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Sample GSM45723 Query DataSets for GSM45723
Status Public on Mar 22, 2006
Title Dr_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 Dr_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 drought stress treatment, seedlings by adding 25% polyethylene glycol 6000 to the planter box were grown for 24 h. 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 = Drought stress
Lot batch = US22502511_16011538011564_S01_A01
 
Submission date Mar 22, 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 -1.32213 1476.68 70.3323 0 0 1 0 1 1 0
2 -1.18491 3169.33 207.044 0 0 0 0 1 1 0
3 0 13.9603 28.745 0 0 0 0 0 1 0
4 -0.0437455 43.5074 39.3385 0 0 0 0 1 1 0
5 -1.4165 1810.07 69.3734 0 0 0 0 1 1 0
6 -1.15308 3183.2 223.762 0 0 0 0 1 1 0
7 0 15.6543 26.2762 0 0 0 0 0 1 0
8 -0.0480141 48.7944 43.6874 0 0 0 0 1 1 0
9 -1.29752 1880.84 94.8042 0 0 0 0 1 1 0
10 -1.08352 2923.7 241.221 0 0 0 0 1 1 0
11 0 16.2239 28.6669 0 0 0 0 0 0 0
12 0 19.1376 37.0535 0 0 0 0 1 0 0
13 -0.891805 1995.93 256.059 0 0 0 0 1 1 0
14 -0.740257 3084.78 561.005 0 0 0 0 1 1 0
15 0 16.0088 26.199 0 0 0 0 0 0 0
16 0 15.8232 36.184 0 0 0 0 1 0 0
17 -0.913195 1997.59 243.955 0 0 0 0 1 1 0
18 -0.764723 3372.18 579.679 0 0 0 0 1 1 0
19 0 12.7668 31.3513 0 0 0 0 0 1 0
20 0 26.552 35.6247 0 0 0 0 1 1 0

Total number of rows: 22575

Table truncated, full table size 996 Kbytes.




Supplementary data files not provided

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