REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
GATA6	Cell Signaling	5851 RRID:AB_10705521
GATA4	Santa Cruz	SC-1237 RRID:AB_2108747
SOX17	RnD	AF1924 RRID:AB_355060
FOXA2	RnD	AF2400 RRID:AB_2294104
EOMES	Cell Signaling	66325 RRID: Unknown
EOMES (RIME analysis)	Abcam	Ab23345 RRID: AB_778267
FLAG	Sigma-Aldrich	F1804 RRID:AB_262044
Normal Mouse IgG	Sigma-Aldrich	12-371 RRID:AB_145840
β-Actin	Sigma-Aldrich	A1978 RRID:AB_476692
Protein G Dynabeads	ThermoFisher Scientific	10004D
Bacterial and virus strains
pzbFGF BL21 Star E. coli	(Ludwig et al., 2006)	N/A
Chemicals, peptides, and recombinant proteins
mTesR	(Ludwig et al., 2006)	N/A
E-cadherin	(Nagaoka et al., 2010)	N/A
RPMI 1640	ThermoFisher Scientific	22400089
Geltrex	ThermoFisher Scientific	A1413302
B-27 Supplement (50x), minus insulin	ThermoFisher Scientific	A1895601
Activin A Recombinant Human Protein	ThermoFisher Scientific	PHC9563
FGF-Basic (AA 10-155) Recombinant Human Protein	ThermoFisher Scientific	PHG0023
Purified recombinant zebrafish FGF-Basic	(Ludwig et al., 2006)	N/A
BMP4 Recombinant Human Protein	ThermoFisher Scientific	PHC9533
Formaldehyde 16%(w/v)	ThermoFisher Scientific	28906
Puromycin	Sigma-Aldrich	P9620
Doxycycline hyclate	Sigma-Aldrich	D9891
ROCK inhibitor Y27632	StemRD	146986-50-7
DAPI	Sigma-Aldrich	D1388
Critical commercial assays
RNeasy mini Kit	QIAGEN	74106
TURBO DNA-freeTM Kit	ThermoFisher/Ambion	AM1907
M-MLV Reverse Transcriptase	ThermoFisher/Invitrogen	28025-013
TaqMan Gene Expression	ThermoFisher/Applied Biosystems	4369016
Pierce BCA protein assay kit	ThermoFisher Scientific	23227
Pierce co-immunoprecipitation kit	ThermoFisher Scientific	87787
SimpleChIP Plus Enzymatic ChIP Kit	Cell Signaling	9005
Transcription Factor Staining Buffer Set	ThermoFisher Scientific/eBioscience	00-5523-00
Experimental models: cell lines
IPSC-K3	(Si-Tayeb et al., 2010b)	N/A
IPSC-K3 GATA6Ex4Δ1/Δ2;indGATA6	(Heslop et al., 2021)	N/A
Oligonucleotides
GATA6	Fwd: TTCGTTTCCTGGTTTGAATTCC Probe: TCATAGCAAGTGGTCTGGGCACC Rev: TGCAATGCTTGTGGACTCTAC	Integrated DNA Technologies
EOMES	Fwd: GTGGCAAAGCCGACAATAAC Probe: CCGAATGAAATCTCCTGTCTCA Rev: ACCCAGAGTCTCCTAATACTGGTTCCC	Integrated DNA Technologies
RPL13a	Fwd: GCCTTCACAGCGTACGA Probe: AGCAGTACCTGTTTAGCCACGATGG Rev: CGAAGATGGCGGAGGTG	Integrated DNA Technologies
Software and algorithms
Graphpad with PRISM	https://www.graphpad.com/	Version 8.4.2
FlowJo	https://www.flowjo.com/	Version 10.5.0
ImageJ	https://imagej.nih.gov	Version 1.53q
EaSEQ	(Lerdrup et al., 2016); https://easeq.net/	Version 1.111
FastQC	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/	Version 0.11.7
Partek Flow	https://www.partek.com/partek-flow/	Version 9.0.20.0526
STAR	Partek Flow	Version 2.6.1d
BOWTIE2	Partek Flow	Version 2.2.5
MACS2	Partek Flow	Version 2.1.1
DiffBind	(Ross-Innes et al., 2012); https://bioconductor.org/packages/DiffBind/	Version 3.13
PANTHER Classification system	(Mi et al., 2013) http://pantherdb.org	Version 17.0
HOMER	(Heinz et al., 2010); http://homer.ucsd.edu/homer/	Version 4.10
Other
ATAC-seq data	(Heslop et al., 2021)	GSE156021
RNA-seq data	(Heslop et al., 2021)	GSE156021
CHIP-seq: GATA6	(Heslop et al., 2021)	GSE156021
CHIP-seq: EOMES	(Heslop et al., 2021)	GSE156021