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Sample GSM332887 Query DataSets for GSM332887
Status Public on Dec 01, 2008
Title Transformants of AK069096 vs Col-0, rep2
Sample type RNA
 
Channel 1
Source name re-transformants of AK069096
Organism Arabidopsis thaliana
Characteristics Aerial parts of re-transformants of AK069096 in T2 generation
Biomaterial provider Mika Kawashima
Growth protocol Plants were grown at 22°C in a cultivation container system (ARACON) in long-day conditions (16 hr light and 8 hr dark) under white fluorescent tubes (FL40SW, Sanyo, Osaka, Japan).
Extracted molecule total RNA
Extraction protocol RNAqueous Kit (Ambion, Inc, USA)
Label Cy3
Label protocol One micro-gram of total RNA was fluorescently labeled using a Low Input RNA Fluorescent Linear Amplification Kit (Agilent Technologies).
 
Channel 2
Source name Col-0
Organism Arabidopsis thaliana
Characteristics Aerial parts of Col-0
Biomaterial provider Mika Kawashima
Growth protocol Plants were grown at 22°C in a cultivation container system (ARACON) in long-day conditions (16 hr light and 8 hr dark) under white fluorescent tubes (FL40SW, Sanyo, Osaka, Japan).
Extracted molecule total RNA
Extraction protocol RNAqueous Kit (Ambion, Inc, USA)
Label Cy5
Label protocol One micro-gram of total RNA was fluorescently labeled using a Low Input RNA Fluorescent Linear Amplification Kit (Agilent Technologies).
 
 
Hybridization protocol Agilent Arabidopsis2 oligo microarray hybridization protocol
Scan protocol Dual-laser Microarray scanner Agilent Technologies, 5µm resolution, 50% PMT
Description Comparison of gene expression between re-transformants of AK069096 and wild-type plants (Col-0).
Data processing Spot intensities on the DNA microarray were quantified by Feature Extraction Software ver.7.1.1 (Agilent Technologies) with default parameters.
 
Submission date Oct 13, 2008
Last update date Oct 15, 2008
Contact name Minami Matsui
E-mail(s) [email protected]
Phone +81-45-503-9623
Fax +81-45-503-9586
Organization name RIKEN
Department Plant Science Center
Lab Plant Functional Genomics Research Team
Street address Suyehirocho 1-7-22 , Tsurumiku
City Yokohama
ZIP/Postal code 230-0045
Country Japan
 
Platform ID GPL888
Series (1)
GSE13165 Transformants of some rice full-length cDNAs vs wild-type Col-0

Data table header descriptions
ID_REF
VALUE Log 10 of ratio of processed signal values for mutant plant over wild-type plant
LogRatioError Standard deviation of log ratio calculated based on error model
PValueLogRatio The level of significance in the differential expression between mutant plant and wild-type plant
gProcessedSignal A signal of mutant plant post dye normalization and background-subtraction used in calculating the log ratio
rProcessedSignal A signal of wild-type plant post dye normalization and background-subtraction used in calculating the log ratio
gProcessedSigError Standard deviation of processed signal of mutant plant
rProcessedSigError Standard deviation of processed signal of wild-type plant
gIsSaturated A boolean flag of 1 indicates that the feature of mutant plant is saturated
rIsSaturated A boolean flag of 1 indicates that the feature of wild-type plant is saturated
gIsFeatNonUnifOL A boolean flag of 1 indicates that the feature of mutant plant is a non-uniformity outlier
rIsFeatNonUnifOL A boolean flag of 1 indicates that the feature of wild-type plant is a non-uniformity outlier
gIsBGNonUnifOL A boolean flag of 1 indicates that the feature of background for mutant plant is a non-uniformity outlier
rIsBGNonUnifOL A boolean flag of 1 indicates that the feature of background for wild-type plant is a non-uniformity outlier
gIsFeatPopnOL A boolean flag of 1 indicates that the feature of mutant plant is a population outlier
rIsFeatPopnOL A boolean flag of 1 indicates that the feature of wild-type plant is a population outlier
gIsBGPopnOL A boolean flag of 1 indicates that the feature of background for mutant plant is a population outlier
rIsBGPopnOL A boolean flag of 1 indicates that the feature of background for wild-type plant is a population outlier
gIsPosAndSignif A boolean flag of 1 indicates that the feature signal of mutant plant is greater than and significant compared to the background signal
rIsPosAndSignif A boolean flag of 1 indicates that the feature signal of wild-type plant is greater than and significant compared to the background signal
gIsWellAboveBG A boolean flag of 1 indicates that the feature of mutant plant is greater than the background plus 2.6-fold of SD of background
rIsWellAboveBG A boolean flag of 1 indicates that the feature of wild-type plant is greater than the background plus 2.6-fold of SD of background

