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Sample GSM185924 Query DataSets for GSM185924
Status Public on Jul 04, 2007
Title DEX1_6HR
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). DESCRIPTION
 
Submission date Apr 30, 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)
GSE7683 Microarray of Dexamethasone-treated primary chondrocytes identifies downstream targets of glucocorticoid signalling
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE Signal intensity
ABS_CALL N/A
DETECTION P-VALUE Statistical confidence

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 46.1879 P 0.00762003
AFFX-BioB-M_at 44.8578 P 0.00110197
AFFX-BioB-3_at 30.7547 P 0.00159257
AFFX-BioC-5_at 101.494 P 0.000126798
AFFX-BioC-3_at 140.453 P 5.16732e-05
AFFX-BioDn-5_at 250.807 P 4.42873e-05
AFFX-BioDn-3_at 556.127 P 0.000224668
AFFX-CreX-5_at 1824.13 P 5.16732e-05
AFFX-CreX-3_at 2035.3 P 4.42873e-05
AFFX-DapX-5_at 8.45396 P 0.0044838
AFFX-DapX-M_at 73.5724 P 0.00359458
AFFX-DapX-3_at 101.743 P 9.4506e-05
AFFX-LysX-5_at 0.974437 A 0.39692
AFFX-LysX-M_at 15.8965 A 0.083592
AFFX-LysX-3_at 43.6817 P 0.000296708
AFFX-PheX-5_at 0.883935 A 0.843268
AFFX-PheX-M_at 5.61577 A 0.300606
AFFX-PheX-3_at 21.0569 P 0.0429619
AFFX-ThrX-5_at 1.6235 A 0.672921
AFFX-ThrX-M_at 9.4211 A 0.0726999

Total number of rows: 45101

Table truncated, full table size 1379 Kbytes.




Supplementary file Size Download File type/resource
GSM185924.CEL.gz 4.0 Mb (ftp)(http) CEL
GSM185924.CHP.gz 243.7 Kb (ftp)(http) CHP
GSM185924.EXP.gz 371 b (ftp)(http) EXP
Raw data provided as supplementary file
Processed data included within Sample table
Processed data provided as supplementary file

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