|
| Status |
Public on Apr 24, 2008 |
| Title |
Arabidopsis, root, longitudinal zone 4, standard conditions, replicate 7 |
| Sample type |
RNA |
| |
|
| Source name |
root tissue
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Ecotype: Columbia
Age: Seedling roots, 5 days after germination
Growth Media: Standard media
|
| Treatment protocol |
Seedlings were grown for 5 days before transfer to standard media or standard media supplemented with 140mM NaCl. One hour after transferring seedlings to media, roots were cut into 4 regions using a razor blade.
|
| Growth protocol |
Seeds were surface sterilized with 50% 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 varying amounts of NaCl added. Nylon mesh was placed on top of the solidified media and seeds were evenly placed on the mesh in a single row at a density of ~2/cm for all experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Approximately 15 sections were dissected for each replicate and pooled. Samples were collected into RNA extraction buffer and briefly sonicated to disrupt the tissue. RNA was extracted using the RNAeasy Micro Kit (Qiagen GmbH).
|
| Label |
biotin
|
| Label protocol |
Fragmented cRNA probes were prepared using the two-cycle amplification protocol by Affymetrix.
|
| |
|
| Hybridization protocol |
Standard Affymetrix protocols. Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.
|
| Scan protocol |
Standard Affymetrix protocols. Samples were submitted to Expression Analysis Inc. (Durham, NC) for hybridization to Affymetrix ATH1 microarrays.
|
| Description |
Gene expression data from longitudinal zone 4 isolated from roots grown under standard conditions for 5 days then transferred to standard media for 1hr
|
| Data processing |
MAS 5
|
| |
|
| Submission date |
Apr 26, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Jose Ramon Dinneny |
| E-mail(s) |
[email protected]
|
| 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 |
GPL198 |
| Series (1) |
| GSE7639 |
Expression analysis of root developmental zones after treatment with salt |
|
| Relations |
| Reanalyzed by |
GSE118579 |
| Reanalyzed by |
GSE119083 |
