|
| Status |
Public on Sep 01, 2013 |
| Title |
Arabidopsis, whole root, standard conditions for 20 hours, replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
whole root
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia
age: Seedling roots, 6 days after germination
growth media: Standard media for 5 days, transferred to standard media for 20 hour
|
| Treatment protocol |
Wild type plants of columbia were germinated and grown for 5 days, and then they were transferred to standard or salt media (standard media with 140mM NaCl added) for 1hr, 3hrs, 20hrs, 2days, 4days and 8days before harvesting.
|
| Growth protocol |
Seeds were surface sterilized with 20% Bleach and 0.1% Tween for 5 minutes and then rinsed 3 times with sterile water. Seeds were stratified at 4˚C for 2 days before being planted on standard media. Standard media is 1X concentration Murashige and Skoog salt mixture (Caisson laboratories), 0.5g/L MES, 1% sucrose, 1% agar and adjusted to pH 5.7 with KOH. Salt media is standard media with 140mM NaCl added. Nylon mesh was placed on top of the solidified media and seeds were evenly placed on the mesh at a density of ~20 seeds/cm in two rows.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNAeasy Mini Kit (Qiagen GmbH).
|
| Label |
Cy3
|
| Label protocol |
Fluorescent cRNA were generated using Agilent's Quick Amp Labeling Kit
|
| |
|
| Hybridization protocol |
Arrays were hybridized, blocked, washed, and post processed with Agilent One Color RNA Spike-In Kit. And the procesures were performed in the microarray facilities located at the Biopolis Shared Facilities, Agency of Science and Technology Research, Singapore
|
| Scan protocol |
The scanned images were analyzed with Feature Extraction Software (Agilent) using default parameters (protocol GE1-v5_10 and Grid:021169_D_F_20080807) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| Description |
Gene expression data from whole roots on standard condition for 20 hour control
|
| Data processing |
Genespring GX10 for data normalization
|
| |
|
| Submission date |
Apr 18, 2013 |
| Last update date |
Sep 01, 2013 |
| Contact name |
Jose Ramon Dinneny |
| E-mail(s) |
jdinneny@carnegiescience.edu
|
| Organization name |
Carnegie Institution for Science, Department of Plant Biology
|
| Department |
Plant Biology
|
| Lab |
Jose R. Dinneny
|
| Street address |
260 Panama St
|
| City |
Stanford |
| State/province |
United States |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL12621 |
| Series (1) |
| GSE46208 |
A spatiotemporal understanding of growth regulation during the salt-stress response (Agilent) |
|
