GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM185964 Query DataSets for GSM185964
Status Public on Jul 04, 2007
Title DEX2_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 protocol Completed according to the London Regional Genomics Centre (LRGC):
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 - 6hr 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
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
Reanalyzed by GSE119085

Data table header descriptions
VALUE Signal intensity
DETECTION P-VALUE Statistical confidence

Data table
AFFX-BioB-5_at 50.8609 P 0.00844047
AFFX-BioB-M_at 61.6661 P 0.000856509
AFFX-BioB-3_at 38.8211 P 0.0103167
AFFX-BioC-5_at 130.152 P 0.00010954
AFFX-BioC-3_at 130.644 P 4.42873e-05
AFFX-BioDn-5_at 264.677 P 4.42873e-05
AFFX-BioDn-3_at 713.112 P 0.000195116
AFFX-CreX-5_at 1814 P 5.16732e-05
AFFX-CreX-3_at 2336.57 P 4.42873e-05
AFFX-DapX-5_at 21.587 P 0.00359458
AFFX-DapX-M_at 104.555 P 0.002867
AFFX-DapX-3_at 161.135 P 0.000195116
AFFX-LysX-5_at 7.57779 A 0.0956669
AFFX-LysX-M_at 28.7662 A 0.0726999
AFFX-LysX-3_at 64.5368 P 7.00668e-05
AFFX-PheX-5_at 6.99853 A 0.544587
AFFX-PheX-M_at 12.8664 A 0.147939
AFFX-PheX-3_at 34.1713 P 0.0464816
AFFX-ThrX-5_at 5.25471 A 0.645547
AFFX-ThrX-M_at 21.095 P 0.0396608

Total number of rows: 45101

Table truncated, full table size 1373 Kbytes.

Supplementary file Size Download File type/resource
GSM185964.CEL.gz 4.0 Mb (ftp)(http) CEL
GSM185964.CHP.gz 244.0 Kb (ftp)(http) CHP
GSM185964.EXP.gz 370 b (ftp)(http) EXP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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