REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Human DPPA5/ESG1 Antibody	R&D Systems	AF3125-SP; RRID: AB_2094168
Human ABCG2 Antibody	R&D Systems	MAB995-SP; RRID: AB_2220316
Chemicals, Peptides, and Recombinant Proteins
Human LIF	Stem Cell Institute, Cambridge	N/A
CHIR99021	Stem Cell Institute, Cambridge	N/A
PD0325901	Stem Cell Institute, Cambridge	N/A
Gö6983	TOCRIS	2285
Penicillin/Streptomycin	Thermo Fisher Scientific	15140122
MEM non-essential amino acids	Thermo Fisher Scientific	11140050
TeSR-E8	STEMCELL Technologies	05990
B27	Thermo Fisher Scientific	17504044
N2	Stem Cell Institute, Cambridge	N/A
DMEM-F12	Thermo Fisher Scientific	11320-033
Neurobasal	Thermo Fisher Scientific	21103049
Accutase	STEMCELL Technologies	07920
Triton X-100	Sigma-Aldrich	T9284
Tween20	Sigma-Aldrich	P9416
DAPI	Thermo Fisher Scientific	62248
RNase Inhibitor	Clontech	2313A
ERCC RNA Spike-In Mix	Ambion	4456740
dNTPs	Thermo Fisher Scientific	10319879
Critical Commercial Assays
AMPure XP beads	Beckman Coulter	A63880
Nextera XT DNA Sample Preparation Kit	Illumina	FC-131-1096
Nextera XT Index Kit	Illumina	FC-131-1001
Superscript II reverse transcriptase	Invitrogen	18064-014
Deposited Data
Raw sequence data and count tables	This study	E-MTAB-6819
Experimental Models: Cell Lines
Human WA09 Embryonic stem cells	Takashima et al., 2014	N/A
Oligonucleotides
Oligo-dT30VN	Picelli et al., 2014	N/A
AAGCAGTGGTATCAACGCAGAGTACT30VN
Template Switching Oligo	Picelli et al., 2014	N/A
AAGCAGTGGTATCAACGCAGAGTACATrGrG+G
ISPCR oligo	Picelli et al., 2014	N/A
AAGCAGTGGTATCAACGCAGAGT
Software and Algorithms
R version 3.5.1 (Feather Spray)	The R Project	https://www.r-project.org
scran	Lun et al., 2016b	https://bioconductor.org/packages/release/bioc/html/scran.html
scater	McCarthy et al., 2017	https://bioconductor.org/packages/release/bioc/html/scater.html
Rtsne	van der Maaten and Hinton, 2008	https://cran.r-project.org/web/packages/Rtsne/index.html
edgeR	Robinson et al., 2010	https://bioconductor.org/packages/release/bioc/html/edgeR.html
subread	Liao et al., 2013	http://subread.sourceforge.net
Rsubread	Liao et al., 2014	https://bioconductor.org/packages/release/bioc/html/Rsubread.html
limma	Ritchie et al., 2015	https://bioconductor.org/packages/release/bioc/html/limma.html