REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse monoclonal GAPDH	Abcam	ab9484
Rabbit polyclonal Requiem	Sigma	SAB4502621
Mouse monoclonal FLAG	Sigma	F1804
Rabbit polyclonal TBX3	Invitrogen	42-4800
Goat polyclonal OCT4	R&D systems	AF1759
Goat polyclonal SOX2	R&D systems	AF2018
Mouse monoclonal NESTIN	BD PharMingen	556309
Mouse monoclonal TUBB3	Promega	G712A
Rabbit polyclonal NANOG	Abcam	Ab80892
Mouse monoclonal P300	Active motif	61401
Mouse monoclonal STAT3	Cell Signaling Technology	9139
Rabbit monoclonal H3K27ac	Abcam	ab177178
Rabbit polyclonal H3K27me3	Millipore	07449
Rabbit polyclonal H3K4me3	Abcam	ab8580
Rabbit polyclonal H3K9ac	Abcam	ab4441
Mouse monoclonal H4-tetraAC	Active motif	39967
Polyclonal goat SOX17	R&D systems	AF1924
Rabbit polyclonal GATA4	Santa Cruz	sc-9053
Goat polyclonal GATA6	R&D systems	AF1700
Rabbit polyclonal SUZ12	Abcam	ab12073
Mouse monoclonal EZH2	BD PharMingen	612667
Rabbit polyclonal EED	Millipore	17-10034
Rabbit monoclonal BRG1	Abcam	ab110641
Mouse IgG	ThermoFisher	A-11032
Alex488-conjugated donkey anti-goat IgG	ThermoFisher	A-11055
Alex594-conjugated donkey anti-rat IgG	ThermoFisher	A-21209
Alex488-conjugated donkey anti-mouse IgG	ThermoFisher	A-21202
Alex594-conjugated donkey anti-rabbit IgG	ThermoFisher	A-21207
DAPI	ThermoFisher	D1306
Bacterial and Virus Strains
DH5a Competent Cells	NEB	C-29871
One Shot TOP10 Chemically Competent E. coli	ThermoFisher	C404010
Chemicals, Peptides, and Recombinant Proteins
LIF	Millipore	ESG1107
BMP4	R&D System	5020-BP-010
Zeocin	ThermoFisher	R25001
G418	ThermoFisher	11811031
Puromycin	ThermoFisher	A1113802
Protease inhibitors	Roche	4693159001
Benzonase	Sigma	E8263-5KU
2x Laemmli Sample Buffer	Bio-Rad	#1610737
3X FLAG peptide	Sigma	F4799-4MG
Trypsin-EDTA (0.25%), phenol red	ThermoFisher	25200056
Paraformaldehyde	Sigma	P6148-500G
Disuccinimidyl glutarate	ThermiFisher	20593
Triton X-100	Sigma	T8787-50ML
4-Hydroxytamoxifen	TOCRIS	3412
Tamoxifen	Sigma	T5648
Annexin-APC	BD PharMingen	550475
7-AAD	BD PharMingen	559925
SYBR Green PCR Master Mix	ThermoFisher	4309155
ABsolute QPCR Mix, ROX	ThermoFisher	AB1139A
SequalPrep Long PCR Kit with dNTPs	ThermoFisher	A10498
Expand Long Template PCR System	Roche	03321053103
Disuccinimidyl glutarate	ThermoFisher	20593
Proteinase K	ThermoFisher	25530049
T4 DNA ligase	NEB	M0202S
Csp6I	Thermo Fisher	FD0214
MboI	Thermo	FD0814
Vivaspin500 PES centrifugal filters	Vivascience	VS0102
KAPA HTP Library Preparation kit	Roche	07961901001
Critical Commercial Assays
AP staining kit	Sigma	SCR004
SequalPrep Long PCR kit	Invitrogen	A10498
BCA Protein Assya Kit	Pierce	23227
ECL Plus	Amersham	RPN2133
RNeasy mini kit	QIAGEN	74104
TotalPrep RNA Amplification Kit	Ambion	AMIL1791
NucleoSpin gDNA Clean-Up kit	Macherey-Nagel	740230.10
