|
| Status |
Public on Apr 02, 2009 |
| Title |
D-glucose_rep1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Rice shoots, treated with 0.5 mM D-glucose.
|
| Organism |
Oryza sativa |
| Characteristics |
cultivar: a Japonica cultivar "Nipponbare"
leaf-stage: 2-leaf-stage
tissue: shoot
|
| Treatment protocol |
Rice plants are treated with 0.5 mM D-allose for 2 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Kit: RNeasy plant mini kit
Manufacturer: Qiagen
|
| Label |
Cy5
|
| Label protocol |
Kit: Low input RNA linear amplification kit
Manufacturer: Agilent Technologies
|
| |
|
| Channel 2 |
| Source name |
Rice shoots, mock-treated.
|
| Organism |
Oryza sativa |
| Characteristics |
cultivar: a Japonica cultivar "Nipponbare"
leaf-stage: 2-leaf-stage
tissue: shoot
|
| Treatment protocol |
Rice plants are mock-treated for 2 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Kit: RNeasy plant mini kit
Manufacturer: Qiagen
|
| Label |
Cy3
|
| Label protocol |
Kit: Low input RNA linear amplification kit
Manufacturer: Agilent Technologies
|
| |
|
| |
| Hybridization protocol |
Kit: in situ hybridization kit plus
Manufacturer: Agilent Technologies
|
| Scan protocol |
Scan protocol Scanner: Agilent DNA microarray scanner
Manufacturer: Agilent Technologies
|
| Description |
An Agilent Rice Oligo Microarray (44k, custom-made; Agilent Technologies, Redwood City, CA, USA) was used for the microarray analysis. By using RNeasy plant mini kit (Qiagen, Hilden, Germany), total RNA was extracted from shoots of two-leaf stage rice plants that had been treated with 0.5 mM D-allose, 0.5 mM D-glucose, or no sugar for 2 days. For each biological replicate, material from at least five rice plants was pooled to provide a single sample for RNA extraction. We performed 3 biological replicates for each treatment. All microarray procedures and data analyses were performed according to the manufacturer’s instructions. RNA integrity was checked using an Agilent 2100 Bioanalyzer (Agilent Technologies, Redwood City, CA, USA). Total RNA (400 ng) was labeled with Cy-3 or Cy-5 using an Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies). Fluorescently labeled targets were hybridized to Agilent Rice Oligo Microarrays for 17 h at 65°C. After hybridization, following wash processes were performed according to the manufacturer’s instructions, and hybridized microarrays were scanned using an Agilent Microarray Scanner (G2505B and software G2565BA; Agilent Technologies).
|
| Data processing |
Feature extraction software (version 9.1; Agilent Technologies) was used to delineate and measure the signal intensity of each spot in the array, and to normalize intensities. The background was measured around each spot as local background, calculated by the Feature Extraction software. Statistical data extraction processes were performed according to the manufacturer’s instructions.
|
| |
|
| Submission date |
Mar 30, 2009 |
| Last update date |
May 15, 2009 |
| Contact name |
Kazuya Akimitsu |
| E-mail(s) |
kazuya@ag.kagawa-u.ac.jp
|
| Phone |
+81-87-891-3131
|
| Fax |
+81-87-891-3021
|
| Organization name |
Kagawa University
|
| Department |
Faculty of Agriculture
|
| Lab |
Plant Pathology
|
| Street address |
2393, Ikenobe
|
| City |
Miki |
| State/province |
Kagawa |
| ZIP/Postal code |
761-0795 |
| Country |
Japan |
| |
|
| Platform ID |
GPL6864 |
| Series (1) |
| GSE15479 |
Rice plants treated with D-allose |
|
