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Status |
Public on Jul 30, 2010 |
Title |
OsMKK4WT DEX 12h 3 |
Sample type |
RNA |
|
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Channel 1 |
Source name |
OsMKK4WT DEX 12h 3
|
Organism |
Oryza sativa |
Characteristics |
protocol: suspension cell culture treatment: Dex time: 12 hr cultivar: Nipponbare cell line: callus of the DEX inducible OsMKK4WT line
|
Treatment protocol |
Suspension cells were treated with Dexamethasone (DEX) (10 micro molar) and harvested at indicated times.
|
Growth protocol |
Calli of O. sativa L. cv. Nipponbare were generated from seed scutellum and suspension-cultured at 25˚C in N6D liquid medium and subcultured in fresh medium every 7 days. For DEX treatment, suspension cell cultures were subcultured for 3 days in a fresh medium.
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was prepared using the Isogen (Nippongene) and RNeasy Plant Mini kit (Qiagen) following the manufacturer's recommendations. The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
Label |
Cy3
|
Label protocol |
Labeled cRNA was prepared from 400 ng RNA using the Low RNA Input Linear Amplification/Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
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Channel 2 |
Source name |
Vector control DEX 12h 3
|
Organism |
Oryza sativa |
Characteristics |
protocol: suspension cell culture treatment: Dex time: 12 hr cultivar: Nipponbare cell line: callus of the vector control line
|
Treatment protocol |
Suspension cells were treated with Dexamethasone (DEX) (10 micro molar) and harvested at indicated times.
|
Growth protocol |
Calli of O. sativa L. cv. Nipponbare were generated from seed scutellum and suspension-cultured at 25˚C in N6D liquid medium and subcultured in fresh medium every 7 days. For DEX treatment, suspension cell cultures were subcultured for 3 days in a fresh medium.
|
Extracted molecule |
total RNA |
Extraction protocol |
RNA was prepared using the Isogen (Nippongene) and RNeasy Plant Mini kit (Qiagen) following the manufacturer's recommendations. The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
Label |
Cy5
|
Label protocol |
Labeled cRNA was prepared from 400 ng RNA using the Low RNA Input Linear Amplification/Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
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Hybridization protocol |
Cy3-labelled cRNA and Cy5-labelled cRNA (825ng each) were mixed, fragmented and hybridized with the rice 4x44K microarray RAP-DB (G2519F#15241) for 17 hours at 65°C using the Agilent Gene Expression Hybridization kit.
|
Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 4x44k array slides.
|
Description |
400 ng RNAs were labeled and 825ng of Cy3- and Cy5-labeled cRNAs were used.
|
Data processing |
The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities.
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Submission date |
Apr 09, 2009 |
Last update date |
Mar 08, 2011 |
Contact name |
Hirohiko Hirochika |
Organization name |
National Institute of Agrobiological Sciences
|
Department |
Division of Genome and Biodiversity Research
|
Street address |
2-1-2 Kannondai
|
City |
Tsukuba |
State/province |
Ibaraki |
ZIP/Postal code |
305-8602 |
Country |
Japan |
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Platform ID |
GPL6864 |
Series (1) |
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