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Sample GSM288879 Query DataSets for GSM288879
Status Public on Jun 15, 2008
Title OsGLK1-FOX 1
Sample type RNA
 
Channel 1
Source name Vector control callus_1
Organism Oryza sativa
Characteristics cultivar: Nipponbare
sample: callus of the vector control line
Growth protocol T1-seeds of the vector control line were sown and grown for 13 days on callus-induction medium containing 2,4-D at 30 mg/l under continuous white fluorescent light.
Extracted molecule total RNA
Extraction protocol RNeasy Plant Mini Kit (Qiagen)
Label Cy3
Label protocol Low RNA inout Lineat Amplification/Labeling Lit (Agilent)
 
Channel 2
Source name OsGLK1-FOX callus_1
Organism Oryza sativa
Characteristics cultivar: Nipponbare
sample: callus of the OsGLK1-FOX line
Growth protocol T1-seeds of the vector control line were sown and grown for 13 days on callus-induction medium containing 2,4-D at 30 mg/l under continuous white fluorescent light.
Extracted molecule total RNA
Extraction protocol RNeasy Plant Mini Kit (Qiagen)
Label Cy5
Label protocol Low RNA inout Lineat Amplification/Labeling Lit (Agilent)
 
 
Hybridization protocol Agilent protocol G4140-90040
Scan protocol Agilent scanner model G2505B, software G2565BA
Description 400 ng RNAs were labeled and 1µg of Cy3- and Cy5-labeled cRNAs were used.
Data processing Data was analyzed by Fearure Extraction software (version 9.1, Agilent)
 
Submission date May 15, 2008
Last update date May 15, 2008
Contact name Hidemitsu Nakamura
E-mail(s) hide7087@affrc.go.jp
Organization name The University of Tokyo
Department Department of Applied Biological Chemistry
Lab Laboratory of Plant Growth Substances
Street address 1-1-1 Yayoi
City Bunkyo-ku
State/province Tokyo
ZIP/Postal code 113-8657
Country Japan
 
Platform ID GPL6864
Series (1)
GSE11451 OsGLK1 regulated genes in rice

Data table header descriptions
ID_REF
VALUE lowess Log 10 based [rProcessedSignal / gProcessedsignal]
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
gBGSubSignal The net CH1 signal following the subtraction of the background from the raw mean CH1 signal
rBGSubSignal The net CH2 signal following the subtraction of the background from the raw mean CH1 signal
gIsSaturated 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
rIsSaturated 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
gIsFeatNonUnifOL Boolean flag indicating if a feature is a NonUniformity Outlier or not. 1 indicates Feature is a non-uniformity outlier in CH1
rIsFeatNonUnifOL Boolean flag indicating if a feature is a NonUniformity Outlier or not. 1 indicates Feature is a non-uniformity outlier in CH2
gIsBGNonUnifOL Boolean flag indicating if a local background is a NonUniformity Outlier or not. 1 indicates local background is a non-uniformity outlier in CH1
rIsBGNonUnifOL Boolean flag indicating if a local background is a NonUniformity Outlier or not. 1 indicates local background is a non-uniformity outlier in CH2
gIsFeatPopnOL Boolean flag indicating if a feature is a Population Outlier or not. 1 indicates Feature is a population outlier in CH1
rIsFeatPopnOL Boolean flag indicating if a feature is a Population Outlier or not. 1 indicates Feature is a population outlier in CH2
gIsBGPopnOL Boolean flag indicating if a local background is a Population Outlier or not. 1 indicates local background is a population outlier in CH1
rIsBGPopnOL 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.

Data table
ID_REF VALUE PValueLogRatio gProcessedSignal rProcessedSignal gBGSubSignal rBGSubSignal gIsSaturated rIsSaturated gIsFeatNonUnifOL rIsFeatNonUnifOL gIsBGNonUnifOL rIsBGNonUnifOL gIsFeatPopnOL rIsFeatPopnOL gIsBGPopnOL rIsBGPopnOL gIsPosAndSignif rIsPosAndSignif gIsWellAboveBG rIsWellAboveBG
1 7.11E-03 9.08E-01 1.95E+03 1.98E+03 1013.31 3088.24 0 0 0 0 0 0 0 0 0 0 1 1 1 1
2 0.00E+00 1.00E+00 5.11E+00 4.19E+00 2.15253 -6.8265 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3 0.00E+00 1.00E+00 5.11E+00 4.19E+00 0.62251 -2.7631 0 0 0 0 0 0 0 0 0 0 0 0 0 0
4 0.00E+00 1.00E+00 5.11E+00 4.18E+00 2.6981 -3.2482 0 0 0 0 0 0 0 0 0 0 0 0 0 0
5 0.00E+00 1.00E+00 5.12E+00 4.18E+00 -1.68226 -0.0611275 0 0 0 0 0 0 0 0 0 0 0 0 0 0
6 0.00E+00 1.00E+00 5.12E+00 4.17E+00 1.9626 -1.25353 0 0 0 0 0 0 0 0 0 0 0 0 0 0
7 -1.72E-01 7.61E-01 6.16E+00 4.14E+00 3.4185 -5.27688 0 0 0 0 0 0 0 0 0 0 1 0 0 0
8 0.00E+00 1.00E+00 5.12E+00 4.17E+00 0.230905 -0.953983 0 0 0 0 0 0 0 0 0 0 0 0 0 0
9 -2.35E-01 6.56E-01 7.06E+00 4.12E+00 3.90347 0.00584262 0 0 0 0 0 0 0 0 0 0 1 0 0 0
10 0.00E+00 1.00E+00 5.12E+00 4.16E+00 2.31583 -0.793128 0 0 0 0 0 0 0 0 0 0 0 0 0 0
11 0.00E+00 1.00E+00 5.11E+00 4.15E+00 0.611795 -4.13424 0 0 0 0 0 0 0 0 0 0 0 0 0 0
12 -4.43E-01 2.85E-01 1.12E+01 4.04E+00 6.09056 0.820306 0 0 0 0 0 0 0 0 0 0 1 0 0 0
13 2.67E-03 9.66E-01 2.83E+02 2.85E+02 139.126 474.093 0 0 0 0 0 0 0 0 0 0 1 1 1 1
14 -1.10E-01 3.47E-01 3.40E+01 2.64E+01 16.7621 43.8785 0 0 0 0 0 0 0 0 0 0 1 1 1 1
15 0.00E+00 1.00E+00 5.11E+00 4.14E+00 1.6815 -7.48343 0 0 0 0 0 0 0 0 0 0 0 0 0 0
16 -6.70E-03 9.13E-01 2.54E+03 2.50E+03 1326.1 3932.79 0 0 0 0 0 0 0 0 0 0 1 1 1 1
17 0.00E+00 1.00E+00 5.10E+00 4.13E+00 1.40529 -2.90035 0 0 0 0 0 0 0 0 0 0 0 0 0 0
18 -2.05E-01 1.47E-03 7.30E+02 4.55E+02 367.762 744.946 0 0 0 0 0 0 0 0 0 0 1 1 1 1
19 -2.99E-01 2.44E-03 5.70E+01 2.86E+01 27.7945 48.4962 0 0 0 0 0 0 0 0 0 0 1 1 1 1
20 0.00E+00 1.00E+00 5.09E+00 4.11E+00 -2.63467 -4.49933 0 0 0 0 0 0 0 0 0 0 0 0 0 0

Total number of rows: 45151

Table truncated, full table size 3803 Kbytes.




Supplementary file Size Download File type/resource
GSM288879.txt.gz 14.2 Mb (ftp)(http) TXT
Processed data included within Sample table
Processed data provided as supplementary file
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