|
| Status |
Public on Oct 15, 2012 |
| Title |
WT 0 mM NaCl, replicate 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
WT 0 mM NaCl
|
| Organism |
Oryza sativa |
| Characteristics |
cultivar: Nipponbare
genotype/variation: wild type
age: day 3
tissue: 1 mm long root tip
|
| Growth protocol |
Wild type and rss3 seedlings were grown on the MS medium in the absence or prescence of 100 mM NaCl for 3 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted from 1-mm root tips by RNeasy mini kit (Qiagen).
|
| Label |
Cy5
|
| Label protocol |
400 ng RNAs were labeled by Low RNA input Linear Amplification/Labeling Kit (Agilent).
|
| |
|
| Channel 2 |
| Source name |
WT 0 mM NaCl (reference)
|
| Organism |
Oryza sativa |
| Characteristics |
cultivar: Nipponbarre
genotype/variation: wild type
age: day 3
tissue: 1 mm long root tip
|
| Growth protocol |
Wild type and rss3 seedlings were grown on the MS medium in the absence or prescence of 100 mM NaCl for 3 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNAs were extracted from 1-mm root tips by RNeasy mini kit (Qiagen).
|
| Label |
Cy3
|
| 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-5- and Cy-3-labeled cRNAs were used for hybridization.
|
| Scan protocol |
Using Agilent scanner model G2505B.
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software v10.5.1.1 (Agilent) to obtain background-subtracted and spatially-detrended Processed Signal intensities. All of the raw Cy-5 and Cy-3 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 subtracting the Cy-5 values by Cy-3 values (reference). Relative log2 expressions were Z-scaled with R software.
|
| |
|
| Submission date |
Oct 10, 2012 |
| Last update date |
Oct 18, 2012 |
| Contact name |
yosuke toda |
| E-mail(s) |
[email protected]
|
| Organization name |
nagoya university
|
| Street address |
furo-cho chikusa-ku
|
| City |
nagoya |
| State/province |
aichi-ken |
| ZIP/Postal code |
464-8601 |
| Country |
Japan |
| |
|
| Platform ID |
GPL6864 |
| Series (1) |
| GSE41442 |
Root tip: WT vs. rss3 and -NaCl vs. +NaCl |
|
