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| Status |
Public on Apr 01, 2008 |
| Title |
Gene expression profiles of various tissues under different physiological conditions |
| Platform organisms |
Oryza sativa; Oryza sativa Japonica Group |
| Sample organism |
Oryza sativa Japonica Group |
| Experiment type |
Expression profiling by array
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| Summary |
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
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| Overall design |
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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| Contributor(s) |
Ooka H, Tasaki K, Yamada-Akiyama H, Lee J, Kikuchi S |
| Citation missing |
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| Submission date |
Apr 16, 2007 |
| Last update date |
Dec 06, 2012 |
| Contact name |
Kouji Satoh |
| Organization name |
NARO/HARC
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| Street address |
Hitsujigaoka 1
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| City |
Sapporo |
| State/province |
Hokkaido |
| ZIP/Postal code |
062-8555 |
| Country |
Japan |
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| Platforms (2) |
| GPL477 |
RICE oligo microarray ver1 |
| GPL892 |
Agilent-012106 Rice Oligo Microarray G4138A (Feature Number version) |
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| Samples (39)
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| Relations |
| BioProject |
PRJNA99401 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE7530_RAW.tar |
190.2 Mb |
(http)(custom) |
TAR (of TXT) |
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