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Series GSE9563 Query DataSets for GSE9563
Status Public on May 14, 2008
Title Translation state array analysis of Mouse embryonic stem cells and embryoid bodies
Organism Mus musculus
Experiment type Expression profiling by array
Summary Stem cell differentiation is known to involve changes in RNA expression, but little is known about translational control during differentiation. We comprehensively profiled gene expression during differentiation of embryonic stem cells (ESCs) into embyroid bodies (EBs) by integrating conventional transcriptome analysis with global assessment of ribosome loading. Differentiation was accompanied by an anabolic switch, characterized by global increases in transcript abundance, polysome content, protein synthesis rates and protein content. Furthermore, 78% of expressed transcripts showed increased ribosome loading, thereby enhancing translational efficiency. Elevated protein synthesis was accompanied by enhanced phosphorylation of eIF-4E binding protein, suggesting regulation by the mTOR pathway.
Some transcripts were under exclusive translational control, including Activated Transcription Factor 5 (ATF5) a b-zip transcription factor, Deleted in Colon Cancer (DCC) the tumor suppressor and Wnt1, the beta-catenin agonist. Parsimonious translation in ESCs may provide a layer of quality control to prevent inappropriate gene expression in the pluripotent state.
Keywords: Translation state array analysis during embryonic stem cell differentiation
 
Overall design Embryonic stem cells (ESC) maintained in an undifferentiated state and day-5 Embryoid bodies (EB) were selected for RNA was extraction and hybridization on Affymetrix 430_2 mouse expression arrays. For polysome fractionation, twelve fractions collected from the gradients were combined to form four pools. One ml of each pool (Pools: 1-4) was used for RNA isolation, labeling and hybridization for undifferentiated ESCs (UD1, UD2, UD3 and UD4) and EBs (EB1, EB2, EB3 and EB4). In parallel, total RNA was also isolated from unfractionated lysates for transcript abundance analysis. Three biological replicates of ESCs and EB cultures were used for polysome fractionation and total RNA analysis.
 
Contributor(s) Sampath P, Pritchard DK, Pabon L, Reinecke H, Schwartz SM, Morris DR, Murry CE
Citation(s) 18462695
Submission date Nov 08, 2007
Last update date Feb 11, 2019
Contact name Charles E Murry
Organization name University of Washington
Department Pathology
Street address 815 Mercer st., Rm # 454
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platforms (1)
GPL1261 [Mouse430_2] Affymetrix Mouse Genome 430 2.0 Array
Samples (30)
GSM241847 ESC, Undifferentiated, Pool-1, Biological Rep-1
GSM241848 ESC, Undifferentiated, Pool-1, Biological Rep-2
GSM241849 ESC, Undifferentiated, Pool-1, Biological Rep-3
Relations
BioProject PRJNA103381

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Supplementary file Size Download File type/resource
GSE9563_RAW.tar 91.4 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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