REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse monoclonal anti-Oct3/4 (C-10)	Santa Cruz	Cat#SC-5279; RRID:AB_628051
Goat polyclonal anti-Oct3/4 (N-19)	Santa Cruz	Cat#SC-8628; RRID:AB_653551
Goat polyclonal anti-Brachyury	R&D systems	Cat#AF2085; RRID:AB_2200235
Rabbit polyclonal anti-Sox1	Cell Signaling Technology	Cat#4194; RRID:AB_1904140
Rabbit polyclonal anti-Stella/Dppa3	Abcam	Cat#ab19878; RRID:AB_2246120
Rat monoclonal anti-Blimp1/Prdm1	Santa Cruz	Cat#SC-47732; RRID:AB_628168
Mouse monoclonal anti-Foxa2	Abnova	Cat#H00003170-M10; RRID:AB_534871
Mouse monoclonal anti-Tuj1	R&D systems	Cat#MAB1195; RRID:AB_357520
Mouse anti-cardiac Troponin T (1C11)	Abcam	Cat#Ab8295; RRID:AB_306445
Goat polyclonal anti-Sox17	R&D systems	Cat#AF1924; RRID:AB_355060
Goat polyclonal anti-Gata4	Santa Cruz	Cat#SC-1237; RRID:AB_2108747
Rabbit polyclonal anti-Eomes	Abcam	Cat#ab23345; RRID:AB_778267
Rat monoclonal anti-Ecadherin (ECCD2)	Kind gift from Prof. M Takeichi	N/A
Rat monoclonal anti-Nanog	eBioscience	Cat#14-5761-80; RRID:AB_763613
Rat monoclonal anti-Sox2	eBioscience	Cat#14-9811-82; RRID:AB_11219471
Mouse monoclonal anti-Oct6 (Pou3f1)	Miilipore	Cat#MABN738; RRID:AB_2876862
Rabbit polyclonal anti-mKusabira Orange	MBL	Cat#PM051M; RRID:AB_2876863
Alexa Fluore 647 anti-SSEA1	BD Bioscience	Cat#562277; RRID:AB_11154583
PE Anti-mouse/rat CD61	Biolegend	Cat#104307; RRID:AB_313084
Anti-CD324 (Ecadherin) eFluor-660	eBioscience	Cat#50-3249-82; RRID:AB_11040003
PE-Cy7 Anti-Ecadherin	Biolegend	Cat#147310; RRID:AB_2564188
APC Anti-mouse CD184 (Cxcr4)	Biolegend	Cat#146508; RRID:AB_2562785
PE Anti-Flk1	Biolegend	Cat#136403; RRID:AB_1967093
Rabbit anti-RFP	Rockland	Cat#600-401-379; RRID:AB_2209751
Rabbit anti-mvh	Abcam	Cat#ab13840; RRID:AB443012
Rabbit anti-phospho Smad2	Cell Signaling Technologies	Cat#3108; RRID:AB_490941
Mouse anti-total Smad2/3	BD Bioscience	Cat#610842; RRID:AB_398161
Mouse anti-Gapdh	Sigma-Aldrich	Cat#G8795; RRID:AB_1078991
Rabbit anti-H3K4me1	Abcam	Cat#ab8895; RRID:AB_306847
Rabbit anti-H3K4me3	Diagenode	Cat#C15410003; RRID:AB_2616052
Rabbit anti-H3K27Ac	Active Motif	Cat#39135; RRID:AB_2614979
Rabbit anti-H3K27me3	Merck	Cat#07-449; RRID:AB_310624
Chemicals, Peptides, and Recombinant Proteins
XAV939	Sigma Aldrich	X-3004
BMS493	Tocris Bio-Techne	3509
A83-01	Generon	A12358-50
SB-505124	Selleckchem	S2186
LDN193189	Axon Medchem	Axon 1509
PD0325901	abcr	AB 253775
CHIR99021	abcr	AB 253776
Y27632	Millipore	Cat 688000
Recombinant Mouse LIF	In house	N/A
Recombinant human LIF	In House	N/A
Recombinant human activin A	Qkine	Qk005
Recombinant zebrafish Fgf2	Qkine	Qk002
Recombinant mouse Stem Cell Factor	BioLegend	579706
Recombinant human BMP2	In House	N/A
N2 Supplement	In house	N/A
B27 Supplement	Thermo Fisher Scientific	17504044
Neurobasal	Thermo Fisher Scientific	11540566
DMEM/F12	Thermo Fisher Scientific	21103049
Human Plasma Fibronectin	Millipore	FC010
Tissue culture Laminin	Millipore	CC095-5MG
Gelatin	Sigma-Aldrich	G-1890
Accutase	Biolegend	423201
M2 medium	Sigma-Aldrich	M-7167
Critical Commercial Assays
NEXTflex Rapid Directional RNA-seq Kit	Bioo Scientific	5138-08
Ribo-Zero rRNA Removal Kit	Illumina	MRZH11124
PureLink RNA Mini kit	Thermo Fisher Scientific	12183018A
PicoPure RNA Isolation kit	Thermo Fisher Scientific	KIT0214
SMARTerR Stranded Total RNA-Seq Kit v2 – Pico InputMammalian	Takara Clontech	634412
