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Sample GSM45729 Query DataSets for GSM45729
Status Public on Mar 22, 2006
Title Cold_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 Cold_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 cold stress treatment, seedlings with planter boxes were incubation at 10 °C 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 = Cold stress
Lot batch = US22502511_16011538011054_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 -2 111174 44.1212 0 0 0 0 1 1 0
2 -2 156885 199.043 0 0 0 0 1 1 0
3 0 45.6247 33.7438 0 0 0 0 0 0 0
4 0 51.5787 33.4509 0 0 0 0 0 0 0
5 -2 112498 40.5815 0 0 0 0 1 1 0
6 -2 163738 204.101 0 0 0 0 1 1 0
7 0 45.0749 34.0621 0 0 0 0 0 1 1
8 0 44.5723 33.1701 0 0 0 0 0 0 0
9 -2 117116 37.6663 0 0 0 0 1 1 0
10 -2 169983 194.323 0 0 0 0 1 1 0
11 0 47.595 34.5295 0 0 0 0 0 0 0
12 0 47.0249 32.6191 0 0 0 0 0 0 0
13 -2 116276 60.2446 0 0 0 0 1 1 0
14 -2 167981 203.056 0 0 0 0 1 1 0
15 0 44.6892 32.8847 0 0 0 0 0 0 0
16 0 43.7618 30.9766 0 0 0 0 0 1 0
17 -2 120375 60.5054 0 0 0 0 1 1 0
18 -2 171585 187.112 0 0 0 0 1 1 0
19 0 39.3824 35.2779 0 0 0 0 0 0 0
20 0 45.6768 32.6666 0 0 0 0 0 0 0

Total number of rows: 22575

Table truncated, full table size 990 Kbytes.




Supplementary data files not provided

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