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Sample GSM126590 Query DataSets for GSM126590
Status Public on Aug 12, 2006
Title myoblast_treated_rep2
Sample type RNA
 
Source name C2C12 myoblasts, treated with 50 mM sodium pyruvate for 72 hr
Organism Mus musculus
Characteristics Undifferentiated C2C12 myoblasts, passage #11

Treatment protocol C2C12 myoblasts were seeded in 100 mm dishes in pyruvate test media and incubated for 72 hr at 37°C. Pyruvate test media: DMEM with no sodium pyruvate supplemented with 10% fetal bovine serum, 1% antibiotics, 4 mM L-glutamine and 50 mM sodium pyruvate.
Growth protocol C2C12 myoblasts were incubated in pyruvate test media for 72 hr at 37°C.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the manufacturer's instructions (Bioarray High yield T7 DNA transcirption kit, ENZO Life Sciences, Inc.)
 
Hybridization protocol Following fragmentation, 10?g of labeled cRNA were hybridized at 45°C for approximately 16 hr to Gene Chip Mouse Genome 430 2.0 Expression Array (Affymetrix). The arrays were stained on Gene Chip Fluidics Workstation 450.
Scan protocol Gene Chips were scanned using the GeneArray Scanner 3000.
Description Gene expression data from undifferentiated C2C12 myoblasts incubated in pyruvate test media for 72 hr.
Data processing The scanned image was converted into numerical values of the signal intensity (Signal) and into categorical expression level measurement (Absolute Call) using the Affymetrix MAS 5.0 software. The MAS 5.0 statistical algorithm parameters used to attribute the Absoute Calls were set to 0.05 for Alpha 1, 0.065 for Alpha 2 and 0.015 for Tau. The software scaled the average intensity of all genes of each chip to a target intenisty of 150.
 
Submission date Aug 10, 2006
Last update date Aug 10, 2006
Contact name Reza Halse
Organization name Novartis Institutes for BioMedical Research
Street address 100 Technology Square
City Cambridge
State/province MA
ZIP/Postal code 02139
Country USA
 
Platform ID GPL1261
Series (1)
GSE5497 Pyruvate induces mitochondrial biogenesis by a PGC-1alpha independent mechanism

Data table header descriptions
ID_REF
VALUE MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
P-VALUE

Data table
ID_REF VALUE ABS_CALL P-VALUE
AFFX-BioB-5_at 174.2 P 0.000446
AFFX-BioB-M_at 267.9 P 0.000044
AFFX-BioB-3_at 162.4 P 0.000081
AFFX-BioC-5_at 561.4 P 0.000052
AFFX-BioC-3_at 644.9 P 0.000044
AFFX-BioDn-5_at 950.4 P 0.000044
AFFX-BioDn-3_at 2847.4 P 0.000044
AFFX-CreX-5_at 5154.1 P 0.000052
AFFX-CreX-3_at 6323.5 P 0.000044
AFFX-DapX-5_at 8.4 A 0.275146
AFFX-DapX-M_at 8.4 A 0.617401
AFFX-DapX-3_at 6.4 A 0.686277
AFFX-LysX-5_at 5.8 A 0.455413
AFFX-LysX-M_at 11.7 A 0.48511
AFFX-LysX-3_at 9.6 M 0.062929
AFFX-PheX-5_at 2.5 A 0.686277
AFFX-PheX-M_at 0.9 A 0.772364
AFFX-PheX-3_at 24.5 A 0.216524
AFFX-ThrX-5_at 9.7 A 0.205732
AFFX-ThrX-M_at 1 A 0.891021

Total number of rows: 45101

Table truncated, full table size 1194 Kbytes.




Supplementary data files not provided

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