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Sample GSM185888 Query DataSets for GSM185888
Status Public on Jul 04, 2007
Title DMSO2_24H
Sample type RNA
 
Source name DMSO-treated embryonic primary chondrocyte cultures, incubated for 24hr.
Organism Mus musculus
Characteristics DMSO-treated embryonic primary chondrocyte cultures, incubated for 24hr.
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 ARRAY-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 -vehicle treatment
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 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 106.736 P 0.000856509
AFFX-BioB-M_at 170.32 P 0.000195116
AFFX-BioB-3_at 105.754 P 0.000195116
AFFX-BioC-5_at 323.418 P 5.16732e-05
AFFX-BioC-3_at 405.799 P 4.42873e-05
AFFX-BioDn-5_at 549.649 P 5.16732e-05
AFFX-BioDn-3_at 1531.1 P 0.000258358
AFFX-CreX-5_at 3758.61 P 5.16732e-05
AFFX-CreX-3_at 3989.02 P 4.42873e-05
AFFX-DapX-5_at 54.1824 P 0.000856509
AFFX-DapX-M_at 70.7521 P 0.00933744
AFFX-DapX-3_at 117.753 P 0.000296708
AFFX-LysX-5_at 8.44264 A 0.083592
AFFX-LysX-M_at 18.7682 A 0.227636
AFFX-LysX-3_at 20.6287 P 7.00668e-05
AFFX-PheX-5_at 2.93427 A 0.772364
AFFX-PheX-M_at 2.61515 A 0.455409
AFFX-PheX-3_at 24.3764 A 0.156732
AFFX-ThrX-5_at 7.2587 A 0.749204
AFFX-ThrX-M_at 19.0309 M 0.0629293

Total number of rows: 45101

Table truncated, full table size 1373 Kbytes.




Supplementary file Size Download File type/resource
GSM185888.CEL.gz 3.9 Mb (ftp)(http) CEL
GSM185888.CHP.gz 243.8 Kb (ftp)(http) CHP
GSM185888.EXP.gz 365 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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