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Sample GSM377046 Query DataSets for GSM377046
Status Public on Apr 30, 2009
Title UO126_3_24HR
Sample type RNA
 
Source name UO126-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 10 uM UO126 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 24 hrs.
Growth protocol 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.
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 49.7169 P 0.0103167
AFFX-BioB-M_at 57.1883 P 0.000753643
AFFX-BioB-3_at 39.4315 P 0.0138105
AFFX-BioC-5_at 162.11 P 7.00668e-05
AFFX-BioC-3_at 168.738 P 4.42873e-05
AFFX-BioDn-5_at 239.942 P 6.02111e-05
AFFX-BioDn-3_at 853.201 P 0.000662269
AFFX-CreX-5_at 2020.35 P 5.16732e-05
AFFX-CreX-3_at 2831.04 P 4.42873e-05
AFFX-DapX-5_at 109.14 P 0.000146581
AFFX-DapX-M_at 189.256 P 0.00141043
AFFX-DapX-3_at 205.848 P 0.00010954
AFFX-LysX-5_at 18.5402 P 0.0012475
AFFX-LysX-M_at 28.4698 A 0.165861
AFFX-LysX-3_at 67.7051 P 0.000224668
AFFX-PheX-5_at 14.5077 A 0.147939
AFFX-PheX-M_at 23.9332 P 0.0336773
AFFX-PheX-3_at 37.627 P 0.00762003
AFFX-ThrX-5_at 23.1073 A 0.083592
AFFX-ThrX-M_at 34.1799 P 0.00687065

Total number of rows: 45101

Table truncated, full table size 1374 Kbytes.




Supplementary file Size Download File type/resource
GSM377046.CEL.gz 3.9 Mb (ftp)(http) CEL
GSM377046.CHP.gz 244.2 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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