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Status |
Public on Aug 12, 2020 |
Title |
Mock vs D-Tagatose in shoot of rice replicate 1 |
Sample type |
RNA |
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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).
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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)
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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 |
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