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Sample GSM185977 Query DataSets for GSM185977
Status Public on Jul 04, 2007
Title DMSO4_6H
Sample type RNA
 
Source name DMSO-treated embryonic primary chondrocyte cultures, incubated for 6hr
Organism Mus musculus
Characteristics DMSO-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) 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 107.843 P 0.000972149
AFFX-BioB-M_at 146.54 P 8.14279e-05
AFFX-BioB-3_at 82.7975 P 5.16732e-05
AFFX-BioC-5_at 321.96 P 5.16732e-05
AFFX-BioC-3_at 400.308 P 4.42873e-05
AFFX-BioDn-5_at 554.463 P 5.16732e-05
AFFX-BioDn-3_at 1351.67 P 8.14279e-05
AFFX-CreX-5_at 3903.98 P 5.16732e-05
AFFX-CreX-3_at 4596.86 P 4.42873e-05
AFFX-DapX-5_at 5.00432 A 0.340661
AFFX-DapX-M_at 7.29833 A 0.354453
AFFX-DapX-3_at 2.14793 A 0.749204
AFFX-LysX-5_at 4.96638 A 0.216524
AFFX-LysX-M_at 6.26781 A 0.41138
AFFX-LysX-3_at 7.2388 M 0.050229
AFFX-PheX-5_at 1.01666 A 0.981719
AFFX-PheX-M_at 0.826299 A 0.868639
AFFX-PheX-3_at 5.12466 A 0.686277
AFFX-ThrX-5_at 1.18949 A 0.883887
AFFX-ThrX-M_at 11.7297 A 0.165861

Total number of rows: 45101

Table truncated, full table size 1380 Kbytes.




Supplementary file Size Download File type/resource
GSM185977.CEL.gz 3.7 Mb (ftp)(http) CEL
GSM185977.CHP.gz 244.8 Kb (ftp)(http) CHP
GSM185977.EXP.gz 373 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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