Data table
ID_REF VALUE LogRatioError PValueLogRatio gProcessedSignal rProcessedSignal gProcessedSigError rProcessedSigError gIsSaturated rIsSaturated gIsFeatNonUnifOL rIsFeatNonUnifOL gIsBGNonUnifOL rIsBGNonUnifOL gIsFeatPopnOL rIsFeatPopnOL gIsBGPopnOL rIsBGPopnOL gIsPosAndSignif rIsPosAndSignif gIsWellAboveBG rIsWellAboveBG
3 4.53E-02 2.12E-01 8.31E-01 6.10E+02 6.77E+02 3.08E+02 6.10E+01 0 0 0 0 0 0 0 0 1 0 1 1 1 1
4 2.58E-01 6.24E-02 3.50E-05 2.95E+03 5.35E+03 3.90E+02 4.29E+02 0 0 0 0 0 0 0 0 1 0 1 1 1 1
5 9.68E-02 2.03E-01 6.34E-01 6.03E+02 7.53E+02 3.09E+02 6.64E+01 0 0 0 0 0 0 0 0 1 0 1 1 1 1
6 -1.78E-02 1.03E-01 8.62E-01 1.54E+03 1.47E+03 3.34E+02 1.21E+02 0 0 0 0 0 0 0 0 1 0 1 1 1 1
8 -8.65E-02 3.85E-01 8.22E-01 3.59E+02 2.94E+02 2.86E+02 3.81E+01 0 0 0 0 0 0 0 0 1 0 1 1 1 1
9 1.14E-01 3.91E-01 7.70E-01 2.80E+02 3.64E+02 2.85E+02 4.18E+01 0 0 0 0 0 0 0 0 1 0 1 1 1 1
10 -2.22E-01 3.37E-01 5.10E-01 4.85E+02 2.91E+02 2.92E+02 3.75E+01 0 0 0 0 0 0 0 0 1 0 1 1 1 1
11 7.55E-02 1.60E-01 6.37E-01 8.10E+02 9.64E+02 3.16E+02 8.19E+01 0 0 0 0 0 0 0 0 0 0 1 1 1 1
12 -1.51E-01 2.20E+00 9.46E-01 4.34E+01 3.07E+01 1.80E+02 4.74E+01 0 0 0 0 0 0 0 0 1 0 1 1 0 0
13 0.00E+00 2.00E+00 1.00E+00 4.27E+01 4.08E+01 1.86E+02 4.58E+01 0 0 0 0 0 0 0 0 1 0 1 1 0 0
15 -2.31E-01 5.15E-01 6.54E-01 2.99E+02 1.76E+02 2.73E+02 3.44E+01 0 0 0 0 0 0 0 0 1 0 1 1 1 1
16 9.60E-03 9.87E-02 9.23E-01 1.57E+03 1.60E+03 3.35E+02 1.31E+02 0 0 0 0 0 0 0 0 1 0 1 1 1 1
17 1.37E-01 6.09E-01 8.22E-01 1.61E+02 2.21E+02 2.63E+02 3.69E+01 0 0 0 0 0 0 0 0 1 0 1 1 1 1
18 0.00E+00 2.20E+00 1.00E+00 3.89E+01 3.47E+01 1.80E+02 4.73E+01 0 0 0 0 0 0 0 0 1 0 0 1 0 0
19 1.83E-01 1.16E-01 1.15E-01 1.05E+03 1.60E+03 3.22E+02 1.31E+02 0 0 0 0 0 0 0 0 0 0 1 1 1 1
20 7.98E-02 9.51E-02 4.01E-01 1.52E+03 1.83E+03 3.34E+02 1.49E+02 0 0 0 0 0 0 0 0 0 0 1 1 1 1
22 -1.63E-01 8.63E-01 8.50E-01 1.49E+02 1.02E+02 2.44E+02 3.59E+01 0 0 0 0 0 0 0 0 0 0 1 1 1 1
23 -1.27E-01 1.77E-01 4.73E-01 9.12E+02 6.81E+02 3.16E+02 6.11E+01 0 0 0 0 0 0 0 0 0 0 1 1 1 1
24 5.64E-02 7.11E-01 9.37E-01 1.48E+02 1.68E+02 2.55E+02 3.60E+01 0 0 0 0 0 0 0 0 1 0 1 1 0 1
25 -2.02E-01 1.28E+00 8.74E-01 9.35E+01 5.86E+01 2.17E+02 3.96E+01 0 0 0 0 0 0 0 0 0 0 1 1 0 0

Total number of rows: 21494

Table truncated, full table size 2035 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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