-cDNA clones as transcriptome resources. However, the cDNA collection did not reveal the transcription activity and specificity of expression. So, we designed 60-mer oligo array based on the array system of Agilent Technologies (GPL477) as custom array. For validation of the array, we tested the reproducibility of labeling and hybridization. After this validation, 22K rice oligo array was supplied from Agilent Technologies (GPL892). 2: reproducibility of hybridization-2: We made a dye-swap experiment to validate dye-effect and data reproducibility between arrays. We hybridized shoot (as control) and stress-treated shoot. This data also indicated the diversity of gene expression profile among stress response. In addition, array data of samples treated for 24 hours have been already published on NCBI-GEO (GSE2415) Keywords: variety among tissues organisms: Oryza sativa ssp. japonica (Nipponbare) tissue: shoot derived from more than 100 plants treatement1: cold stress (10 degreeC) time course1: 48, 72 hours tissue1: shoot treatment2: drought stress (25% polyethylene glycol 6000) time course2: 1, 9 hours tissue: shoot treatment3: flood and lay-down stress time course3: 1, 6, 24, 48 hours tissue3: shoot treatment4: flood stress time course4: 1, 24, 48, 72 hours tissue4: shoot treatment5: lay-down stress for 24 hours tissue5: shoot hybridization : two dye method hybridization: Dye-swap experiment replication: samples were not replicated. array: 2 array per 1 experiment (total 26 arrays)
2008-04-01 | E-GEOD-7532 | biostudies-arrayexpress
Project description:Rice is one of important crop and, the genome has been already completely sequenced. Moreover we collected more than 30K rice FL-cDNA clones as transcriptome resources. However, the cDNA collection did not reveal the transcription activity and specificity of expression. So, we designed 60-mer oligo array based on the array system of Agilent Technologies (GPL477) as custom array. For validation of the array, we tested the reproducibility of labeling and hybridization. After this validation, 22K rice oligo array was supplied from Agilent Technologies (GPL892). 1: reproducibility of labeling: mRNA of shoot sample was amplified and labeled more than 10 times with Cy3 and Cy5, and both Cy3- and Cy5-labeled cRNA was hybridized on a slide (self-hybridization), and validate the reproducibility of labeling. In addition, we also amplified and labeled mRNA of other samples with Cy3 and Cy5, and made a self-hybridization. The intensity data of these array was also indicated transcription activity of genes in these samples. Keywords: variety among tissues organisms: Oryza sativa ssp. japonica (Nipponbare) tissue: shoot, root, germinated seed, panicle, callus derived from more than 100 plants treatement1: cold stress (10 degreeC) time course1: 24, 48, 72 hours tissue1: shoot treatment2: drought stress (25% polyethylene glycol 6000) time course2: 1, 9, 24 hours tissue: shoot treatment3: flood and lay-down stress time course3: 1, 6, 24, 48 hours tissue3: shoot treatment4: flood stress time course4: 1, 24, 48, 72 hours tissue4: shoot treatment5: osmotic stress (260mM mannitol) for 24 hours tissue5: shoot treatment6: 150mM NaCl for 24 hours tissue6: shoot hybridization : two dye method hybridization: self-hybridization replication: Hybridization of shoot replicated 11 times, and germinated seed was twice. Other samples did not replicated. array: 1 array per 1 experiment (total 39 arrays)
2008-04-01 | E-GEOD-7530 | biostudies-arrayexpress
Project description:Rare sugars are monosaccharides that are rarely present in nature. One of the rare sugars, D-psicose, had a negative effect on shoot growth of rice. This negative effect to rice growth was observed previously with D-allose, but not observed in other tested rare sugars. To clarify the response to D-psicose in rice at the 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, treatment of D-psicose caused high induction of many defense-related genes including pathogenesis-related (PR) genes in rice.
2010-01-31 | GSE19595 | GEO
Project description:Rare sugars are monosaccharides that are rarely present in nature. One of the rare sugars, D-allose had a negative effect on shoot growth of rice. This negative effect to rice growth was not observed in other tested rare sugars. To clarify the response to the D-allose 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, treatment of D-allose caused high induction of many defense-related genes including pathogenesis-related (PR) genes in rice.
