REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse monoclonal anti-Oct4	Santa Cruz	Cat#SC-5279; RRID: AB_628051
Goat polyclonal anti-Otx2	R & D	Cat#AF1979; RRID: AB_2157172
Goat polyclonal anti-Sox1	R & D	Cat#AF3369; RRID: AB_2239879
Goat polyclonal anti-Sox17	R & D	Cat#AF1924; RRID: AB_355060
Mouse monoclonal anti-β Catenin (Active form)	Merck-Millipore	Cat#05-665; RRID: AB_309887
Goat polyclonal anti-β Catenin (Total)	R & D	Cat#AF1329; RRID: AB_354736
Mouse monoclonal anti-α Tubulin	Sigma	Cat#T6199; RRID: AB_477583
Rabbit polyclonal anti-Histone H3	Sigma	Cat#H0164; RRID: AB_532248
Goat polyclonal anti-Nanog (human)	R & D	Cat#AF1997; RRID: AB_355097
Biological Samples
Naive human cell lysates	Dr Peter Rugg-Gunn	N/A
Chemicals, Peptides, and Recombinant Proteins
ActivinA	Dr Marko Hyvönen, Cambridge University	N/A
FGF2	Dr Marko Hyvönen, Cambridge University	N/A
Ms LIF	Dr Marko Hyvönen, Cambridge University	N/A
BMP4	R & D	Cat#314-BP
CHIR99021	Tocris Bioscience	Cat#4423/10
PD0325901	Tocris Bioscience	Cat#4192
LY294002	Promega	Cat#V1201
Retinoic Acid	Sigma	R2625
IWP2	Tocris	Cat# 3533/10
Critical Commercial Assays
Kapa Sybr Fast Low Rox	Sigma	Cat#KK4622
Dual Luciferase Reporter Assay	Promega	Cat#E1910
Total β Catenin ELISA kit	Life Technologies	Cat#KHO1211
GenElute Total Mammalian RNA Extraction Kit	Sigma	Cat#RTN350
Click-iT EdU Pacific Blue Flow Cytometry Assay Kit	ThermoFisher	Cat#C10418
Deposited Data
Raw data	This paper	http://dx.doi.org/10.17632/gy6t9rv8jd.1
Single Cell RNA Seq Raw data	This paper	ArrayExpress: E-MTAB-8844
Mouse Embryonic Fibroblast (MEF) scRNA Seq data	Zhao et al., 2018	BIG: CRA000932; GEO: GSE114952
Bulk RNA Seq data	Skelly et al., 2020	ArrayExpress: E-MTAB-7730, E-MTAB-7728 (founder inbred strain mESC RNA-Seq and diversity outcross mESC RNA-Seq)
Mouse strain SNP datasets	Wellcome Trust Sanger Institute	ftp://ftp-mouse.sanger.ac.uk/current_snps/mgp.v5.merged.snps_all.dbSNP142.vcf.gz
Mouse genome dataset C57BL/6NJ	Keane et al., 2011	EMBL-EBI: ERP000041
Mouse genome dataset C3H/HeJ	Keane et al., 2011	EMBL-EBI: ERP000040
Mouse genome dataset CAST/EiJ	Keane et al., 2011	EMBL-EBI: ERP000042
The Molecular Signature Database Hallmark Gene Set Collection (MSigDB)	Liberzon et al., 2015	https://www.gsea-msigdb.org/gsea/msigdb/genesets.jsp?collection=H
Experimental Models: Cell Lines
Mouse: C57BL/6J	Jackson Laboratory	Strain ID JR#000664; RRID: CVCL_ZL17
Mouse: C3H/HeJ	Jackson Laboratory	Strain ID JR#000659; RRID: CVCL_2H67
Mouse: CAST/EiJ	Jackson Laboratory	Strain ID JR#000928; RRID: CVCL_ZL18
Mouse: PWD/PhJ	Jackson Laboratory	Strain ID JR#004660; RRID: CVCL_2H68
Oligonucleotides
See Primers Table for Oligonucleotide sequences used in this study		N/A
Recombinant DNA
M50 Super 8x TOPFlash	Veeman et al., 2003	Addgene plasmid#12456; RRID:Addgene_12456
pGL4.74[hRluc/TK] vector	Promega	Cat#E6931
Software and Algorithms
ImageJ	https://imagej.net/Welcome	RRID:SCR_003070
Python	Python Software Foundation	https://www.python.org; RRID:SCR_008394
Scanpy (1.4.4.post1)		https://scanpy.readthedocs.io/en/stable/index.html; RRID:SCR_018139
topGO	Alexa and Rahnenführer, 2019	https://bioconductor.org/packages/release/bioc/html/topGO.html; RRID:SCR_014798