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Sample GSM9858 Query DataSets for GSM9858
Status Public on Jan 08, 2004
Title 50uM GA_05
Sample type RNA
 
Channel 1
Source name GA treated sample labeled by green (Cy3)
Organism Oryza sativa
Extracted molecule total RNA
 
Channel 2
Source name Non treated sample labeled by red (Cy5)
Organism Oryza sativa
Extracted molecule total RNA
 
 
Description The callus used for total RNA extraction was derived from the scutellum of the japonica rice variety Nipponbare and cultivated in Murashige and Skoog medium* containing 10 microM 2,4 dichlorophenoxyacetic acid. Such callus maintains the ability to develop roots and leaves. After the calli had been cultured in the medium for 30 d, they were transferred to a medium containing the plant hormone GA (Gibberellin) and cultured for 3 d. The concentration of the plant hormone was adjusted to 50 microM. After culturing, we used an RNeasy Plant Mini Kit (QIAGEN, Tokyo, Japan) to extract total RNA from the hormone-treated calli and from the controls. Messenger RNA (mRNA) was isolated with an Oligotex-dt30 (Super) mRNA purification kit (TaKaRa, Shiga, Japan). Purified mRNA was amplified, labeled, and hybridized 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 hormone-treated callus by the signal intensity of that from untreated callus.
*Murashige, T. and Skoog, F. 1962, A revised medium for rapid growth and bio assays with tobacco tissue cultures, Physiologia Plantarum, 15, 473–497.

Keywords = Rice
Keywords = Callus
Keywords = Phytohormone
Keywords = Gibberellin
Keywords = Germination
Lot batch = 16011538011005_S01_A01
 
Submission date Sep 08, 2003
Last update date Sep 08, 2006
Contact name Junshi Yazaki
E-mail(s) yaz@nias.affrc.go.jp
Phone 81-29-838-7007
Fax 81-29-838-7007
URL http://cdna01.dna.affrc.go.jp/RMOS/index.html
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)
GSE661 ABA or GA calli 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 1indicates Feature is a non-uniformity outlier in green channel. Flag indicating if a feature is a NonUniformity Outlier or not.
QUALITY4 1indicates Feature is a non-uniformity outlier in red channel. Flag indicating if a feature is a NonUniformity Outlier or not.
QUALITY5 1indicates 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 1indicates 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.

Data table
ID_REF VALUE NormCH1 NormCH2 QUALITY1 QUALITY2 QUALITY3 QUALITY4 QUALITY5 QUALITY6
1 -0.102103 118587 93741.8 0 0 0 0 1 1
2 -0.168945 89897.1 60925.6 0 0 0 0 1 1
3 -0.149882 133.312 94.4035 0 0 0 0 1 1
4 0 13.9985 10.8867 0 0 0 0 0 0
5 -0.105358 131102 102861 0 0 0 0 1 1
6 -0.164142 93719.3 64222.5 0 0 0 0 1 1
7 0 13.6569 11.1591 0 0 0 0 1 1
8 -0.327427 24.0403 11.3113 0 0 0 0 1 1
9 -0.103534 135008 106371 0 0 0 0 1 1
10 -0.156474 98730.3 68861.5 0 0 0 0 1 1
11 0 13.7822 11.0576 0 0 0 0 1 1
12 0 14.783 10.309 0 0 0 0 0 0
13 -0.110353 140784 109195 0 0 0 0 1 1
14 -0.149499 96182.2 68170.4 0 0 0 0 1 1
15 -0.107762 14.8064 11.5528 0 0 0 0 1 1
16 0 14.0119 10.8763 0 0 0 0 0 0
17 -0.120204 148234 112394 0 1 0 0 1 1
18 -0.147662 103545 73700.3 0 0 0 0 1 1
19 0 13.9976 10.8875 0 0 0 0 0 1
20 0 14.5224 10.494 0 0 0 0 0 0

Total number of rows: 22575

Table truncated, full table size 960 Kbytes.




Supplementary data files not provided

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