|
| Status |
Public on Apr 24, 2008 |
| Title |
Arabidopsis, root cells, columella root cap, standard conditions, replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
Protoplasted and FACS sorted root cells
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Ecotype: Columbia
Age: Seedling roots, 6 days after germination
GFP-reporter: PET111
Growth Media: Standard media
|
| Treatment protocol |
Samples were prepared as in Birnbaum et al. (2005) for roots grown under standard conditions. For salt treated samples, roots were transferred to 140 mM NaCl for 1hr before protoplasting. Three replicates were performed per cell type, per condition. In order to test for the effects of sorting, Col-0 roots were protoplasted after being treated for 1 hour with or without salt treatment. Cells were passed through the FACS device with all cells being collected.
|
| 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 at a density of ~20 seeds/cm in two rows.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
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 isolated columella root cap cells
|
| Data processing |
MAS 5
|
| |
|
| Submission date |
Apr 26, 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) |
| GSE7641 |
Expression analysis of root cell-types after treatment with salt |
|
| Relations |
| Reanalyzed by |
GSE118579 |
| Reanalyzed by |
GSE119083 |
