|
| Status |
Public on Mar 15, 2010 |
| Title |
High Temperature during Grain Filling of Rice, Biological Replicate 1, Dye Swap 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
High temperature, Replicate 1
|
| Organism |
Oryza sativa |
| Characteristics |
experimental condition: high temperature
|
| Treatment protocol |
Five days after flowering (DAF), the plants were transferred to either a 33°C/28°C or 25°C/20°C chamber for high temperature or control treatment, respectively, and then the temperature was maintained at 25°C/20°C from 20 DAF to maturity. Ten and 12 DAF for high temperature and control plots, respectively, developing caryopses were detached from the ear at midday (6 h after illumination was started), immediately frozen in liquid nitrogen, and stored at -80°C.
|
| Growth protocol |
Rice (Oryza sativa ssp. japonica) ‘Nipponbare’ was grown at 27°C/22°C (12-h-day/12-h-night photoperiod) until flowering in a plant incubator (model FLI-301NH; Eyela, Tokyo, Japan) equipped with a sodium lamp, which allows illumination at an intensity of 560 µmol photons m-2 s-1. Six plants were grown in a plastic container (15 × 10 × 6 cm) filled with 600 ml of rice nursery culture soil (containing 0.15 g each of nitrogen, phosphate, and potassium), and each plant was restricted to the main culm by the removal of tillers. Approximately 15 to 20 d before heading, 3 g of a fertilizer (containing 0.18 g nitrogen, 0.24 g phosphate, 0.18 g potassium, and 0.06 g magnesium) was supplied per container.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 12 developing caryopses harvested from 25°C/20°C- and 33°C/28°C-treated plants using the method of Chang et al. (1993) (3 biologically independent replicates, each). The yield and RNA purity were determined spectrophotometrically. Integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
|
| Label |
Cy5
|
| Label protocol |
Total RNA (400 ng) was labeled with Cy3 or Cy5 using an Agilent Quick Amp Labeling kit (Agilent Technologies).
|
| |
|
| Channel 2 |
| Source name |
Control, Replicate 1
|
| Organism |
Oryza sativa |
| Characteristics |
experimental condition: control
|
| Treatment protocol |
Five days after flowering (DAF), the plants were transferred to either a 33°C/28°C or 25°C/20°C chamber for high temperature or control treatment, respectively, and then the temperature was maintained at 25°C/20°C from 20 DAF to maturity. Ten and 12 DAF for high temperature and control plots, respectively, developing caryopses were detached from the ear at midday (6 h after illumination was started), immediately frozen in liquid nitrogen, and stored at -80°C.
|
| Growth protocol |
Rice (Oryza sativa ssp. japonica) ‘Nipponbare’ was grown at 27°C/22°C (12-h-day/12-h-night photoperiod) until flowering in a plant incubator (model FLI-301NH; Eyela, Tokyo, Japan) equipped with a sodium lamp, which allows illumination at an intensity of 560 µmol photons m-2 s-1. Six plants were grown in a plastic container (15 × 10 × 6 cm) filled with 600 ml of rice nursery culture soil (containing 0.15 g each of nitrogen, phosphate, and potassium), and each plant was restricted to the main culm by the removal of tillers. Approximately 15 to 20 d before heading, 3 g of a fertilizer (containing 0.18 g nitrogen, 0.24 g phosphate, 0.18 g potassium, and 0.06 g magnesium) was supplied per container.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 12 developing caryopses harvested from 25°C/20°C- and 33°C/28°C-treated plants using the method of Chang et al. (1993) (3 biologically independent replicates, each). The yield and RNA purity were determined spectrophotometrically. Integrity was verified using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
|
| Label |
Cy3
|
| Label protocol |
Total RNA (400 ng) was labeled with Cy3 or Cy5 using an Agilent Quick Amp Labeling kit (Agilent Technologies).
|
| |
|
| |
| Hybridization protocol |
Fluorescently labeled targets were hybridized to Agilent rice 44-K oligo DNA microarrays (Agilent Technologies). The hybridization and washing were performed according to the manufacturer’s instructions.
|
| Scan protocol |
Hybridized microarrays were scanned using an Agilent Microarray Scanner (Agilent Technologies).
