E-GEOD-7363 - Transcription profiling of mouse embryonic fibroblast serum response

Status
Submitted on 26 March 2007, released on 15 June 2008, last updated on 10 June 2011
Organism
Mus musculus
Samples (10)
Array (1)
Protocols (12)
Description
Expression data from specific translational activity and cytoplasmic localization (nuclear retention) of mRNAs of primary mouse embryonic fibroblasts (MEF) early in response to serum. The goal of the study was to roughly discriminate between different levels of RNA regulation, namely mRNA de-novo transcription, mRNA stability and degradation, mRNA nuclear retention, mRNA translation as well as miRNA expression within a defined cellular system and time point and to link these levels together in order to get a more detailed analysis of the complex RNA regulation system, the ?RNA regulome?. To make the data more stringent the same microarray platform (Affymetrix GeneChip system) for all analyses except the miRNA expression profiling were used. Nuclear and cytoplasmic RNA fractions were separated in order to get more insight into potential nuclear retention of mRNAs. In addition the cytoplasmic mRNA pool was fractionated by its polyribosomal load using sucrose density gradients. Likewise the small RNA was specifically analyzed for miRNA precursor expression and mature miRNA expression. As study system the early serum response model of primary mouse embryonal fibroblast cells was used. Affymetrix GeneChip microarrays were used to detail regulatory mechanisms of mRNA translation and localization in response to serum (2h). Experiment Overall Design: The gene expression and regulation program at the RNA level early (2h) in response to serum was studied. mRNAs was isolated from serum starved and 2h serum treated MEF cells. This experiment allowed detailed regulatory mechanisms of mRNA translational activity and cytoplasmic localization (nuclear retention) of mRNAs of MEF cells in early response to serum.
Experiment types
transcription profiling by array, unknown experiment type
Contact
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-7363.idf.txt
Sample and data relationshipE-GEOD-7363.sdrf.txt
Raw data (1)E-GEOD-7363.raw.1.zip
Processed data (1)E-GEOD-7363.processed.1.zip
Array designA-AFFY-6.adf.txt
R ExpressionSetE-GEOD-7363.eSet.r
Links