|
| Status |
Public on Jan 15, 2009 |
| Title |
pineal gland, mid-day, rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
pineal gland, mid-day
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: pineal gland
time: mid-day
strain: Sprague-Dawley
age: 2-3 months
|
| Treatment protocol |
Pineal glands and tissues were stored at -80oC prior to RNA extraction.
|
| Growth protocol |
Rats were kept on a 14 hr light:10 hr dark (14:10 LD) cycle. Pineals were taken at Zeitgeber time (ZT) 7 and ZT19. Cultured pineal glands were kept in BGJb medium for 48 hours before being treated with a vehicle (norepinephrine (1 μM), dibutyryl cAMP (0.5 or 1 mM), or forskolin (10 μM)) for 6 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions. Total RNA was subjected to DNase treatment using Turbo DNA-free.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 4 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45oC to an Affymetrix rat RAE230 2.0 GeneChip Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.
|
| Description |
in vivo pineal gland
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
|
| |
|
| Submission date |
Aug 05, 2008 |
| Last update date |
Apr 30, 2010 |
| Contact name |
David C. Klein |
| E-mail(s) |
[email protected]
|
| Phone |
3014966915
|
| Fax |
3014803526
|
| Organization name |
NICHD/NIH
|
| Department |
PDEGEN
|
| Lab |
Sect. Neuroendo.
|
| Street address |
49 Convent Dr.
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL1355 |
| Series (2) |
| GSE12343 |
Expt. C; Daily Rhythm in Expression of >600 Genes in the Rodent Pineal Gland: Dominant Role of Adrenergic/cAMP Signaling |
| GSE12344 |
Daily Rhythm in Expression of over 600 Genes in the Rodent Pineal Gland: Dominant Role of Adrenergic/cAMP Signaling |
|
