|
| Status |
Public on Jul 04, 2007 |
| Title |
DEX4_6H |
| Sample type |
RNA |
| |
|
| Source name |
DEX-treated embryonic primary chondrocyte cultures, incubated for 6hr
|
| Organism |
Mus musculus |
| Characteristics |
DEX-treated embryonic primary chondrocyte cultures, incubated for 6hr
|
| Biomaterial provider |
Mouse supplier: Charles River. Cultures were completed in Frank Beiers laborartory by Veronica Ulici and Claudine James
|
| Treatment protocol |
Primary monolayer chondrocytes were treated with 10-7 M dexamethasone (DEX) or the DMSO control (vehicle) diluted in fresh media supplemented with 0.25 mM ascorbic acid (Sigma) and 1 mM beta-glycerophosphate (Sigma) and incubated for up to 24 hrs
|
| Growth protocol |
Tibiae, femurs and humeri were isolated from E15.5 mouse embryos and placed in alpha-MEM media (Invitrogen) containing 0.2% Bovine Serum Albumin (BSA), 1 mM beta-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.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy extraction
|
| Label |
ONE COLOUR: SAPE
|
| Label protocol |
Completed according to the London Regional Genomics Centre (LRGC): http://www.lrgc.ca/
|
| |
|
| Hybridization protocol |
According to standard protocols used in London Regional Genomics Centre. Ontario, Canada
|
| Scan protocol |
According to standard protocols used in London Regional Genomics Centre. Ontario, Canada
|
| Description |
-6 HR TIME POINT
|
| Data processing |
Microarray data were pre-processed using the GC-RMA algorithm in Genespring GX* Expression values were further filtered by retaining only those probe sets with expression values of at least 50 in at least 25% of all conditions,
thus generating a list of 22 091 probe sets. To assess differential gene expression between treatments at both the 6 and 24 hr time points, a Welch ANOVA test with a p-value cut-off of 0.01 and a 5% false discovery rate (FDR)
reduced the data to 1158 probe sets. Subsequent 1.5-, 5- and 10-fold change filters produced lists of 162, 21 and 7 probe sets for the 6 hr time point and 399, 53 and 19 probe sets for the 24 hr time point, respectively.
The same data set was normalized in parallel using Robust Multichip Analysis using 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).
|
| |
|
| Submission date |
May 01, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Claudine James |
| E-mail(s) |
[email protected], [email protected]
|
| 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) |
| GSE7683 |
Microarray of Dexamethasone-treated primary chondrocytes identifies downstream targets of glucocorticoid signalling |
|
| Relations |
| Reanalyzed by |
GSE119085 |
