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Sample GSM376952 Query DataSets for GSM376952
Status Public on Apr 30, 2009
Title DMSO3_24HR
Sample type RNA
 
Source name DMSO-treated embryonic primary chondrocyte cultures, incubated for 24hrs.
Organism Mus musculus
Characteristics strain: CD1
tissue: cartilage
developmental stage: embryonic 15.5 days
Biomaterial provider Mouse supplier: Charles River. Cultures were completed in Frank Beier's laboratory by Veronica Ulici and Claudine James and Lee-Anne Stanton
Treatment protocol Primary monolayer chondrocytes were treated with the DMSO control (vehicle) and diluted in fresh media supplemented with 0.25 mM ascorbic acid (Sigma) and 1 mM ß-glycerophosphate (Sigma) and incubated for 24 hrs.
Growth protocol Tibiae, femurs and humeri were isolated from E15.5 mouse embryos and placed in a-mem media (Invitrogen) containing 0.2% bovine serum albumin (BSA), 1 mm ß-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 biotin
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 DMSO is the vehicle for the pharmacological inhibitors LY294002, TSA, UO126, SB202190 and represents the experimental control.
Data processing MAS 5.0 Algorythm : "The procedure is to construct a plot of each chip's probes against the corresponding probes on the baseline chip; eliminate the highest 1% of probes (and for symmetry the lowest 1%), and fit a regression line to the middle 98% of probes (ie. estimate slope and intercept: two parameters). Transform the values in each probe, by subtracting the intercept, and dividing by the slope, so that the regression line becomes the identity ( y = x ) line." http://discover.nci.nih.gov/microarrayAnalysis/Affymetrix.Preprocessing.jsp
 
Submission date Mar 02, 2009
Last update date Apr 21, 2009
Contact name veronica ulici
E-mail(s) verau79@yahoo.com
Phone 1-519-661-3387
URL http://www.schulich.uwo.ca/research/skeletal-web/beier/old_news.htm
Organization name University of Western Ontario
Department Physiology and Pharmacology
Lab Dr. Frank Beier
Street address 1151 Richmond Street
City London
State/province Ontario
ZIP/Postal code N6A5C1
Country Canada
 
Platform ID GPL1261
Series (1)
GSE15069 Inhibitor trials in chondrocytes - MAS 5.0 normalization

Data table header descriptions
ID_REF
VALUE MAS5.0 signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), or marginal (M)
DETECTION P-VALUE detection p-value, p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 51.8533 P 0.0166701
AFFX-BioB-M_at 63.0088 P 0.00141043
AFFX-BioB-3_at 26.2402 P 0.026111
AFFX-BioC-5_at 149.458 P 0.000195116
AFFX-BioC-3_at 146.789 P 5.16732e-05
AFFX-BioDn-5_at 217.804 P 7.00668e-05
AFFX-BioDn-3_at 832.452 P 0.00110197
AFFX-CreX-5_at 2113.27 P 5.16732e-05
AFFX-CreX-3_at 2826.6 P 4.42873e-05
AFFX-DapX-5_at 70.3327 P 0.000389797
AFFX-DapX-M_at 121.468 P 0.00499819
AFFX-DapX-3_at 133.861 P 0.000126798
AFFX-LysX-5_at 11.9058 P 0.0182725
AFFX-LysX-M_at 29.296 A 0.108979
AFFX-LysX-3_at 40.4294 P 8.14279e-05
AFFX-PheX-5_at 11.3407 A 0.5
AFFX-PheX-M_at 15.5532 A 0.0676785
AFFX-PheX-3_at 24.3477 A 0.147939
AFFX-ThrX-5_at 18.5426 A 0.0780018
AFFX-ThrX-M_at 29.4814 P 0.00556451

Total number of rows: 45101

Table truncated, full table size 1374 Kbytes.




Supplementary file Size Download File type/resource
GSM376952.CEL.gz 3.9 Mb (ftp)(http) CEL
GSM376952.CHP.gz 244.3 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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