Differentially expressed genes from different developmantal stages in rice
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa Oryza sativa Japonica Group
PROVIDER: GSE7531 | GEO | 2008/04/01
SECONDARY ACCESSION(S): PRJNA99403
REPOSITORIES: GEO
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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
2008-04-01 | GSE7532 | 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)
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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
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