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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
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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) |
- Schiro MM, Stauber SE, Peterson TL, Krueger C et al. Mutations in protein-binding hot-spots on the hub protein Smad3 differentially affect its protein interactions and Smad3-regulated gene expression. PLoS One 2011;6(9):e25021. PMID: 21949838
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Submission date |
Jul 06, 2011 |
Last update date |
Mar 04, 2019 |
Contact name |
Michael Hoffmann |
E-mail(s) |
fmhoffma@wisc.edu
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Organization name |
University of Wisconsin-Madison
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Street address |
1400 University Ave
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City |
Madison |
State/province |
WI |
ZIP/Postal code |
53706 |
Country |
USA |
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Platforms (1) |
GPL6246 |
[MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version] |
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Samples (4)
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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 |
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Relations |
BioProject |
PRJNA143549 |