|
| Status |
Public on Jan 31, 2008 |
| Title |
SB90_1 |
| Sample type |
RNA |
| |
|
| Source name |
SB90-treated embryonic primary chondrocyte cultures, incubated for 24hrs.
|
| Organism |
Mus musculus |
| Characteristics |
Tibiae, femurs and humeri were isolated from E15.5 mouse embryos and placed in α-MEM media (Invitrogen) containing 0.2% Bovine Serum Albumin (BSA), 1 mM β-glycerophosphate,
0.05 mg/ml ascorbic acid and penicillin/streptomycin incubated at 37°C in a humidified 5% CO2 incubator overnight. The following morning media was removed and the bones placed in 4 ml
of 0.25% trypsin-EDTA (Invitrogen) for 15 min at 37oC. Trypsin was subsequently replaced with 1 mg/ml collagenase P (Roche) in DMEM / 10% fetal bovine serum (Invitrogen), and cells
were incubated at 37°C with rotation at 100 rpm for 90 min. Following digestion, the cell suspension was centrifuged for 5 min at 1000 rpm, and the collagenase containing supernatant was decanted.
Chondrocytes were resuspended in media containing 2:3 DMEM:F12, 10% fetal bovine serum, 0.5 mM L-glutamine, and penicillin/streptomycin (25 units/ml).
Cells were seeded in 6-well NUNC plates at a density of 2.5X104 cells per ml and incubated overnight. Primary monolayer chondrocytes were treated with 10 µM
SB90 reconstituted in DMSO and diluted in fresh media supplemented with 0.25 mM ascorbic acid (Sigma) and 1 mM β-glycerophosphate (Sigma) and incubated for up to 24 hrs.
|
| Biomaterial provider |
Mouse supplier: Charles River. Cultures were completed in Frank Beier's laboratory by Veronica Ulici and Claudine James and Lee-Anne Stanton
|
| Treatment protocol |
SEE CHARACTERISTICS
|
| Growth protocol |
SEE CHARACTERISTICS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy extraction
|
| Label |
SAPE
|
| Label protocol |
Completed according to the London Regional Genomics Centre (LRGC): http://www.lrgc.ca/
|
| |
|
| Hybridization protocol |
LRGC specifications
|
| Scan protocol |
M.A.S. 5.0-see LRGC specifications
|
| Description |
AFFY544
|
| Data processing |
Microarray data were pre-processed RMAEXPRESS software v.0.4.1 developed by B. Bolstad, University of California, Berkeley. Background adjustment and quantile
normalization parameters were selected for data processing. Logarithmically transformed expression values were used to implement Gene Set Enrichment Analysis (GSEA) (Subramanian et al., 2005, PNAS).
|
| |
|
| Submission date |
Jul 11, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Claudine James |
| E-mail(s) |
claudinegj@hotmail.com, fbeier@uwo.ca
|
| Phone |
(519)661-3387
|
| Fax |
(519)850-2459
|
| Organization name |
University of Western Ontario
|
| Department |
Physiology and Pharmacology
|
| Lab |
Frank Beier/ CIHR Group in Skeletal Development and Remodeling
|
| Street address |
1151 Richmond Street, Suite 2
|
| City |
London |
| State/province |
Ontario |
| ZIP/Postal code |
N6A 5C1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
|
| Relations |
| Reanalyzed by |
GSE119085 |
