Comment[ArrayExpressAccession]	E-GEOD-43420
MAGE-TAB Version	1.1							
Public Release Date	2013-03-01
Investigation Title	Transcriptional responses to Wnt pathway stimulation in mouse embryonic stem cells cultured in serum+LIF condition							
Comment[Submitted Name]	Transcriptional responses to Wnt pathway stimulation in mouse embryonic stem cells cultured in serum+LIF condition
Experiment Description	The objective of this study was to identify genes regulated by canonical Wnt signaling in  mouse embryonic stem cells (ESCs).Canonical Wnt signaling supports the pluripotency of mouse ESCs but also promotes differentiation of early mammalian cell lineages. To explain these paradoxical observations, we explored the gene regulatory networks at play. Canonical Wnt signaling is intertwined with the pluripotency network comprising Nanog, Oct4, and Sox2 in mouse ESCs. In defined media supporting the derivation and propagation of mouse ESCs, Tcf3 and β-catenin interact with Oct4; Tcf3 binds to Sox motif within Oct-Sox composite motifs that are also bound by Oct4-Sox2 complexes. Further, canonical Wnt signaling up-regulates the activity of the Pou5f1 distal enhancer via the Sox motif in mouse ESCs. When viewed in the context of published studies on Tcf3 and β-catenin mutants, our findings suggest that Tcf3 counters pluripotency by competition with Sox2 at these sites, and Tcf3 inhibition is blocked by β-catenin entry into this complex. Wnt pathway stimulation also triggers β-catenin association at regulatory elements with classic Lef/Tcf motifs associated with differentiation programs. The failure to activate these targets in the presence of a MEK/ERK inhibitor essential for mouse ESC culture suggests that MEK/ERK signaling and canonical Wnt signaling combine to promote mouse ESC differentiation. Triplicates of mouse embryonic stem cells cultured with GSK3 inhibitor CHIR99021 or with Wnt pathway inhibitor XAV939.							
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	Zhang	Ohba	McMahon					
Person First Name	Xiaoxiao	Shinsuke	Andrew					
Person Mid Initials			P					
Person Email	zhangxiaoxiaozxx@gmail.com							
Person Affiliation	Harvard University							
Person Address	Molecular and Cellular Biology, Harvard University, 7 Divinity Ave., Cambridge, MA, USA							
Person Roles	submitter							
Protocol Name	P-GSE43420-1	P-GSE43420-6	P-GSE43420-3	P-GSE43420-8	P-GSE43420-7	P-GSE43420-2	P-GSE43420-4	P-GSE43420-5
Protocol Description	ID_REF =  VALUE = RMA normalized	10 mg of fragmented biotinylated cRNA was fragmented and hybridized for 16 hr at 45C on mouse genechip 1.0 st arrays. Arrays were washed and stained in the Affymetrix Fluidics Station 450.	All ESCs were maintained in complete ES media (15% fetal bovine serum, 0.1 mM non-essential amino acids, 0.1 mM b-mercaptoethanol, 2 mM L-glutamine, 10^3 units/ml LIF, and 1X nucleotide mix in DMEM high glucose) with feeder cells isolated from DR4 mice	Data were analyzed by RMA in R.	Arrays were scanned with the GeneChip Scanner 3000 7G.	Cells were treated for 24 hours with CHIR99021 (3μM) or XAV939 (1 μM)	Total RNA was isolated using TRIZOL Reagent (Invitrogen, 15596-026) and purified by RNeasy Mini Kit (QIAGEN, 74104).	300 ng of total RNA were labeled for each sample using the GeneChip WT cDNA Synthesis and Amplification Kit and WT Terminal Labeling Kit (Affymetrix, 900673 and 900671).
Protocol Type	bioassay_data_transformation	hybridization	grow	feature_extraction	image_aquisition	specified_biomaterial_action	nucleic_acid_extraction	labeling
Experimental Factor Name	TREATMENT							
Experimental Factor Type	treatment							
Comment[SecondaryAccession]	GSE43420							
Comment[GEOReleaseDate]	2013-03-01							
Comment[ArrayExpressSubmissionDate]	2013-01-10							
Comment[GEOLastUpdateDate]	2013-03-03							
Comment[AEExperimentType]	transcription profiling by array							
SDRF File	E-GEOD-43420.sdrf.txt