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Sample GSM45501 Query DataSets for GSM45501
Status Public on Mar 22, 2006
Title FS_24h_1
Sample type RNA
 
Channel 1
Source name Untreated sample labeled by green (Cy3)
Organism Oryza sativa
Extracted molecule total RNA
 
Channel 2
Source name FS_24h treated sample labeled by red (Cy5)
Organism Oryza sativa
Extracted molecule total RNA
 
 
Description The japonica rice variety Nipponbare was grown under hydroponic condition for 10-days (untreated seedling sample). Seedlings were exposed to once stress conditions for 24 hours(stress treated sample). In the flooded standing (FS) treatment, seedlings with planter boxes were submerged vertically. Total RNAs were prepared from each sample using an RNeasy Midi Kit (Qiagen, Tokyo, Japan) and the mRNAs were purified with an Oligotex-dT30 Kit (Takara, Shiga, Japan). Purified mRNA was amplified and labeled and we hybridized the 1-mg fluorescent liner amplified Cy3- and Cy5-labeled cRNAs (each cRNA was 500 ng) to the NIAS RICE 22K oligonucleotide array ver1 according to the manufacturer’s protocols (Agilent Technologies; http://www.chem.agilent.com/). We calculated the expression ratio that applied to LOWESS normalization after dividing the signal intensity of mRNA from stress-treated seedling by the signal intensity of that from untreated seedling.

Keywords = Rice
Keywords = Flooded standing stress
Lot batch = US22502511_16011538011502_S01_A01
 
Submission date Mar 17, 2005
Last update date Oct 28, 2005
Contact name Shoshi Kikuchi
E-mail(s) skikuchi@nias.affrc.go.jp
Phone 81-298-38-7007
Fax 81-298-38-7007
URL http://cdna01.dna.affrc.go.jp/cDNA/
Organization name National Institute of Agrobiological Sciences
Department Molecular Genetics
Lab Gene Expression
Street address 2-1-2 Kan-nondai
City Tsukuba
State/province Ibaraki
ZIP/Postal code 305-8602
Country Japan
 
Platform ID GPL477
Series (1)
GSE2415 Rice Seedling Stress treatment

Data table header descriptions
ID_REF
VALUE log(REDsignal/GREENsignal) per feature
NormCH1 Dye-normalized signal per channel green, used for computation of log ratio
NormCH2 Dye-normalized signal per channel red, used for computation of log ratio
QUALITY1 1 = Saturated or 0 = Not saturated, Flag indicating if a feature is saturated or not in green channel.
QUALITY2 1 = Saturated or 0 = Not saturated, Flag indicating if a feature is saturated or not in red channel.
QUALITY3 1 indicates Feature is a non-uniformity outlier in green channel. Flag indicating if a feature is a NonUniformity Outlier or not.
QUALITY4 1 indicates Feature is a non-uniformity outlier in red channel. Flag indicating if a feature is a NonUniformity Outlier or not.
QUALITY5 1 indicates feature is positive and significant above background in green channel. Flag indicating if the mean signal of a feature is greater than the corresponding background.
QUALITY6 1 indicates feature is positive and significant above background in red channel. Flag indicating if the mean signal of a feature is greater than the corresponding background.
QUALITY7 1 = Feature used

Data table
ID_REF VALUE NormCH1 NormCH2 QUALITY1 QUALITY2 QUALITY3 QUALITY4 QUALITY5 QUALITY6 QUALITY7
1 -1.63288 4549.39 105.943 0 0 0 0 1 1 0
2 -1.0879 7051.89 575.975 0 0 0 0 1 1 0
3 0 18.007 15.8982 0 0 0 0 0 1 0
4 0 20.4746 14.9296 0 0 0 0 0 0 0
5 -1.59116 4304.36 110.344 0 0 0 0 1 1 0
6 -1.25547 7245.3 402.337 0 0 0 0 1 1 0
7 0 18.2035 16.3398 0 0 0 0 0 1 0
8 0 19.211 16.2221 0 0 0 0 0 0 0
9 -1.54587 4635.54 131.895 0 0 0 0 1 1 0
10 -1.25883 7980.85 439.761 0 0 0 0 1 1 0
11 0.0291826 14.6442 15.662 0 0 0 0 0 1 0
12 -0.358284 36.9372 16.1875 0 0 0 0 1 1 0
13 -1.61215 5348.05 130.63 0 0 0 0 1 1 0
14 -1.25999 8023.81 440.955 0 0 0 0 1 1 0
15 0 15.2994 15.2358 0 0 0 0 0 1 0
16 -0.326631 33.4996 15.791 0 0 0 0 1 1 0
17 -1.6183 6012.58 144.799 0 0 0 0 1 1 0
18 -1.25954 9068.24 498.87 0 0 0 0 1 1 0
19 0 16.1964 16.0912 0 0 0 0 0 1 0
20 -0.41775 42.9193 16.4022 0 0 0 0 1 1 0

Total number of rows: 22575

Table truncated, full table size 997 Kbytes.




Supplementary data files not provided

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