SuperscriptIII reverse transcriptase	Invitrogen	18080093
Click-iT EdU Pacific Blue flow cytometry Assay Kit	Invitrogen	C10636
Pierce BCA Protein Assay Kit	Invitrogen	23225
Deposited Data
ChIP-seq	This study	E-MTAB-6165
RNA-seq	This study	E-MTAB-6166
4C	This study	E-MTAB-6167
Experimental Models: Cell Lines
E14 ESCs	This study	N/A
R26::CreERT2 - E14 ESCs	This study	N/A
R26::CreERT2 Dpf2 fl/fl E14 ESCs	This study	N/A
Eed −/− R26::CreERT2 Dpf2 fl/fl E14 ESCs	This study	N/A
Ezh2 −/− R26::CreERT2 Dpf2 fl/fl E14 ESCs	This study	N/A
Tbx3 DE KO ESCs	This study	N/A
Tbx3 IE KO ESCs	This study	N/A
Experimental Models: Organisms/Strains
SCID mice	Hans Scholer’s Group	N/A
Deposited Data
ChIP-seq data	This study	E-MTAB-6165 (ArrayExpress)
RNA-seq data	This study	E-MTAB-6166 (ArrayExpress)
4C data	This study	E-MTAB-6167 (ArrayExpress)
Proteomics data	This study	PXD011806 (ProteomeXchange)
Oligonucleotides
Oct4	TaqMan	Mm00658129_gH
Klf4	TaqMan	Mm00516104_m1
Nanog	TaqMan	Mm02384862_g1
Rex1	TaqMan	Mm03053975_g1
Nr0b1	TaqMan	Mm00431729_m1
Klf2	TaqMan	Mm01244979_g1
Klf5	TaqMan	Mm00456521_m1
Gapdh	TaqMan	4352339E
Tbx3	TaqMan	Mm01195726_m1
GATA6	TaqMan	Mm00802636_m1
GATA4	TaqMan	Mm00484689_m1
Sox17	TaqMan	Mm00488363_m1
FGF5	TaqMan	Mm00438918_m1
Sox1	TaqMan	Mm00486299_s1
Pax6	TaqMan	Mm00443072_m1
Brachyury	TaqMan	Mm01318252_m1
Tubb3	TaqMan	Mm00727586_s1
Dpf2	TaqMan	Mm00599980_m1
Nestin	TaqMan	Mm00450205_m1
Pdgfra	TaqMan	Mm00440701_m1
GATA2	TaqMan	Mm00492301_m1
Bmp4	TaqMan	Mm00432087_m1
Hand1	TaqMan	Mm00433931_m1
Sox21	TaqMan	Mm00844350_s1
Gjb3	TaqMan	Mm00433647_m1
Lama1	TaqMan	Mm01226102_m1
Ncam1	TaqMan	Mm01149710_m1
Pcdh17	TaqMan	Mm00977568_m1
See Table S5 for qPCR and gRNA sequences	This Study	N/A
Recombinant DNA
Dpf2 targeting vector	EUCOMM resource	N/A
C-FTAP-tag Dpf2 knockin vector	This study	N/A
pPyCAG-Dpf2-IZ	Hitoshi Niwa	N/A
pPyCAG-Tbx3-IN	Hitoshi Niwa	N/A
pCAGGs-FlpE	This study	N/A
Nanog shRNA	Wu Qiang	N/A
Tbx3 shRNA	April Kartikasari	N/A
Reagent or Resource
GMEM	Sigma-Aldrich	G2549
FCS	GIBCO	10439024
Non-essential amino acid	GIBCO	11140050
Sodium pyruvate	GIBCO	11360070
2-mercaptoethanol	GIBCO	21985023
L-glutamine	GIBCO	25030081
TCEP	Sigma	75259
Iodoacetamide	Sigma	I6125
colloidal Coomassie	Sigma	B2025
AggreWell 400 plates	STEMCELL Technoligies	34421
Dynabeads Protein G	Invitrogen	10003D
4-12% Bis-Tris Novex gel	Invitrogen	NP0321BOX
PVDF membranes	Biorad	1620177
Software and Algorithms
ChromHMM v1.1.0	Chronis et al., 2017	N/A
Bowtie2 v2.2.1	Langmead et al., 2009	N/A
Cufflinks v2.2.1	Trapnell et al., 2010	N/A
MACS2 v20140616	Zhang et al., 2008	N/A
BedTools v2.27	Quinlan and Hall, 2010	N/A
HOMER v4.9.0	Heinz et al., 2010	N/A
Metascape	http://metascape.org	N/A
Proteome Discover 1.4	Thermofisher	N/A
Tophat version 2.0.13	Trapnell et al., 2009	N/A
Mascot 2.5	Matrix Science	N/A