Comment[ArrayExpressAccession]	E-GEOD-42539
MAGE-TAB Version	1.1							
Public Release Date	2013-02-08
Investigation Title	Gene expression changes in embryonic stem cells in response to Tcf15-E47							
Comment[Submitted Name]	Gene expression changes in embryonic stem cells in response to Tcf15-E47
Experiment Description	We set out to identify genes that respond rapidly to overexpression of a Tcf15-E47 heterodimeric transcription factor in mouse embryonic stem cells. Dox inducible Tcf15-E47 mouse embryonic stem cells were exposed to dox for 0, 8, 12, 24h and samples collected in duplicate.  Control parental cells were exposed to dox for 0 or 8 h and samples collected in duplicate. Total 12 samples.							
Term Source Name	ArrayExpress	EFO
Term Source File	http://www.ebi.ac.uk/arrayexpress/	http://www.ebi.ac.uk/efo/efo.owl						
Person Last Name	Lowell	Lowell	Lin					
Person First Name	Sally	Sally	Chia-Yi					
Person Email	geo@ncbi.nlm.nih.gov							
Person Affiliation	University of Edinburgh							
Person Address	MRC Centre for Regenerative Medicine, University of Edinburgh, 5 Little France Drive, Edinburgh, United Kingdom							
Person Roles	submitter							
Protocol Name	P-GSE42539-1	P-GSE42539-6	P-GSE42539-3	P-GSE42539-8	P-GSE42539-7	P-GSE42539-2	P-GSE42539-4	P-GSE42539-5
Protocol Description	ID_REF =  VALUE = limma quantile normalised log2 transformed data	Standard Illumina hybridization protocol	GMEM + LIF + FCS	Raw data was processed in R using the beadarray (Dunning et al., 2007) and limma (Smyth, 2005) packages from the Bioconductor suite (Gentleman et al., 2004). Briefly, we removed low-quality probes from the input data. The data was subsequently quantile-normalized and log2-transformed before assessing differential expression with the limma algorithms. We considered genes differentially expressed which had an FDR-adjusted p-value of at most 0.05 and a fold change of 1.5 or more for at least one time point in comparison to the 0-hour baseline.	Standard Illumina scanning protocol	Addition of 1μg/mL dox	RNA was prepared using Absolutely RNA Purification Kits (Agilent).	100 ng of RNA were reverse transcribed into ds cDNA and transcribed/amplified into biotin labeled cRNA using an Illumina TotalPrep RNA Amplification Kit (AMIL1791, Ambion)
Protocol Type	bioassay_data_transformation	hybridization	grow	feature_extraction	image_aquisition	specified_biomaterial_action	nucleic_acid_extraction	labeling
Experimental Factor Name	CELL TYPE							
Experimental Factor Type	cell type							
Publication Title	Tcf15 Primes Pluripotent Cells for Differentiation.							
Publication Author List	Davies OR, Lin CY, Radzisheuskaya A, Zhou X, Taube J, Blin G, Waterhouse A, Smith AJ, Lowell S							
PubMed ID	23395635							
Publication DOI	10.1016/j.celrep.2013.01.017							
Comment[SecondaryAccession]	GSE42539							
Comment[GEOReleaseDate]	2013-02-08							
Comment[ArrayExpressSubmissionDate]	2012-11-27							
Comment[GEOLastUpdateDate]	2013-02-14							
Comment[AEExperimentType]	transcription profiling by array							
Comment[AdditionalFile:Data1]	GSE42539_fold_change.txt							
Comment[AdditionalFile:Data2]	GSE42539_non_normalized.txt							
SDRF File	E-GEOD-42539.sdrf.txt