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Sample GSM390831 Query DataSets for GSM390831
Status Public on Jul 30, 2010
Title OsMKK4WT DEX 12h 3
Sample type RNA
 
Channel 1
Source name OsMKK4WT DEX 12h 3
Organism Oryza sativa
Characteristics protocol: suspension cell culture
treatment: Dex
time: 12 hr
cultivar: Nipponbare
cell line: callus of the DEX inducible OsMKK4WT line
Treatment protocol Suspension cells were treated with Dexamethasone (DEX) (10 micro molar) and harvested at indicated times.
Growth protocol Calli of O. sativa L. cv. Nipponbare were generated from seed scutellum and suspension-cultured at 25˚C in N6D liquid medium and subcultured in fresh medium every 7 days. For DEX treatment, suspension cell cultures were subcultured for 3 days in a fresh medium.
Extracted molecule total RNA
Extraction protocol RNA was prepared using the Isogen (Nippongene) and RNeasy Plant Mini kit (Qiagen) following the manufacturer's recommendations. The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol Labeled cRNA was prepared from 400 ng RNA using the Low RNA Input Linear Amplification/Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
Channel 2
Source name Vector control DEX 12h 3
Organism Oryza sativa
Characteristics protocol: suspension cell culture
treatment: Dex
time: 12 hr
cultivar: Nipponbare
cell line: callus of the vector control line
Treatment protocol Suspension cells were treated with Dexamethasone (DEX) (10 micro molar) and harvested at indicated times.
Growth protocol Calli of O. sativa L. cv. Nipponbare were generated from seed scutellum and suspension-cultured at 25˚C in N6D liquid medium and subcultured in fresh medium every 7 days. For DEX treatment, suspension cell cultures were subcultured for 3 days in a fresh medium.
Extracted molecule total RNA
Extraction protocol RNA was prepared using the Isogen (Nippongene) and RNeasy Plant Mini kit (Qiagen) following the manufacturer's recommendations. The protocol includes an on-column DNase digestion. RNA was quantified using a NanoDrop ND-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy5
Label protocol Labeled cRNA was prepared from 400 ng RNA using the Low RNA Input Linear Amplification/Labeling kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
 
 
Hybridization protocol Cy3-labelled cRNA and Cy5-labelled cRNA (825ng each) were mixed, fragmented and hybridized with the rice 4x44K microarray RAP-DB (G2519F#15241) for 17 hours at 65°C using the Agilent Gene Expression Hybridization kit.
Scan protocol Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using two color scan setting for 4x44k array slides.
Description 400 ng RNAs were labeled and 825ng of Cy3- and Cy5-labeled cRNAs were used.
Data processing The scanned images were analyzed with Feature Extraction Software 9.1.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended processed signal intensities.
 
Submission date Apr 09, 2009
Last update date Mar 08, 2011
Contact name Hirohiko Hirochika
Organization name National Institute of Agrobiological Sciences
Department Division of Genome and Biodiversity Research
Street address 2-1-2 Kannondai
City Tsukuba
State/province Ibaraki
ZIP/Postal code 305-8602
Country Japan
 
Platform ID GPL6864
Series (1)
GSE15613 OsMKK4 regulated genes

Data table header descriptions
ID_REF
VALUE lowess Log10 based [gProcessedSignal/rProcessedSignal]
gProcessedSignal The propagated feature signal of CH1 (Cy3), used for computaion of log ratio
rProcessedSignal The propagated feature signal of CH2 (Cy5), used for computaion of log ratio
gIsFound Boolean flag of CH1
rIsFound Boolean flag of CH2

Data table
ID_REF VALUE gProcessedSignal rProcessedSignal gIsFound rIsFound
1 -0.118 1.69E+03 2.22E+03 1 1
2 0 0
3 0.24 3.60E+00 2.07E+00 1 1
4 0.265 3.84E+00 2.09E+00 1 1
5 0.00E+00 2.95E+00 2.11E+00 1 1
6 0.00E+00 2.96E+00 2.12E+00 1 1
7 0.00E+00 2.97E+00 2.13E+00 1 1
8 0.00E+00 2.98E+00 2.14E+00 1 1
9 0.00E+00 2.99E+00 2.15E+00 1 1
10 0.151 3.06E+00 2.16E+00 1 1
11 0.00E+00 3.01E+00 2.17E+00 1 1
12 0.00E+00 3.01E+00 2.18E+00 1 1
13 0.00879 4.03E+02 3.95E+02 1 1
14 0.174 2.26E+02 1.52E+02 1 1
15 0.00E+00 3.03E+00 2.20E+00 1 1
16 -0.207 1.46E+03 2.36E+03 1 1
17 0.219 3.65E+00 2.21E+00 1 1
18 0.104 3.33E+02 2.63E+02 1 1
19 -0.104 4.08E+01 5.19E+01 1 1
20 -0.172 3.06E+00 4.55E+00 1 1

Total number of rows: 45151

Table truncated, full table size 1509 Kbytes.




Supplementary file Size Download File type/resource
GSM390831.txt.gz 13.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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