|
| Status |
Public on May 02, 2017 |
| Title |
4C_12h_12h |
| Sample type |
RNA |
| |
|
| Source name |
T87 cultured cell
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
cell line: T87
|
| Treatment protocol |
Cells were collected prior to the cordycepin treatment (0 h) and 0.5, 2, 4 h after cordycepin addition in the control cells. Incubation time after cordycepin addition was 4, 8 and 12 h in the cold treated cell.
|
| Growth protocol |
Arabidopsis T87 suspension cells derived from Columbia ecotype were grown in JPL media (Axelos et al. 1992) at 22°C under constant light (80 μmol m–2 s–1) with orbital shaking (120 rpm). Cells were transferred to new medium every two weeks at ~20-fold dilution. Seven days after subculturing, cells were divided into two conditions. Control cells were grown under the same condition, and the cold treated cells were transferred to 4°C under dim light (40 μmol m–2 s–1) and cultured for 12, 24 and 36 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the cells by using RNeasy Plant Mini kit (Qiagen)
|
| Label |
biotin
|
| Label protocol |
All procedures were carried out following the Affymetrix GeneChip Expression Analysis Technical Manual.
|
| |
|
| Hybridization protocol |
All procedures were carried out following the Affymetrix GeneChip Expression Analysis Technical Manual.
|
| Scan protocol |
All procedures were carried out following the Affymetrix GeneChip Expression Analysis Technical Manual.
|
| Data processing |
Data were analyzed by Bioconductor of R. To extract the expression level of the probe set, the Robust Multichip Average (RMA) method implemented in the Affy package was used. Log-transformed RMA value was delogged and then normalized with the average expression level of poly(A) RNA controls derived from Bacillus subtilis genes.
|
| |
|
| Submission date |
May 16, 2016 |
| Last update date |
May 02, 2017 |
| Contact name |
Katsuhiko Mineta |
| E-mail(s) |
katsuhiko.mineta@kaust.edu.sa
|
| Organization name |
King Abdullah University of Science and Technology
|
| Street address |
4700 KAUST
|
| City |
Thuwal |
| ZIP/Postal code |
23955-6900 |
| Country |
Saudi Arabia |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE81477 |
Coordinated Regulations of mRNA Synthesis and Decay during Cold Acclimation in Arabidopsis Cells. |
|
