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Sample GSM209843 Query DataSets for GSM209843
Status Public on Jan 31, 2008
Title TSA_1
Sample type RNA
 
Source name TSA-treated embryonic primary chondrocyte cultures, incubated for 24hrs.
Organism Mus musculus
Characteristics Tibiae, femurs and humeri were isolated from E15.5 mouse embryos and placed in α-MEM media (Invitrogen) containing 0.2% Bovine Serum Albumin (BSA), 1 mM β-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. Primary monolayer chondrocytes were treated with 100 µM
TSA reconstituted in DMSO and diluted in fresh media supplemented with 0.25 mM ascorbic acid (Sigma) and 1 mM β-glycerophosphate (Sigma) and incubated for up to 24 hrs.
Biomaterial provider SB90-treated embryonic primary chondrocyte cultures, incubated for 24hrs.
Treatment protocol SEE CHARACTERISTICS
Growth protocol SEE CHARACTERISTICS
Extracted molecule total RNA
Extraction protocol Qiagen RNeasy extraction
Label SAPE
Label protocol Completed according to the London Regional Genomics Centre (LRGC): http://www.lrgc.ca/
 
Hybridization protocol LRGC specifications
Scan protocol M.A.S. 5.0-see LRGC specifications
Description AFFY543
Data processing Microarray data were pre-processed 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) (Subramanian et al., 2005, PNAS).
 
Submission date Jul 11, 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)
GSE8488 Inhibitor Trials
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE RMAExpress-processed signal intensity

Data table
ID_REF VALUE
1415670_at 10.597436
1415671_at 11.965004
1415672_at 11.519104
1415673_at 8.785246
1415674_a_at 10.027695
1415675_at 10.062095
1415676_a_at 12.479217
1415677_at 10.184
1415678_at 10.620778
1415679_at 10.850957
1415680_at 9.405112
1415681_at 10.723121
1415682_at 9.19625
1415683_at 11.371754
1415684_at 9.838172
1415685_at 8.785565
1415686_at 10.611551
1415687_a_at 11.707153
1415688_at 10.590118
1415689_s_at 9.022551

Total number of rows: 45101

Table truncated, full table size 899 Kbytes.




Supplementary file Size Download File type/resource
GSM209843.CEL.gz 3.9 Mb (ftp)(http) CEL
Processed data included within Sample table
Raw data provided as supplementary file

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