|
| Status |
Public on Jun 24, 2007 |
| Title |
CCA1-34_dark_late_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
CCA1-34 6 day old seedling, 120 minutes after transfer to darkness, night
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
Strain: CCA1-34 (CCA1-OX)
Age: 6 Days
Tissue: Whole Seedling
|
| Growth protocol |
About 100 seedlings were grown on a filter paper laid on 1xMSMO, 3% sucrose, 0.9% agar (Cat # A1296, Sigma) in 6 cm round Petri dishes. Seeds were stratified for four days at 4 ˚C and then incubated for four days at 20˚C under short day (8 hours light: 16 hours dark) conditions. The Petri dishes were tilted about 30˚ from vertical in a growth chamber equipped with red and blue LEDs (70.7 µE red light and 15.3 µE blue light). Starting from subjective dawn at day five, cycles of 160 min light and 320 min dark were given for three days. This sample was collected 1240 minutes after subjective dawn on the sixth day; 120 minutes after lights-off.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples were transferred to 1.5 ml tube and immediately frozen by liquid nitrogen and stored at –80˚C. Samples were collected using infra-red (IR) goggles (Night Vision model NCB4, Night Owl Optics, NY) to avoid light exposure. 100 mg frozen tissue samples were ground by pestle and electric motor. Total RNA was extracted using RNeasy Plant Mini kit (Qiagen, CA).
|
| Label |
biotin
|
| Label protocol |
From 5 µg of total RNA, cRNA was made and labeled with biotin (Affymetrix, CA) according to protocol described by Schmid, M. et al. Nat. Genet. 37, 501-506 (2005).
|
| |
|
| Hybridization protocol |
Hybridization was performed in a Affymetrix 640 Hybridization Oven using standard Affymetrix protocols.
|
| Scan protocol |
Scans were performed on a Affymetrix GeneChip 3000 scanner.
|
| Description |
Seedlings were entrained in short days for four days and then transferred to cycles of 160 min light and 320 min dark for three days. This sample was collected two hours after lights off, 1240 minutes after dawn on the sixth day.
|
| Data processing |
Data was normalized using the RMA protocol.
|
| |
|
| Submission date |
Jan 29, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Julin N Maloof |
| E-mail(s) |
jnmaloof@ucdavis.edu
|
| Phone |
(530) 752-8077
|
| Fax |
(530) 752-5410
|
| URL |
http://malooflab.openwetware.org/
|
| Organization name |
University of California, Davis
|
| Department |
Plant Biology
|
| Street address |
One Shields Ave
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL198 |
| Series (1) |
| GSE6906 |
Rhythmic growth explained by coincidence between internal and external cues |
|
| Relations |
| Reanalyzed by |
GSM540924 |
| Reanalyzed by |
GSE118579 |
| Reanalyzed by |
GSE119083 |
