REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse anti-hOCT-4	Santa Cruz	Cat# sc-5279; RRID: AB_628051
AlexaFluor 488 goat anti-mouse IgG	Thermo Fisher Scientific	Cat# A11029; RRID: AB_2534088
Mouse anti-hTRA-1-60 (PE-conjugated)	Thermo Fisher Scientific	Cat# MA-1-023-PE; RRID: AB_2536704
Mouse anti-TRA-1-60	Abcam	Cat# ab16288; RRID: AB_778563
AlexaFluor 488 goat anti-mouse IgM	Thermo Fisher Scientific	Cat# A21042: RRID: AB_2535711
Chemicals, peptides, and recombinant proteins
DMEM, high glucose	Life Technologies	Cat# 11965118
Fetal Bovine Serum, qualified	Life Technologies	Cat# 26140079
L-glutamine (200mM)	Life Technologies	Cat# 25030081
Penicillin-Streptomycin (10,000 U/ml)	Life Technologies	Cat# 15140122
TeSR™-E7™	StemCell Technologies	Cat# 05914
CellAdhere™ Dilution Buffer	StemCell Technologies	Cat# 07183
Vitronectin™	StemCell Technologies	Cat# 07180
StemFlex™	Life Technologies	Cat# A3349401
DPBS, no calcium, no magnesium	Life Technologies	Cat# 14190250
ReLeSR™	StemCell Technologies	Cat# 05873
DMEM/F-12	Life Technologies	Cat# 11320082
L-glutamine (200mM)	Life Technologies	Cat# 25030081
MEM Non-Essential Amino Acids solution (100x)	Life Technologies	Cat# 11140050
Corning® Matrigel® basement membrane matrix	VWR	Cat# 734-1100
B-27 supplement (50x)	Life Technologies	Cat# 17504044
FGF basic protein, human recombinant	Merck	Cat# GF003
Neurobasal™ medium	Life Technologies	Cat# 21103049
GlutaMAX™ supplement	Life Technologies	Cat# 35050061
D-(+)-Glucose solution 45 % in H2O	Sigma	Cat# D8769
N-2 supplement (100x)	Life Technologies	Cat# 17502048
Bovine Serum Albumin	Sigma	Cat# A4503-50G
Critical commercial assays
MycoAlert mycoplasma detection kit	Lonza	Cat# LT07-318
Human Dermal Fibroblasts Nucleofector™ Kit	Lonza	Cat# VVPD-1001
LS columns	Miltenyi Biotec	Cat# 130-042-401
MidiMACS Separator	Miltenyi Biotec	Cat# 130-42-301
MACSQuant Analyzer 10	Miltenyi Biotec	Cat# 130-096-343
Anti-TRA-1-60 microbeads, human	Miltenyi Biotec	Cat# 130-100-832
Papain Dissociation System	Worthington Biochemical Corporation	Cat# LK003153
Countess II™ Fl Automated cell counter	Thermo Fisher Scientific	Cat# AMQAF1000
QIAamp DNA Mini kit	Qiagen	Cat# 51306
SimpliNano™ Spectrophotometer	GE Life Sciences	Cat# 29061711
Chromium™ Single Cell 3’ Library, Gel Bead & Multiplex Kit, 16 rxns	10X Genomics	Cat# PN-120233
Dynabeads™ MyOne™ Silane	Thermo Fisher Scientific	Cat# 37002D
SPRIselect beads	Beckman Coulter	Cat# B23318
NovaSeq 6000 S4 Reagent kit	Illumina	Cat# 20039236
Deposited data
Single-cell RNA-seq	This manuscript (https://data.humancellatlas.org)	77780d56-03c0-481f-aade-2038490cef9f
Experimental models: cell lines
Human iPSCs	This manuscript (https://data.humancellatlas.org)	77780d56-03c0-481f-aade-2038490cef9f
Software and algorithms
NovaSeq Control Software v1.6	Illumina	https://support.illumina.com/sequencing/sequencing_instruments/novaseq-6000/downloads.html
GenomeStudio v2.0.4	Illumina	https://support.illumina.com/array/array_software/genomestudio/downloads.html
GenomeStudio PLINK Input Report Plug-in v2.1.4	Illumina
10x Cellranger	10X Genomics	https://www.10xgenomics.com/software/
Minimac3	Das et al., 201688	https://github.com/Santy-8128/Minimac3
Eagle v2.3	Loh et al., 201689	https://data.broadinstitute.org/alkesgroup/Eagle/
ascend R package	Senabouth et al., 201990	https://github.com/powellgenomicslab/ascend
demuxlet	Kang et al., 201891	https://github.com/statgen/demuxlet
scrublet	Wolock et al., 201992	https://github.com/AllonKleinLab/scrublet
Monocle 3 R package	Cao et al., 201993	http://cole-trapnell-lab.github.io/monocle-release/monocle3
Seurat 3.1 R package	Butler et al., 201894 and Stuart et al., 201995	https://github.com/satijalab/seurat
UMAP	Becht et al., 201896	https://github.com/lmcinnes/umap
Slingshot 1.4.0 R package	Street et al., 201856	https://github.com/kstreet13/slingshot
tradeSeq 0.99.80	Van den Berge et al., 202057	https://statomics.github.io/tradeSeq/index.html
limma 3.42.2 R package	Ritchie et al., 201597	https://bioconductor.org/packages/release/bioc/html/limma.html