|
| Status |
Public on Mar 01, 2010 |
| Title |
WT rice leaf blade vs. GS1;1 mutant rice leaf blade, dye-swap |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
GS1;1 mutant rice leaf blade
|
| Organism |
Oryza sativa |
| Characteristics |
cultivar: Nipponbare GS1;1 knock out mutant
mutant line: Tos17 insertion mutant NC2373
age: 18 days after sowing
tissue: 3rd leaf blade
|
| Growth protocol |
growth: hydroponic culture
growth enviroment: greenhouse
growth substrates: The germinated seedlings were grown hydroponically in one-fourth concentration of the hydroponic culture solution in the presence of 1.0 mM NH4Cl as nitrogen source. The culture solution was replaced as new one every morning at 10:00 am.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from leaf blade using the RNeasy plant mini kit (Qiagen). RNA profile and integrity of RNA was checked by Agilent’s Bioanalyzer.
|
| Label |
Cy3
|
| Label protocol |
The total RNA extracted (750 ng) from leaf blade was labeled with Cy-3 using an Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent, USA).
|
| |
|
| Channel 2 |
| Source name |
WT rice leaf blade
|
| Organism |
Oryza sativa |
| Characteristics |
cultivar: Nipponbare
age: 18 days after sowing
tissue: 3rd leaf blade
|
| Growth protocol |
growth: hydroponic culture
growth enviroment: greenhouse
growth substrates: The germinated seedlings were grown hydroponically in one-fourth concentration of the hydroponic culture solution in the presence of 1.0 mM NH4Cl as nitrogen source. The culture solution was replaced as new one every morning at 10:00 am.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from leaf blade using the RNeasy plant mini kit (Qiagen). RNA profile and integrity of RNA was checked by Agilent’s Bioanalyzer.
|
| Label |
Cy5
|
| Label protocol |
The total RNA extracted (750 ng) from leaf blade was labeled with Cy-5 using an Agilent Low RNA Input Fluorescent Linear Amplification Kit (Agilent, USA).
|
| |
|
| |
| Hybridization protocol |
hybridization_Kit: in situ hybridization plus
hybridization_Manufacturer: Agilent Technologies
hybridization_Manual: Agilent Technologies
|
| Scan protocol |
Scanner: Agilent DNA microarray Scaner (G2565AA)
Manufacturer: Agilent Technologies
Software: Scanner Control software
Manual: Agilent Technologies
|
| Description |
Comparison of gene expression between a GS1;1 mutant and wild-type plants in leaf blade at the 18-day-old.
|
| Data processing |
Software: Feature Extraction Software Version A.7.5.1
Manufacturer: Agilent Technologies
Manual: Agilent Technologies
|
| |
|
| Submission date |
Mar 05, 2009 |
| Last update date |
Mar 13, 2009 |
| Contact name |
Tomoyuki Yamaya |
| E-mail(s) |
tyamaya@biochem.tohoku.ac.jp
|
| Organization name |
Tohoku University
|
| Department |
Gladuate School of Agricultural Science
|
| Street address |
1-1Tsutsumidori-Amamiyamachi, Aoba-ku
|
| City |
Sendai |
| ZIP/Postal code |
981-8555 |
| Country |
Japan |
| |
|
| Platform ID |
GPL892 |
| Series (1) |
| GSE15122 |
Gene expression of cytosolic glutamine synthetase 1;1 knock-out mutant rice |
|
| Data table header descriptions |
| ID_REF |
|
| VALUE |
log10 based [gProcessedSignal / rProcessedSignal] |
| LogRatioError |
Standard deviation of log ratio calculated based on error model |
| PValueLogRatio |
The level of significance in the differential expression between CH1 and CH1 |
| gProcessedSignal |
A signal of CH1 post dye normalization and background-subtraction used in calculating the log ratio |
| rProcessedSignal |
A signal of CH2 post dye normalization and background-subtraction used in calculating the log ratio |
| gProcessedSigError |
Standard deviation of processed signal of CH1 |
| rProcessedSigError |
Standard deviation of processed signal of CH2 |
| gIsSaturated |
A boolean flag of 1 indicates that the feature of CH1 is saturated |
| rIsSaturated |
A boolean flag of 1 indicates that the feature of CH2 is saturated |
| gIsFeatNonUnifOL |
A boolean flag of 1 indicates that the feature of CH1 is a non-uniformity outlier |
| rIsFeatNonUnifOL |
A boolean flag of 1 indicates that the feature of CH2 is a non-uniformity outlier |
| gIsBGNonUnifOL |
A boolean flag of 1 indicates that the feature of background for CH1 is a non-uniformity outlier |
| rIsBGNonUnifOL |
A boolean flag of 1 indicates that the feature of background for CH2 is a non-uniformity outlier |
| gIsFeatPopnOL |
A boolean flag of 1 indicates that the feature of CH1 is a population outlier |
| rIsFeatPopnOL |
A boolean flag of 1 indicates that the feature of CH2 is a population outlier |
| gIsBGPopnOL |
A boolean flag of 1 indicates that the feature of background for CH1 is a population outlier |
| rIsBGPopnOL |
A boolean flag of 1 indicates that the feature of background for CH2 is a population outlier |
| gIsPosAndSignif |
A boolean flag of 1 indicates that the feature signal of CH1 is greater than and significant compared to the background signal |
| rIsPosAndSignif |
A boolean flag of 1 indicates that the feature signal of CH2 is greater than and significant compared to the background signal |
| gIsWellAboveBG |
A boolean flag of 1 indicates that the feature of CH1 is greater than the background plus 2.6-fold of SD of background |
| rIsWellAboveBG |
A boolean flag of 1 indicates that the feature of CH2 is greater than the background plus 2.6-fold of SD of background |
| INV_VALUE |
log10 based [rProcessedSignal / gProcessedSignal] |