Nextera DNA Library Preparation Kit	Illumina	FC-121-1030
SAGE Warming Kit	CooperSurgical Fertility & Genomic Solutions	ART-8030
NEXTflex Rapid DNA-Seq Kit 2.0 bundle with 96 HT barcodes	PerkinElmer	NOVA-5188-13
Mouse Xist Stellaris RNA FISH Probe with Quasar 670 Dye	BioSearch Technologies	VSMF-3095-5
10 CIRCLE, 7MM ID, FROSTED, HEAVY TEFLON COATED Slide	Roboz Surgical Instrument	F107-HTC
TransIT LT1	Mirus	MIR2304
Alkaline Phaphatase Kit	Sigma Aldrich	86R-1KIT
Deposited Data
RNA-seq	This paper	GEO: GSE131566
ATAC-seq	This paper	GEO: GSE131566
scRNA-seq	This paper	GEO: GSE156589
ChIP-seq	This paper	GEO: GSE156261
Experimental Models: Cell Lines
5ar1 (mFS)	This paper	N/A
5ar2 (mFS)	This paper	N/A
5ar3 (mFS)	This paper	N/A
5ar5 (mFS)	This paper	N/A
5cdr1 (mFS)	This paper	N/A
5cdr2 (mFS)	This paper	N/A
NBRA3.2 (mFS)	This paper	N/A
5a6 (mFS)	This paper	N/A
E14Tg2a (mES)	Hooper et al., 1987	N/A
Rd2 (mES)	Kalkan et al., 2017	N/A
Sox1::GFP (mES)	Stavridis and Smith, 2003	N/A
AFX6 (mEpiSC)	This paper	N/A
AFX33 (mEpiSC)	This paper	N/A
AF32 (mEpiSC)	This paper	N/A
OEC2 (mEpiSC)	Guo et al., 2009	N/A
HNES1 (hES)	Guo et al., 2016	N/A
cR-H9 (hES)	Guo et al., 2017	N/A
cR-Shef6 (hES)	Guo et al., 2017	N/A
Etv4/5 dKO ES	This paper	N/A
Otx2 KO ES	This paper	N/A
hFS1	This paper	N/A
hFS2	This paper	N/A
hFS3	This paper	N/A
Experimental Models: Organisms/Strains
Mouse/CD-1	Charles River	022
Mouse/129aa	WT-Gurdon Institute	N/A
Mouse/ ROSAmT/mG	Jackson Laboratory	007576
Mouse/C57BL/6	WT-Gurdon Institute	N/A
Oligonucleotides
gRNA sequences	See Table S3	N/A
Genotyping primers	See Table S3	N/A
Taqman probes and UPL primers for qRT-PCR	See Table S3	N/A
Recombinant DNA
pPBCAG-mKO2-IP	This paper	N/A
pPBCAG-GFP-IP	This paper	N/A
pPBCAG-Cas9-IN	This paper	N/A
pCML32	This paper	N/A
Software and Algorithms
Tophat2 v2.1.0	Kim et al., 2013	https://ccb.jhu.edu/software/tophat/index.shtml
TrimGalore v0.4.5	N/A	https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
FeatureCounts v1.5.0	Liao et al., 2019	http://subread.sourceforge.net/
R v3.6.2	N/A	https://www.R-project.org/
DESeq2 v1.18.1	Love et al., 2014	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Pheatmap	N/A	https://cran.r-project.org/web/packages/pheatmap/index.html
ggplot2	N/A	https://ggplot2.tidyverse.org/
DeepTools	Ramirez et al., 2016	https://doi.org/10.1093/nar/gkw257
Diffbind v2.6.6	N/A	https://bioconductor.org/packages/release/bioc/html/DiffBind.html
MACS2	Zhang et al., 2008	N/A
DAVID v6.8	Huang et al., 2009	https://david.ncifcrf.gov/
HOMER v4.10	Heinz et al., 2010	http://homer.ucsd.edu/homer/
Bismark	Krueger and Andrews, 2011	https://www.bioinformatics.babraham.ac.uk/projects/bismark/
MarkDuplicates	Picard tools	N/A
Seurat v3.1.0	Butler et al., 2018	https://satijalab.org/seurat/
STAR v2.7.3a	Dobin et al., 2013	https://github.com/alexdobin/STAR
Wiggletools	Zerbino et al., 2014	https://github.com/Ensembl/WiggleTools
Bowtie	Langmead and Salzberg, 2012	N/A
Samtools v1.9	N/A	http://www.htslib.org/
FastQC v0.11.3	N/A	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
MultiQC v1.8	N/A	https://multiqc.info/
Methpipe	Song et al., 2013	http://smithlabresearch.org/software/methpipe/
Venny 2.1	N/A	https://bioinfogp.cnb.csic.es/tools/venny/index.html
FCS Express 7 Research	N/A	De Novo Software