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| Status |
Public on Apr 24, 2008 |
| Title |
Microarray analysis of rice plants fumigated with ozone |
| Platform organism |
Oryza sativa Japonica Group |
| Sample organism |
Oryza sativa |
| Experiment type |
Expression profiling by array
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| Summary |
In this study, integrated transcriptomics, proteomics and metabolomics approaches were applied to investigate the molecular responses of O3 in the leaves of two-weeks old rice (cv. Nipponbare) seedlings exposed to 0.2 ppm O3 for a period of 24 h. Based on the morphological alteration of O3-exposed rice leaves, transcript profiling of rice genes was performed in leaves exposed for 1, 12 and 24 h using rice DNA microarray chip, proteomics and metabolomics. This systematic survey showed that O3 triggers a chain reaction of altered gene, protein and metabolite expressions involved in multiple cellular processes in rice.
Also investigated were the molecular responses in the leaves of two-weeks old rice (cv. Nipponbare) seedlings under continuous light and pure air (as a positive control for ozone exposure experiments) for a period of 24 h. Transcript profiling of rice genes was performed in leaves exposed for 1, 12 and 24 h using rice DNA microarray chip, proteomics and metabolomics. This systematic survey showed that continuous light and growth for 24 h also triggers a chain reaction of altered gene expressions involved in multiple cellular processes in rice, but different from those against ozone, in general.
Keywords: Ozone fumigation response
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| Overall design |
Ozone-treated Samples: An in vivo 14-days-old rice seedling model system was used, where whole seedlings were used for exposure/fumigation to the ozone (0.2 ppm). Dye-swap or reverse labeling with Cy3 and Cy5 dyes procedure was applied followed by hybridization and wash processes, and the hybridized microarrays (G4138A) were scanned using a GenePix microarray scanner followed by the Gene Pix 4000 analysis application program for image analysis and data extraction processes. The GeneSpring Ver. 4 software was used for normalization.
Control Samples: An in vivo 14-days-old rice seedling model system was used, where whole seedlings were used for exposure to continuous light and pure air. Dye-swap or reverse labeling with Cy3 and Cy5 dyes procedure was applied followed by hybridization and wash processes, and the hybridized microarrays (G4138A) were scanned using a Standard protocol of Agilent DNA Microarray Scanner and data processing was done by Feature Extraction software Version 8.1 from Agilent Technologies.
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| Contributor(s) |
Rakwal R |
| Citation(s) |
18517257 |
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| Submission date |
Apr 13, 2008 |
| Last update date |
Dec 06, 2012 |
| Contact name |
Randeep Rakwal |
| E-mail(s) |
rakwal-68@aist.go.jp
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| Fax |
+81 29 861 6066
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| Organization name |
AIST
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| Lab |
MST, HTRC lab
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| Street address |
AIST WEST, Onagawa 16-1
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| City |
Tsukuba |
| State/province |
Ibaraki |
| ZIP/Postal code |
305-8569 |
| Country |
Japan |
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| Platforms (1) |
| GPL892 |
Agilent-012106 Rice Oligo Microarray G4138A (Feature Number version) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA106843 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE11157_RAW.tar |
43.8 Mb |
(http)(custom) |
TAR (of GPR, TXT) |
| Processed data included within Sample table |
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