2009-04-02 | GSE15479 | GEO
Project description:Rare sugars are monosaccharides that are rarely present in nature. One of the rare sugars, D-psicose, had a negative effect on shoot growth of rice. This negative effect to rice growth was observed previously with D-allose, but not observed in other tested rare sugars. To clarify the response to D-psicose in rice at the 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, treatment of D-psicose caused high induction of many defense-related genes including pathogenesis-related (PR) genes in rice. An Agilent Rice Oligo Microarray (44k, custom-made; Agilent Technologies, Redwood City, CA, USA) was used for the microarray analysis. By using the RNeasy plant mini kit (Qiagen, Hilden, Germany), total RNA was extracted from shoots of two-leaf stage rice plants that had been treated with 0.5 mM D-psicose or no sugar for 2 days. For each biological replicate, material from at least five 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 manufacturer’s instructions. RNA integrity was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Redwood City, CA, USA). Total RNA (400 ng) was labeled with Cy3 or Cy5 using an Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). Fluorescently labeled targets were hybridized to Agilent Rice Oligo Microarrays for 17 h at 65°C. After hybridization, wash processes were performed according to the manufacturer’s instructions, and hybridized microarrays were scanned using an Agilent Microarray Scanner (G2505B and software G2565BA; Agilent Technologies). Feature extraction software (version 9.1; 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 manufacturer’s instructions.
2010-01-30 | E-GEOD-19595 | biostudies-arrayexpress
Project description:Rare sugars are monosaccharides that are rarely present in nature. One of the rare sugars, D-allose had a negative effect on shoot growth of rice. This negative effect to rice growth was not observed in other tested rare sugars. To clarify the response to the D-allose 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, treatment of D-allose caused high induction of many defense-related genes including pathogenesis-related (PR) genes in rice. An Agilent Rice Oligo Microarray (44k, custom-made; Agilent Technologies, Redwood City, CA, USA) was used for the microarray analysis. By using RNeasy plant mini kit (Qiagen, Hilden, Germany), total RNA was extracted from shoots of two-leaf stage rice plants that had been treated with 0.5 mM D-allose, 0.5 mM D-glucose, or no sugar for 2 days. For each biological replicate, material from at least five 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 manufacturer’s instructions. RNA integrity was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Redwood City, CA, USA). Total RNA (400 ng) was labeled with Cy-3 or Cy-5 using an Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). Fluorescently labeled targets were hybridized to Agilent Rice Oligo Microarrays for 17 h at 65°C. After hybridization, following wash processes were performed according to the manufacturer’s instructions, and hybridized microarrays were scanned using an Agilent Microarray Scanner (G2505B and software G2565BA; Agilent Technologies). Feature extraction software (version 9.1; 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 manufacturer’s instructions.
2009-04-02 | E-GEOD-15479 | biostudies-arrayexpress
Project description:Expression of the sense-antisense transcripts (SATs). Methods: The sequences of 60mer DNA specific to the sense and antisense genes were chosen by K.K. DNAFORM (Japan), and Agilent Technologies manufactured custom oligo DNA microarray chips by using this information. RNA was labeled and hybridized using Fluorescent Direct Label Kits (oligo dT-primed labeling) (Agilent Technologies), according to the manufacturer's protocols. For labeling with random nanomers, we used the CyScribe First-Strand cDNA Labeling Kit (Amersham). The RNA samples used for microarray experiments were from mouse ES cells, SL10 cells (fibroblast cell line), brain, heart, and testis. The total RNA of brain, heart, and testis for array experiments was purchased from Ambion. The total RNA of ES and fibroblast cells was isolated using Trizol reagent (Invitrogen). The same total RNA samples were reciprocally labeled with Cy3 or Cy5, hybridized to the oligo DNA on the chip, and dye-normalized, and processed signals were obtained using Feature Extraction software (Agilent Technologies). Keywords: parallel sample
2005-03-31 | GSE2185 | GEO
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.
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