|
| Description |
US22502590_251524111384_S01_GE2-v4_95_Feb07_1_2.txt
|
| Data processing |
Feature Extraction software (version 9.1; Agilent Technologies) was employed for the data extraction and normalization processes. 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 |
Feb 16, 2010 |
| Last update date |
Mar 15, 2010 |
| Contact name |
Hiromoto Yamakawa |
| E-mail(s) |
hy741220@affrc.go.jp
|
| Phone |
+81-25-526-3245
|
| Fax |
+81-25-524-8578
|
| URL |
http://narc.naro.affrc.go.jp/
|
| Organization name |
National Agricultural Research Center
|
| Department |
Hokuriku Research Center
|
| Lab |
Rice Physiology Research Team
|
| Street address |
Inada 1-2-1
|
| City |
Joetsu |
| State/province |
Niigata |
| ZIP/Postal code |
943-0193 |
| Country |
Japan |
| |
|
| Platform ID |
GPL6864 |
| Series (1) |
| GSE20345 |
Gene expression profile in rice developing caryopsis exposed to high temperature |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
normalized log10 ratio Cy5/Cy3 (high/control temperature) |
| PValueLogRatio |
Significance level of the Log Ratio computed for a feature |
| gProcessedSignal |
The propagated feature signal of CH1, used for computation of log ratio |
| rProcessedSignal |
The propagated feature signal of CH2 , used for computation of log ratio |
| gIsSaturated |
The net CH1 signal following the subtraction of the background from the raw mean CH1 ignal |
| rIsSaturated |
The net CH2 signal following the subtraction of the background from the raw mean CH1 signal |
| gIsFeatNonUnifOL |
Boolean flag indicating if a feature of CH1 is saturated or not. A feature is saturated IF 50% of the pixels in a feature are above the saturation threshold |
| rIsFeatNonUnifOL |
Boolean flag indicating if a feature of CH2 is saturated or not. A feature is saturated IF 50% of the pixels in a feature are above the saturation threshold |
| gIsBGNonUnifOL |
Boolean flag indicating if a feature is a NonUniformity Outlier or not. 1 indicates Feature is a non-uniformity outlier in CH1 |
| rIsBGNonUnifOL |
Boolean flag indicating if a feature is a NonUniformity Outlier or not. 1 indicates Feature is a non-uniformity outlier in CH2 |
| gIsFeatPopnOL |
Boolean flag indicating if a local background is a NonUniformity Outlier or not. 1 indicates local background is a non-uniformity outlier in CH1 |
| rIsFeatPopnOL |
Boolean flag indicating if a local background is a NonUniformity Outlier or not. 1 indicates local background is a non-uniformity outlier in CH2 |
| gIsBGPopnOL |
Boolean flag indicating if a feature is a Population Outlier or not. 1 indicates Feature is a population outlier in CH1 |
| rIsBGPopnOL |
Boolean flag indicating if a feature is a Population Outlier or not. 1 indicates Feature is a population outlier in CH2 |
| gBGSubSignal |
Boolean flag indicating if a local background is a Population Outlier or not. 1 indicates local background is a population outlier in CH1 |
| rBGSubSignal |
Boolean flag indicating if a local background is a Population Outlier or not. 1 indicates local background is a population outlier in CH2 |
| gIsPosAndSignif |
Boolean flag indicating if the mean signal of a feature is greater than the corresponding background and if this difference is significant. 1 indicates Feature of CH1 is positive and significant above background |
| rIsPosAndSignif |
Boolean flag indicating if the mean signal of a feature is greater than the corresponding background and if this difference is significant. 1 indicates Feature of CH2 is positive and significant above background |
| gIsWellAboveBG |
Boolean flag indicating if a feature is WellAbove Background or not. 1 indicates Feature of CH1 passes gIsPosAndSignif and additionally the gBGSubSignal is greater than 2.6 x gBG_SD. |
| rIsWellAboveBG |
Boolean flag indicating if a feature is WellAbove Background or not. 1 indicates Feature of CH2 passes rIsPosAndSignif and additionally the rBGSubSignal is greater than 2.6 x rBG_SD. |
