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Sample GSM142313 Query DataSets for GSM142313
Status Public on Oct 25, 2007
Title RDA RSV 2
Sample type RNA
 
Channel 1
Source name NIL37 RSV 2
Organism Oryza sativa
Characteristics leaves of 14-day old seedling
Treatment protocol Leaves of 7-day old seedlings were inoculated 3 small brown planthoppers carrying rice stripe virus for 24 hours. Leaves were harvested 7 days after inoculation.
Growth protocol Seedlings were grown in a greenhouse for 14 days.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with Trizol according to the manufaturer's instruction.
Label Cy3
Label protocol Agilent Low RNA input fluorescent linear amplification kit according to the manufacturer's instrcution.
 
Channel 2
Source name NIL22 RSV 2
Organism Oryza sativa
Characteristics leaves of 14-day old seedling
Treatment protocol Leaves of 7-day old seedlings were inoculated 3 small brown planthoppers carrying rice stripe virus for 24 hours. Leaves were harvested 7 days after inoculation.
Growth protocol Seedlings were grown in a greenhouse for 14 days.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted with Trizol according to the manufaturer's instruction.
Label Cy5
Label protocol Agilent Low RNA input fluorescent linear amplification kit according to the manufacturer's instrcution.
 
 
Hybridization protocol in-situ Hybridization Kit Plus (Agilent Technologies) according to the manufacturer's instrcution.
Scan protocol DNA microarray scanner (Agilent Technologies) according to the manufacturer's instrcution.
Description NIL37 and NIL22 were sister NIL (BC4) derived from the cross between varieties Ilpum (recurrent parent) and Shinkwang (donor parent). NIL37 is susceptible to rice stripe virus (RSV), and NIL22 is resistant to RSV.
Data processing Feature Extraction Vert. 8.1 (Agilent Technologies)
 
Submission date Oct 25, 2006
Last update date Nov 06, 2006
Contact name IL-RYONG CHOI
E-mail(s) ichoi@cgiar.org
Organization name International Rice Research Institute
Street address DAPO Box 7777
City Metro Manila
ZIP/Postal code 0000
Country Philippines
 
Platform ID GPL892
Series (1)
GSE6126 Comparative gene expression analysis between virus-susceptible and -resistant rice lines (NIL37 and NIL22)

Data table header descriptions
ID_REF
VALUE log10 based [rProcessedSignal / gProcessedSignal]
PValueLogRatio Significance level of the value computed for a feature
gProcessedSignal normalized CH1 signal intensity
rProcessedSignal normalized CH2 signal intensity
gBGSubSignal Raw CH1 intensity subtracted background intensity
rBGSubSignal Raw CH2 intensity subtracted background intensity

Data table
ID_REF VALUE PValueLogRatio gProcessedSignal rProcessedSignal gBGSubSignal rBGSubSignal
1 -1.04E+00 2.55E-29 1.45E+04 1.33E+03 1109.89 333.747
2 -1.62E-01 9.04E-01 4.87E+01 3.35E+01 4.11214 8.35025
3 -4.68E-02 8.73E-01 1.99E+02 1.79E+02 15.6838 43.5274
4 7.71E-02 9.14E-01 7.00E+01 8.36E+01 5.7313 19.5698
5 6.07E-02 3.22E-01 1.39E+03 1.60E+03 105.509 403.925
6 -6.91E-03 9.44E-01 6.49E+02 6.38E+02 49.5706 160.192
7 -1.72E+00 3.58E-34 1.46E+04 2.79E+02 1106.7 70.425
8 9.64E-02 1.59E-01 1.03E+03 1.29E+03 78.3914 325.019
9 5.72E-02 2.48E-01 1.12E+04 1.28E+04 863.406 3173.48
10 0.00E+00 1.00E+00 4.03E+01 3.65E+01 2.4365 8.1693
11 -1.23E-01 1.40E-02 2.41E+04 1.82E+04 1867.83 4499.07
12 1.42E-02 9.23E-01 3.89E+02 4.01E+02 30.0526 99.5611
13 -1.02E-02 9.71E-01 1.98E+02 1.94E+02 15.6083 47.2212
14 -1.86E+00 1.46E-34 1.50E+04 2.05E+02 1139.08 51.9143
15 1.30E-02 7.98E-01 4.48E+03 4.61E+03 342.61 1156.38
16 -3.53E-02 4.85E-01 4.89E+03 4.51E+03 374.664 1130.85
17 -4.96E-03 9.89E-01 1.54E+02 1.53E+02 12.2401 36.8941
18 -5.78E-02 3.92E-01 1.26E+03 1.11E+03 95.9588 279.058
19 -4.93E-01 6.86E-16 8.30E+05 2.67E+05 65272.6 65170.9
20 1.13E-01 5.70E-01 2.48E+02 3.21E+02 19.3461 79.0165

Total number of rows: 22575

Table truncated, full table size 1274 Kbytes.




Supplementary file Size Download File type/resource
GSM142313.txt.gz 4.2 Mb (ftp)(http) TXT

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