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Status |
Public on Mar 11, 2011 |
Title |
rss1-2,+NaCl_3 / WT,-NaCl_3 |
Sample type |
RNA |
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|
Channel 1 |
Source name |
rss1-2,+NaCl(test)
|
Organism |
Oryza sativa |
Characteristics |
genotype: rss1 mutant treatment: salt-stress (+NaCl)
|
Growth protocol |
Wild type and rss1-2 seedlings were grown on the MS medium in the absence or prescence of 150 mM NaCl for 7 days.
|
Extracted molecule |
total RNA |
Extraction protocol |
RNAs were extracted from 1-cm shoot basal tissues by RNeasy mini kit (Qiagen) .
|
Label |
Cy3
|
Label protocol |
400 ng RNAs were labeled by Low RNA input Linear Amplification/Labeling Kit (Agilent).
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|
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Channel 2 |
Source name |
WT,-NaCl (reference)
|
Organism |
Oryza sativa |
Characteristics |
genotype: wild type treatment: non-stress (-NaCl)
|
Growth protocol |
Wild type and rss1-2 seedlings were grown on the MS medium in the absence or prescence of 150 mM NaCl for 7 days.
|
Extracted molecule |
total RNA |
Extraction protocol |
RNAs were extracted from 1-cm shoot basal tissues by RNeasy mini kit (Qiagen) .
|
Label |
Cy5
|
Label protocol |
400 ng RNAs were labeled by Low RNA input Linear Amplification/Labeling Kit (Agilent).
|
|
|
|
Hybridization protocol |
Agilent protocol G4140-90050. 825 ng of each Cy-3- and Cy-5-labeled cRNAs were used for hybridization.
|
Scan protocol |
Agilent scanner model G2505B
|
Data processing |
The scanned images were analyzed with Feature Extraction Software v9.5.3.1 (Agilent) to obtain background-subtracted and spatially detrended Processed Signal intensities. All of raw Cy-3 and Cy-5 signals (gBGSubSignal and rBGSubSignal, respectively) were normalized by variance stabilization normalization method using R software (http://www.r-project.org/). After normalization, the relative expression levels of genes were calculated by dividing the Cy-3 values(test) by Cy-5 values(reference).
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Submission date |
Mar 10, 2011 |
Last update date |
Mar 15, 2011 |
Contact name |
Daisuke Ogawa |
Organization name |
Nagoya University
|
Department |
Bioscience and Biotechnology Center
|
Lab |
Plant Cell Function
|
Street address |
Furou-Chou, Chikusa
|
City |
Nagoya |
ZIP/Postal code |
464-8601 |
Country |
Japan |
|
|
Platform ID |
GPL6864 |
Series (1) |
GSE27884 |
Transcriptional profiling of rice salt sensitive 1 (rss1) mutant |
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