|
| Status |
Public on Mar 11, 2011 |
| Title |
rss1-2,+NaCl_1 / WT,-NaCl_1 |
| Sample type |
RNA |
| |
|
| 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).
|
| |
|
| 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).
|
| |
|
| 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 |
|
