|
| Status |
Public on Apr 24, 2008 |
| Title |
Arabidopsis, whole roots, 140 mM NaCl, 16 hour, replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
whole roots
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Ecotype: Columbia
Age: Seedling roots, 5 days after germination
Growth Media: Standard media for 4 days then transferred to media supplemented with 140 mM NaCl
Treatment length: 16 hours
|
| Treatment protocol |
Seedlings were grown for 4-5 days before transfer to standard media supplemented with 140 mM NaCl. Transfers were staggered such that all roots were harvested within 3 hours of each other on the sixth day of growth. Roots were cut with a razor blade 0.5 mm below the root/hypocotyl junction and collected into RNA extraction buffer. Approximately 15 roots were collected per replicate, with two biological replicates being performed per time point. Samples were briefly sonicated to disrupt the tissue.
|
| 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 roots were collected per replicate. Samples were 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 whole roots grown under standard conditions for 5 days and transferred to media supplemented with 140 mM NaCl for 16 hours
|
| 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) |
| GSE7642 |
Time course expression analysis of the salt stress response in Arabidopsis roots |
|
| Relations |
| Reanalyzed by |
GSE118579 |
| Reanalyzed by |
GSE119083 |
