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Sample GSM4044533 Query DataSets for GSM4044533
Status Public on Aug 12, 2020
Title Mock vs D-Tagatose in shoot of rice replicate 1
Sample type RNA
 
Channel 1
Source name Rice shoot, treated with D-Tagatose at 2-leaf stage
Organism Oryza sativa
Characteristics cultivar: cv. Nipponbare
treatment: grown for 5 days with water, then for 2 days with D-Tagatose
tissues: shoot
tissues: shoot
Treatment protocol Seedlings of two-leaf-stage rice plants were cultured in Kimura-B liquid medium with or without 0.5 mM D-Tagatose for 2 days.
Growth protocol Seeds were germinated in 0.2%Benlate for 1 day and deionized water for 1 day at 30°C under dark, and grown for 5 days on water.
Extracted molecule total RNA
Extraction protocol Matufacture's instruction of Qiagen RNeasy Plant Mini Kit
Label Cy5
Label protocol Low RNA Input Linear Amplification/Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions
 
Channel 2
Source name Rice shoot, non-sugar-treated at 2-leaf stage
Organism Oryza sativa
Characteristics cultivar: cv. Nipponbare
treatment: grown for 5 days with water, then for 2 days with water
Treatment protocol Seedlings of two-leaf-stage rice plants were cultured in Kimura-B liquid medium with or without 0.5 mM D-Tagatose for 2 days.
Growth protocol Seeds were germinated in 0.2%Benlate for 1 day and deionized water for 1 day at 30°C under dark, and grown for 5 days on water.
Extracted molecule total RNA
Extraction protocol Matufacture's instruction of Qiagen RNeasy Plant Mini Kit
Label Cy3
Label protocol Low RNA Input Linear Amplification/Labeling Kit (Agilent Technologies) according to the manufacturer’s instructions
 
 
Hybridization protocol Cy3- and Cy5-labbelled samples (500 μl) were equally mixed and used for hyblidaization. Hybridization was conducted at 65°C, 10 rpm, 17h
Scan protocol The plate was washed with SSC series, removed excess of buffer with N2 gus and scanned with an Agilent Microarray Scanner (Agilent Technologies).
Description Biological replicate 1 of 3
Data processing Feature extraction software (version 9.1; Agilent Technologies) was used to delineate and measure the signal intensity of each spot in the array, and to normalize intensities. The background was measured around each spot as local background, calculated by the Feature Extraction software. Statistical data extraction processes were performed according to the manufacturer’s instructions.
Please note that each processed data file contains the following additional data columns:
NormCH1: Dye-normalized signal intensity of CH1 (rProcessedSignal)
NormCH2: Dye-normalized signal intensity of CH2 (gProcessedSignal)
MeanSignalCH1: Raw mean CH1 signal of feature (rMeanSignal)
MeanSignalCH2: Raw mean CH2 signal of feature (gMeanSignal)
 
Submission date Aug 26, 2019
Last update date Aug 12, 2020
Contact name Kazuya Akimitsu
E-mail(s) akimitsu.kazuya@kagawa-u.ac.jp
Phone +81-87-891-3131
Organization name Kagawa University
Department Faculty of Agriculture
Lab Plant pathology
Street address Ikenobe 2393
City Miki
State/province Kagawa
ZIP/Postal code 761-0795
Country Japan
 
Platform ID GPL6864
Series (1)
GSE136313 Rice plants treated with D-Tagatose

Data table header descriptions
ID_REF
VALUE log10 (NormCH1 / NormCH2) (LogRatio); Significance P value of the value computed for a feature
Pvalue

Data table
ID_REF VALUE Pvalue
1 0.091178757 0.141287443
2 0 1
3 0 1
4 0 1
5 0 1
6 0 1
7 0 1
8 0 1
9 0 1
10 0 1
11 0 1
12 -0.185933941 0.190697774
13 0.106796422 0.131532759
14 0.282203339 0.019201637
15 0 1
16 0.013120499 0.831781805
17 -0.069007902 0.265501141
18 0.025023561 0.71347269
19 -0.036677958 0.860750541
20 0 1

Total number of rows: 45151

Table truncated, full table size 1196 Kbytes.




Supplementary file Size Download File type/resource
GSM4044533_D-tagatose_2D_rep1_matrix-file.xls.gz 2.7 Mb (ftp)(http) XLS
GSM4044533_US22502560_251524111387_S01_GE2-v5_95_Feb07_1_1.txt.gz 14.1 Mb (ftp)(http) TXT
Processed data included within Sample table

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