|
| Status |
Public on Apr 24, 2008 |
| Title |
At_NaCl_Col-2 |
| Sample type |
RNA |
| |
|
| Source name |
root tips
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Ecotype: Columbia
Genotype: wild type
Age: Seedling roots, 5 days after germination
Growth Media: Standard media for 5 days then transferred to media supplemented with 140 mM NaCl
Treatment length: 1 hour
|
| Treatment protocol |
Seedlings were grown for 5 days before being transferred to standard media or media supplemented with 140mM NaCl. One hour after transfer, a razor blade was used to cut the root ~5 mm above the root tip. Approximately 30 roots were pooled per replicate. Two biological replicates were performed per genotype, per condition. 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 30 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 one-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 root tips of wild type plants grown under standard conditions for 5 days and transferred to standard media supplemented with 140mM NaCl for 1 hour
|
| Data processing |
MAS 5
|
| |
|
| Submission date |
Aug 15, 2007 |
| Last update date |
Aug 28, 2018 |
| 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 |
GPL198 |
| Series (1) |
| GSE8787 |
Expression analysis of the salt stress response in Arabidopsis mutants with defects in hair patterning |
|
| Relations |
| Reanalyzed by |
GSE118579 |
| Reanalyzed by |
GSE119083 |
