Comment[ArrayExpressAccession]	E-GEOD-46227
MAGE-TAB Version	1.1						
Public Release Date	2013-09-15
Investigation Title	Developmental equivalence of epiblast stem cells (EpiSCs)						
Comment[Submitted Name]	Developmental equivalence of epiblast stem cells (EpiSCs)
Experiment Description	Epiblast stem cells (EpiSCs) were derived from the epiblast or the ectoderm (epi/ect) of pre-gastrula stage to late-bud stage mouse embryos. To identify if the EpiSCs retain any original stage specific characteristics or which developmental stage of epi/ect they most closely related to, we performed microarray analysis to compare the gene expression profile of multiple EpiSC lines with that of epi/ect of 7 different stages. Eighteen EpiSC lines established from R1-129 embryos of different stages and 1 line (EpiSC9) imported were harvested in triplicate cultured separately for 3 days. The * marks the subline thawed at a different time and harvested but originated from the same embryo. EpiSC9_T is an RNA sample provided by Dr Tesar. ESCs, iPSCs and MEFs were prepared accordingly. For the epiblast samples, in order to avoid the averaging effect by pooling samples, we linearly amplified the RNA starting from a single epiblast or ectoderm.						
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	Kojima	Kojima	Tam				
Person First Name	Yoji	Yoji	Patrick				
Person Mid Initials			P				
Person Email	ykojima@cmri.org.au						
Person Affiliation	CMRI						
Person Address	Embryology, CMRI, 214 Hawkesbury Road, Westmead, NSW, Australia						
Person Roles	submitter						
Protocol Name	P-GSE46227-1	P-GSE46227-5	P-GSE46227-6	P-GSE46227-2	P-GSE46227-3	P-GSE46227-4	P-GSE46227-7
Protocol Description	Raw data of 45281 probes were extracted with BeadStudio and quantile normalized with Beadarray package on R. Non-annotated probes in Bioconductor illuminaMousev2.db package were removed and remaining 31646 probes were used for the analysis. ID_REF =  VALUE = Quantile normalized signal intensity	Standard Illumina protocol using Illumina TotalPrep kit (Ambion) starting from 230 ng total RNA. For amplified RNA, First round amplification was performed with MessageAmp II aRNA kit (Ambion) and labelled with Illumina TotalPrep kit starting from 10 ng aRNA with second round protocol in MessageAmp II aRNA kit.	Standard Illumina protocol. RNA labelling, hybridization and scanning were performed by Australian Genome Research Facility	EpiSCs were treated with collagenase to lift of from fibroblast layer. Epiblast samples were digested with trypsin followed by mechanical dissection.	Epiblast stem cells (EpiSCs) were collected between 10th to 20th passage. Epiblast samples were dissected from E5.5 to E8.25 embryos classified by morphological criteria.	Total RNA was extracted using QIAGEN RNeasy columns following standard protocol. Concentration and integrity were tested by spectrophotometry with Bioanalyser.	iScan with iScan Control Software
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	STRAIN OR LINE	CELL TYPE	PASSAGE	STAGE			
Experimental Factor Type	strain or line	cell type	passage	Stage			
Comment[SecondaryAccession]	GSE46227						
Comment[GEOReleaseDate]	2013-09-15						
Comment[ArrayExpressSubmissionDate]	2013-04-19						
Comment[GEOLastUpdateDate]	2013-09-15						
Comment[AEExperimentType]	transcription profiling by array						
Comment[AdditionalFile:Data1]	GSE46227_non-normalized_data.txt						
SDRF File	E-GEOD-46227.sdrf.txt