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Gene expression profiles of various tissues under different physiological conditions

ABSTRACT: 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

ORGANISM(S): Oryza sativa Oryza sativa Japonica Group

PROVIDER: GSE7530 | GEO | 2008/04/01

SECONDARY ACCESSION(S): PRJNA99401

REPOSITORIES: GEO

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Gene expression profiles of various tissues under different physiological conditions

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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