|
| Status |
Public on Mar 14, 2007 |
| Title |
RDV_1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Mock_inoculation1
|
| Organism |
Oryza sativa |
| Characteristics |
cultivar : Nipponbare
Age: 18 days
Tissue : shoot
|
| Treatment protocol |
Nine-day-old rice seedlings were exposed to approximately fifty virus-free insects (leafhoppers)
|
| Growth protocol |
Ten rice seeds (Oryza sativa L. cv. Nipponbare) were sown in a pot that has been filled with a commercial soil mixture (Bonsol; Sumitomo Chemical, Osaka, Japan). The pot was then submerged in water inside a container and was kept in a growth chamber at 25±3°C under natural sunlight for 9 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
kit : RNeasy maxi kit
Manufacture : Qiagen
|
| Label |
Cy3
|
| Label protocol |
kit : Low input RNA linear amplification kit
Manufacture : Agilent Technologies
|
| |
|
| Channel 2 |
| Source name |
RDV_infection1
|
| Organism |
Oryza sativa |
| Characteristics |
cultivar : Nipponbare
Age: 18 days
Tissue : shoot
|
| Treatment protocol |
Nine-day-old rice seedlings were exposed to approximately fifty viruliferous insects (leafhoppers)
|
| Growth protocol |
Ten rice seeds (Oryza sativa L. cv. Nipponbare) were sown in a pot that has been filled with a commercial soil mixture (Bonsol; Sumitomo Chemical, Osaka, Japan). The pot was then submerged in water inside a container and was kept in a growth chamber at 25±3°C under natural sunlight for 9 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
kit : RNeasy maxi kit
Manufacture : Qiagen
|
| Label |
Cy5
|
| Label protocol |
kit : Low input RNA linear amplification kit
Manufacture : Agilent Technologies
|
| |
|
| |
| Hybridization protocol |
Kit : in situ hybridization kit plus
Manufacture : Agilent Technologies
|
| Scan protocol |
Scanner : Agilent DNA microarray scanner
Manufacture: Agilent Technologies
|
| Description |
Keyword : Oryza sativa
Keyword : Rice Dwarf virus
|
| Data processing |
Feature Extraction ver 8.1.1.1 (Agilent Technologies)
|
| |
|
| Submission date |
Jul 11, 2006 |
| Last update date |
Mar 14, 2007 |
| Contact name |
Takumi SHIMIZU |
| E-mail(s) |
[email protected]
|
| Phone |
+81-29-838-8932
|
| Fax |
+81-29-838-8929
|
| Organization name |
National Agricultural Research Center
|
| Street address |
Kannondai 3-1-1
|
| City |
Tsukuba |
| ZIP/Postal code |
305-8666 |
| Country |
Japan |
| |
|
| Platform ID |
GPL892 |
| Series (1) |
| GSE5286 |
Rice plants infected by Rice dwarf virus |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
log10 [normalized Ch2 / normalized Ch1] |
| PVALUE |
Significance level of the value computed for a feature |
| NORM_SIG_CH1 |
Dye-normalized signal intensity of CH1 |
| NORM_SIG_CH2 |
Dye-normalized signal intensity of CH2 |
| MeanSignal_CH1 |
Raw mean CH1 signal of feature |
| MeanSignal_CH2 |
Raw mean CH2 signal of feature |
| BGMeanSignal_CH1 |
Mean local background CH1 signal |
| BGMeanSignal_CH2 |
Mean local background CH2 signal |
