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Sample GSM142446 Query DataSets for GSM142446
Status Public on Oct 31, 2009
Title P-def_rep3
Sample type RNA
 
Channel 1
Source name Nipponbare_P-def_rep3; without Phosphorus
Organism Oryza sativa
Characteristics root tissues sampled in 40 day-old plants
Growth protocol Plants were grown in 12L pots filled with soil (Andosol) without Phosphorus
Extracted molecule total RNA
Extraction protocol Total RNA of root tissues (1.6 g) was collected and purified by RNeasy midi kit according to manufacturer's protocol.
Label Cy3
Label protocol Labelled cRNA was synthesized by Low RNA Input Linear Amplification kit (Agilent Technlogies) according to manufacturer's protocol.
 
Channel 2
Source name 6-4_P-def_rep3; without Phosphorus
Organism Oryza sativa
Characteristics root tissues sampled in 40 day-old plants
Growth protocol Plants were grown in 12L pots filled with soil (Andosol) without Phosphorus
Extracted molecule total RNA
Extraction protocol Total RNA of root tissues (1.6 g) was collected and purified by RNeasy midi kit according to manufacturer's protocol.
Label Cy5
Label protocol Labelled cRNA was synthesized by Low RNA Input Linear Amplification kit (Agilent Technlogies) according to manufacturer's protocol.
 
 
Hybridization protocol Both 1 micro gram labelled cRNA were hybridized on a slide by In-situ Hybridization Kit Plus (Agilent Technologies) according to manufacturer's protocol.
Scan protocol After hybridization, the slide was washed twice according to manufacturer's protocol. the slide was scanned by DNA microarray scaner according to manufacturer's protocol.
Description Keyword: Nipponbare
Keyword: 6-4 (NIL with inserts from cv. Kasalath (indica))
Keyword: Comparison between line
Keyword: Phosphorus deficiency
Keyword: Root
Data processing Feature Extraction ver 8.1 (Agilent Technologies)
 
Submission date Oct 26, 2006
Last update date Mar 24, 2009
Contact name Matthias Wissuwa
E-mail(s) wissuwa@affrc.go.jp
Phone +81-29-838-6354
Fax +81-29-838-6354
Organization name JIRCAS
Street address 1-1 Ohwashi
City Tsukuba
ZIP/Postal code 305-8686
Country Japan
 
Platform ID GPL892
Series (1)
GSE6187 Comparative gene expression analysis between Nipponbare and 6-4 under two conditions

Data table header descriptions
ID_REF
VALUE Log10 based [Norm_CH2 / Norm_CH1]
PVALUE Significance level of the value computed for a feature
Norm_CH1 Dye-normalized signal intensity of CH1
Norm_CH2 Dye-normalized signal intensity of CH2
Raw_CH1 Raw CH1 intensity subtracted background CH1 intensity
Raw_CH2 Raw CH2 intensity subtracted background CH2 intensity

Data table
ID_REF VALUE PVALUE Norm_CH1 Norm_CH2 Raw_CH1 Raw_CH2
1 -1.27E+00 6.47E-30 3.85E+03 2.08E+02 765.044 109.593
2 0.00E+00 1.00E+00 1.66E+01 1.42E+01 2.64362 -3.39744
3 -3.08E-01 7.74E-01 4.94E+01 2.43E+01 10.556 11.9148
4 -1.30E-01 9.59E-01 1.74E+01 1.29E+01 3.81276 5.78083
5 2.37E-04 9.97E-01 1.68E+03 1.68E+03 333.299 884.064
6 -5.69E-02 8.79E-01 1.09E+02 9.58E+01 22.618 48.4014
7 -1.81E+00 1.69E-32 4.00E+03 6.25E+01 800.809 32.6967
8 4.15E-02 8.50E-01 1.69E+02 1.85E+02 34.4171 95.1525
9 -4.01E-03 9.45E-01 1.21E+03 1.20E+03 240.576 633.129
10 -5.57E-02 8.90E-01 1.01E+02 8.87E+01 20.9418 44.7532
11 2.38E-02 6.56E-01 1.77E+03 1.87E+03 351.281 983.606
12 -2.28E-02 9.31E-01 1.50E+02 1.42E+02 30.7176 72.5144
13 -3.79E-02 9.35E-01 8.52E+01 7.80E+01 17.7488 39.2033
14 -1.78E+00 1.49E-32 4.12E+03 6.83E+01 823.355 35.8015
15 -6.68E-02 7.00E-01 2.46E+02 2.11E+02 49.9591 108.961
16 5.74E-02 7.11E-01 2.41E+02 2.75E+02 48.7787 142.435
17 4.76E-02 4.19E-01 1.11E+03 1.24E+03 220.394 653.333
18 -5.12E-02 3.19E-01 2.78E+03 2.47E+03 551.566 1306.59
19 -1.19E-02 9.74E-01 1.06E+02 1.03E+02 21.8842 51.9973
20 -9.63E-03 8.56E-01 1.96E+03 1.92E+03 389.842 1011.04

Total number of rows: 22575

Table truncated, full table size 1274 Kbytes.




Supplementary file Size Download File type/resource
GSM142446.txt.gz 5.2 Mb (ftp)(http) TXT

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