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Sample GSM375568 Query DataSets for GSM375568
Status Public on Mar 31, 2009
Title dye-swap experiment between EG4 and Nipponbare 2
Sample type RNA
 
Channel 1
Source name Gimbozu EG4 replicate 2
Organism Oryza sativa Japonica Group
Characteristics age: 7-day-old seedling
disease state: healthy
cultivar: Gimbozu EG4
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 Nipponbare replicate 2
Organism Oryza sativa Japonica Group
Characteristics age: 7-day-old seedling
disease state: healthy
cultivar: Nipponbare
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 Feb 26, 2009
Last update date Mar 05, 2009
Contact name Ken Naito
E-mail(s) knaito@plantbio.uga.edu
Phone 706-542-1857
Organization name University of Georgia
Department Plant Biology
Lab Wessler Lab
Street address 4505 Miller Plant Sciences Building
City Athens
State/province GA
ZIP/Postal code 30602
Country USA
 
Platform ID GPL6864
Series (1)
GSE15021 Microarray analysis of strain EG4 vs. Nipponbare

Data table header descriptions
ID_REF
VALUE Log10 ratio of EG4/Nipponbare
PValueLogRatio Significance level of Log Ratio computed for a feature
gProcessedSignal The propagated feature signal of CH1, used for computation fo Log Ratio
rProcessedSignal The propagated feature signal of CH1, used for computation fo Log Ratio
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 as a NonUniformity Outlier or not. 1 indicates Feature is a non-uniformity outlier in CH1
rIsFeatNonUnifOL Boolean flag indicating if a feature as 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 indicats local background is a non-uniformity outlier in CH1
rIsBGNonUnifOL Boolean flag indicating if a local background is a NonUniformity Outlier or not. 1 indicats local background is a non-uniformity outlier in CH2
gIsFeatPopnOL Boolean flag indicating if a feature is a Population Outlier or not. 1 indicats Feature is a Population outlier in CH1
rIsFeatPopnOL Boolean flag indicating if a feature is a Population Outlier or not. 1 indicats Feature is a Population outlier in CH2
gIsBGPopnOL Boolean flag indicating if a local background is a Population Outlier or not. 1 indicats local background is a Population outlier in CH1
rIsBGPopnOL Boolean flag indicating if a local background is a Population Outlier or not. 1 indicats local background is a Population outlier in CH2
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 CH2 signal
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 gIsPosAndSignif and additionally the rBGSubSignal is greater than 2.6 x rBG_SD
INV_VALUE Log10 ratio of rProcessedSignal/gProcessedSigna

Data table
ID_REF VALUE PValueLogRatio gProcessedSignal rProcessedSignal gIsSaturated rIsSaturated gIsFeatNonUnifOL rIsFeatNonUnifOL gIsBGNonUnifOL rIsBGNonUnifOL gIsFeatPopnOL rIsFeatPopnOL gIsBGPopnOL rIsBGPopnOL gBGSubSignal rBGSubSignal gIsPosAndSignif rIsPosAndSignif gIsWellAboveBG rIsWellAboveBG INV_VALUE
1 -0.173 6.25E-03 2.20E+03 3.29E+03 0 0 0 0 0 0 0 0 1 0 2134.42 7619.13 1 1 1 1 1.73E-01
2 0.00E+00 1.00E+00 3.62E+00 2.92E+00 0 0 0 0 0 0 0 0 1 0 -0.803087 2.66287 0 0 0 0 0.00E+00
3 0.00E+00 1.00E+00 3.68E+00 2.97E+00 0 0 0 0 0 0 0 0 1 0 0.97996 -0.858475 0 0 0 0 0.00E+00
4 0.00E+00 1.00E+00 3.73E+00 3.00E+00 0 0 0 0 0 0 0 0 1 0 0.511616 -1.18493 0 0 0 0 0.00E+00
5 0.00E+00 1.00E+00 3.78E+00 3.04E+00 0 0 0 0 0 0 0 0 1 0 -1.07882 -0.261815 0 0 0 0 0.00E+00
6 0.00E+00 1.00E+00 3.82E+00 3.06E+00 0 0 0 0 0 0 0 0 1 0 0.28659 -6.0668 0 0 0 0 0.00E+00
7 0.00E+00 1.00E+00 3.85E+00 3.09E+00 0 0 0 0 0 0 0 0 1 0 3.1508 -6.19998 0 0 0 0 0.00E+00
8 0.00E+00 1.00E+00 3.88E+00 3.11E+00 0 0 0 0 0 0 0 0 1 0 0.425041 -1.30843 0 0 0 0 0.00E+00
9 0.00E+00 1.00E+00 3.91E+00 3.13E+00 0 0 0 0 0 0 0 0 0 0 -2.42365 -3.38765 0 0 0 0 0.00E+00
10 0.00E+00 1.00E+00 3.93E+00 3.14E+00 0 0 0 0 0 0 0 0 0 0 1.05594 -3.17775 0 0 0 0 0.00E+00
11 0.00E+00 1.00E+00 3.94E+00 3.15E+00 0 0 0 0 0 0 0 0 0 0 1.45221 -4.85128 0 0 0 0 0.00E+00
12 -0.238 1.17E-03 4.89E+01 8.45E+01 0 0 0 0 0 0 0 0 0 0 46.9536 162.439 1 1 1 1 2.38E-01
13 -0.0259 6.77E-01 2.25E+02 2.38E+02 0 0 0 0 0 0 0 0 0 0 207.688 474.772 1 1 1 1 2.59E-02
14 0.226 4.96E-04 1.61E+03 9.55E+02 0 0 0 0 0 0 0 0 0 0 1405.71 2009.48 1 1 1 1 -2.26E-01
15 0.00E+00 1.00E+00 3.96E+00 3.15E+00 0 0 0 0 0 0 0 0 0 0 3.46836 -0.372064 0 0 0 0 0.00E+00
16 0.586 1.07E-12 4.37E+02 1.13E+02 0 0 0 0 0 0 0 0 0 0 404.645 226.097 1 1 1 1 -5.86E-01
17 -0.0798 1.99E-01 3.46E+02 4.15E+02 0 0 0 0 0 0 0 0 0 0 315.18 845.292 1 1 1 1 7.98E-02
18 -0.187 5.03E-03 8.79E+01 1.35E+02 0 0 0 0 0 0 0 0 0 0 83.6746 265.364 1 1 1 1 1.87E-01
19 0.241 6.45E-01 5.44E+00 3.12E+00 0 0 0 0 0 0 0 0 0 0 5.30195 0.862485 1 0 0 0 -2.41E-01
20 0.00E+00 1.00E+00 3.91E+00 3.10E+00 0 0 0 0 0 0 0 0 0 0 1.63839 1.29003 0 0 0 0 0.00E+00

Total number of rows: 45151

Table truncated, full table size 4117 Kbytes.




Supplementary file Size Download File type/resource
GSM375568.txt.gz 13.7 Mb (ftp)(http) TXT
Processed data included within Sample table
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