REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Polyclonal goat IgG anti-human SOX2	RnD Bio-Techne	Cat#AF2018; RRID:AB_355110
Polyclonal rabbit IgG anti-human CDX2	Cell Signaling Technology	Cat#3977S; RRID:AB_2077043
Monoclonal rabbit IgG anti-human GATA3	Abcam	Cat#ab199428 (EPR16651); RRID:AB_2819013
Polyclonal goat IgG anti-human E-cadherin	RnD Bio-Techne	Cat#AF748; RRID:AB_355568
Monoclonal mouse IgG2b anti-human POU5F1	Santa Cruz	Cat#sc-5279 (C-10); RRID:AB_628051
Monoclonal rabbit IgG anti-human Smad1	Cell Signaling Technology	Cat#6944 (D59D7); RRID:AB_10858882
Monoclonal rabbit IgG anti-human phospho-Smad1/5/9	Cell Signaling Technology	Cat#13820 (D5B10); RRID:AB_2493181
Mouse monoclonal IgG anti-human Hsp90	Abcam	Cat#ab13492 (AC88); RRID:AB_300396
Mouse monoclonal IgG anti-human PAX6 conjugated with PE	BD Biosciences	Cat#561552 (O18-1330); RRID:AB_10714781
Rabbit monoclonal IgG anti-human AIF	Cell Signaling Technology	Cat#5318 (D39D2); RRID:AB_10634755
Rabbit monoclonal IgG anti-human PDI	Cell Signaling Technology	Cat#3501 (C81H6); RRID:AB_2156433
Rabbit monoclonal IgG anti-human LAMP1	Cell Signaling Technology	Cat#9091 (D2D11); RRID:AB_2687579
Mouse monoclonal IgG anti-human CD55 conjugated with FITC	Biolegend	Cat#311305 (JS11); RRID:AB_314862
Mouse monoclonal IgG anti-human CD90 (THY1) conjugated with Alexa Fluor647	Biolegend	Cat#328115 (5E10); RRID:AB_893439
Mouse monoclonal IgG anti-human CD24 conjugated with APC	eBioscience, Invitrogen	Cat#17-0247-42 (SN3 A5-2H10); RRID:AB_10718833
Mouse monoclonal IgG anti-human VTCN1 (B7-H4) conjugated with SuperBright436	eBioscience, Invitrogen	Cat#62-5949-41 (H74); RRID:AB_2784834
Chemicals, peptides, and recombinant proteins
MAPK inhibitor PD032590	Cambridge Stem Cell Institute facility	N/A
aPKC inhibitor Gö6983	Tocris Bio-Techne	Cat. 2285
Tankyrase inhibitor XAV939	Tocris Bio-Techne	Cat. 3748
Human leukemia inhibitory factor	Cambridge Stem Cell Institute facility	N/A
ROCK inhibitor Y-27632	Millipore	Cat. 688000
Activin receptor inhibitor A8301	Tocris Bio-Techne	Cat. 2939
BMP receptor inhibitor LDN193189 (DM3189)	Axon Medchem	Cat. 1509
Critical commercial assays
Chromium Single Cell 3′ Library & Gel Bead Kit v3	10x Genomics	PN-1000075
Chromium Chip B Kit	10x Genomics	PN-1000073
Nextera XT kit	Illumina	FC-131-1024
Deposited data
Raw and analysed data	This paper	GEO: GSE179309
Single-cell RNAseq of human in vitro cultured embryos	Xiang et al., 2020	GEO: GSE136447
Single-cell RNAseq of macaque in vitro cultured embryos	Ma et al., 2019	GEO: GSE130114
Single-cell RNAseq of human gastrula	Tyser et al, 2021	Array Express: E-MTAB-9388
Bulk RNAseq of the time course of naïve hPSC differentiation to TE-like cells	Guo et al., 2021	GEO: GSE166401
Bulk RNAseq of the time course of naïve hPSC differentiation to TE-like cells and primed hPSC differentiation to AME-L-like cells	Io et al., 2021	GEO: GSE144994
Single-cell RNAseq of in vitro-derived amnion-like epithelial cells	Zheng et al., 2019	GEO: GSE134571
Experimental models: Cell lines
Human: HNES1	Guo et al., 2016	Naïve hPSC line HNES1
Human: cR-H9-EOS	Guo et al., 2017	Chemically reset hPSC line cR-H9-EOS
Human: H9 (WA09)	WiCell	hPSC line H9
Oligonucleotides
Primers used in Figures 2, 4, and S4 and see Table S4	This paper	N/A
Software and algorithms
RStudio	R Core Team, 2020	N/A
CellRanger v3.1.0	Zheng et al., 2017	N/A
Seurat V4.0.1	Hao et al., 2021	N/A
Ggplot	Wickham et al., 2019	N/A
Factoextra 1.0.7	Kassambara and Mundt, 2020	N/A
DESeq2	Love et al., 2014	N/A
Pheatmap	Kolde, 2019	N/A
SCINA	Zhang et al., 2019	N/A
DeconRNASeq	Gong and Szustakowski, 2013	N/A
Destiny	Angerer et al., 2016	N/A
ImageJ	Schneider et al., 2012	N/A
NIS-Elements	Nikon	N/A
Imaris	Oxford Instruments	N/A