|
| Status |
Public on Dec 01, 2013 |
| Title |
S. pimpinellifolium, population 1630, control treatment, rep 3 |
| Sample type |
RNA |
| |
|
| Source name |
lateral root tissue, control treatment
|
| Organism |
Solanum pimpinellifolium |
| Characteristics |
organism: S. pimpinellifolium
tissue: lateral root tissue
population: population 1630
treatment: control treatment
|
| Treatment protocol |
Control plants were watered to keep the soil moist at all times. Drought plants were watered until the soil is fully hydrated and left unwatered until all leaves showed sign of wilting. This cycle was repeated three times.
|
| Growth protocol |
Plants were grown in commercial garden soil with natural lighting at a temperature range of 22-30oC until they started to form flower buds.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from tomato root tissue by grinding to a powder in liquid nitrogen using a modified protocol of Griffiths et al. (1999, J Exp Bot 50:793).
|
| Label |
biotin
|
| Label protocol |
100 ng of total RNA was biotin-labeled using the Affymetrix Genechip IVT Express kit (Affymetrix) following the manufacturer’s instructions.
|
| |
|
| Hybridization protocol |
The purified and labeled aRNA was fragmented and hybridized to the Affymetrix Tomato Genome Arrays overnight in Affymetrix 450 hybridization oven. The chips were washed, stained on Affymetrix Fluidics Station 450 in the following day.
|
| Scan protocol |
Chips were scanned with Affymetrix Genechip scanner 3000.
|
| Description |
P1630C3
|
| Data processing |
Arrays were normalized using the dChip software with the default setting using P1597D2 as a baseline array, which had the median probe intensity.
|
| |
|
| Submission date |
Aug 06, 2012 |
| Last update date |
Dec 01, 2013 |
| Contact name |
Takuya Nakazato |
| E-mail(s) |
nakazato.takuya1@gmail.com
|
| Phone |
(901)678-5539
|
| URL |
https://umdrive.memphis.edu/tnkazato/public/home.htm
|
| Organization name |
The University of Memphis
|
| Department |
Biological Sciences
|
| Lab |
Nakazato
|
| Street address |
3774 Walker Avenue
|
| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38152 |
| Country |
USA |
| |
|
| Platform ID |
GPL4741 |
| Series (1) |
| GSE39894 |
Comparative transcriptome analysis of responses to water deficit in Solanum lycopersicum and S. pimpinellifolium roots |
|
