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| Status |
Public on Oct 21, 2011 |
| Title |
Expression data from C2C12 cells with or without Smad3 overexpression |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
|
| Summary |
The goal of this study was to identify genes in C2C12 myoblasts whose expression was altered by overexpression of Smad3.
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| Overall design |
Four total samples were analyzed. Two biological replicates were prepared from C2C12 cells infected with retroviral vector encoding wildtype Smad3 and exposed for 24 hours to 100 pM TGF-β. Two biological replicates were prepared from C2C12 cells infected with a control retrovirus that did not encode Smad3 (empty vector, EV) and exposed for 24 hours to 100pM TGF-β. To identify genes with altered expression between empty vector controls and cells overexpressing wild-type Smad3, we first pre-processed the four arrays using robust multiarray averaging as implemented in the R software package ‘xps’, version 1.10.2 (http://www.bioconductor.org/packages/release/bioc/html/xps.html). This preprocessing corrects for background noise and array effects, and aggregates probe data to 28,836 genes. Duplicates were averaged on the base-2 logarithm scale, and then we took differences between the averages to obtain logarithm-scale fold changes. Genes were selected which showed at least a two-fold change (raw scale) between wild-type and empty vector expressing cells. Due to the limited sample size, we did not apply any statistical tests to estimate false-discovery rate. This resulted in 79 genes that were at least two-fold higher in the wild-type Smad3-expressing C2C12 cells compared to empty vector cells and 25 genes that were at least two-fold lower in the wild-type Smad3-expressing cells than the in the empty vector cells.
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| Contributor(s) |
Hoffmann FM, Schiro MM |
| Citation(s) |
21949838 |
| Submission date |
Jul 06, 2011 |
| Last update date |
Mar 04, 2019 |
| Contact name |
Michael Hoffmann |
| E-mail(s) |
fmhoffma@wisc.edu
|
| Organization name |
University of Wisconsin-Madison
|
| Street address |
1400 University Ave
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL6246 |
[MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version] |
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| Samples (4)
|
| GSM821026 |
C2C12 infected with control EV; 24hr TGF-beta; replicate 1 |
| GSM821027 |
C2C12 infected with control EV; 24hr TGF-beta; replicate 2 |
| GSM821028 |
C2C12 infected with Smad3 retrovirus; 24hr TGF-beta; replicate 1 |
| GSM821029 |
C2C12 infected with Smad3 retrovirus; 24hr TGF-beta; replicate 2 |
|
| Relations |
| BioProject |
PRJNA143549 |
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