|
| Status |
Public on Jul 13, 2007 |
| Title |
Arabidopsis roots, air treatment, replica 2 |
| Sample type |
RNA |
| |
|
| Source name |
Arabidopsis roots. Air treatment control.
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Wild-type Arabidopsis seeds (Col-0) were germinated in the dark for 72 hours in sterile vertical plates. Hydrocarbon-free air was flushed through the plates with seedlings for four additional hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIzol Reagent (Invitrogene Life Technologies) and then further purified using RNasy Mini Kit (QIAGEN)
|
| Label |
biotin
|
| Label protocol |
cRNA synthesis and labeling were performed according to manufacturers' (Affymetrix)
recommendations, except that the labeling reactions were scaled down 50%.
|
| |
|
| Hybridization protocol |
Hybridization and washes were performed according to Affymetrix recommendations.
Affymetrix GeneChip Fluidics Station and Afymetrix GeneChip hybridization Oven 640 were used.
|
| Scan protocol |
The Affymetrix GeneChip Scanner was used according to the manufactirers' recommendations.
|
| Description |
Wild-type Col-0 seeds were surface-sterilized and deposited onto a Nylon membrane (Sefar filtration, 03-100/47) that had been previously autoclave-sterilized and laid on the surface of sterile AT plates. Seeds were stratified for three days at 4ºC in the dark, and then exposed to light for one hour at room temperature. Plates with seeds were placed in a vertical orientation and incubated for three days in the dark at 22ºC.
Hydrocarbon-free air was flushed through the plates with seedlings for four hours. 50 ml of RNAlater solution was poured into the plates and the membranes with the seedlings were transferred to new plates containing 50 ml of fresh RNAlater solution. Using a razorblade, the roots were dissected from the hypocotyls while still submerged into the RNAlater solution, transferred to a microfuge tube and frozen at –80ºC.
|
| Data processing |
Data from Cel files were normalized using the gcRMA package from Bioconductor.
|
| |
|
| Submission date |
Apr 02, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Jose M Alonso |
| E-mail(s) |
[email protected]
|
| Phone |
919-515-5729
|
| Organization name |
North Carolina State University
|
| Department |
Genetics
|
| Street address |
|
| City |
Raleigh |
| State/province |
NC |
| ZIP/Postal code |
27695 |
| Country |
USA |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE7432 |
Ethylene and auxin interactions in the roots of Arabidopsis seedlings |
|
| Relations |
| Reanalyzed by |
GSE118579 |
| Reanalyzed by |
GSE119083 |
