Project name: Mus musculus

Description: The goal of this study was to identify genes in C2C12 myoblasts whose expression was altered by overexpression of Smad3.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.

Data type: Transcriptome or Gene expression

Sample scope: Multiisolate

Relevance: ModelOrganism

Release date: 2011-10-21

Last updated: 2011-07-06