NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM310039 Query DataSets for GSM310039
Status Public on Jan 15, 2009
Title pineal gland, mid-night, rep 1
Sample type RNA
 
Source name pineal gland, mid-night
Organism Rattus norvegicus
Characteristics tissue: pineal gland
time: mid-night
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

Data table header descriptions
ID_REF
VALUE MAS 5.0-calculated signal intensity
ABS_CALL Call in an absolute analysis that indicates if the signal was present (P), absent (A), or marginal (M)

Data table
ID_REF VALUE ABS_CALL
1367452_at 1234.59253 P
1367453_at 556.967957 P
1367454_at 1600.50134 P
1367455_at 1207.99402 P
1367456_at 1333.87415 P
1367457_at 388.798706 P
1367458_at 131.591431 P
1367459_at 2195.96069 P
1367460_at 1426.27722 P
1367461_at 667.254089 P
1367462_at 486.176025 P
1367463_at 486.087006 P
1367464_at 394.436615 P
1367465_at 1809.83313 P
1367466_at 925.309448 P
1367467_at 622.199219 P
1367468_at 397.697479 P
1367469_at 2021.16895 P
1367470_at 671.4021 P
1367471_at 917.667908 P

Total number of rows: 31099

Table truncated, full table size 697 Kbytes.




Supplementary file Size Download File type/resource
GSM310039.CEL.gz 2.8 Mb (ftp)(http) CEL
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap