REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, peptides, and recombinant proteins
Vitronectin (VTN-N)	Thermo Fisher Scientific	Cat # A14700
CultureSure® Y-27632	FUJIFILM WAKO	Cat # 036-24023
Dimethyl sulfoxide, for molecular biology	Sigma-Aldrich	Cat # D8418
2,5-Hexanedione	Sigma-Aldrich	Cat # 00770-50ml
Acrylamide(monomer)	NACALAI TESQUE	Cat # 06114-24
Amiodarone Hydrochloride	TCI (Tokyo Chemical Industry)	Cat # A2530
Amitriptyline hydrochloride	Sigma-Aldrich	Cat # A8404
Atorvastatin Calcium Salt Trihydrate	TCI (Tokyo Chemical Industry)	Cat # A2476
Axitinib	Selleck Chemicals	Cat # S1005
Bucillamine	Toronto Research Chemicals	Cat # B689375
Butylated hydroxyanisole	Sigma-Aldrich	Cat # B1253-5G
(+)-Chlorpheniramine Maleate	FUJIFILM WAKO	Cat # 030-13271
Chlorpromazine Hydrochloride	FUJIFILM WAKO	Cat # 033-10581
cis-Diammineplatinum(II) dichloride crystalline	Sigma-Aldrich	Cat # P4394-250MG
Cyclopamine hydrate	SIGMA	Cat # C4116-1MG
Ciclosporin A	FUJIFILM WAKO	Cat # 031-24931
Digoxin	Sigma-Aldrich	Cat # D6003-1G
Doxorubicin (hydrochloride)	Cayman Chemical	Cat # 15007
Gentamicin sulfate	Sigma-Aldrich	Cat # G3632-1G
Ibuprofen	FUJIFILM WAKO	Cat # 098-02641
Itraconazole	Sigma-Aldrich	Cat # I6657-100MG
Lithocholic acid	Sigma-Aldrich	Cat # L6250-10G
Methapyrilene HCl	Sigma-Aldrich	Cat # 442641
Sunitinib malate	Tocris Bioscience	Cat # 510-86011
Thioacetamide	Sigma-Aldrich	Cat # 172502-25G
Valproic acid	SIGMA	Cat # PHR1061-1G
Verapamil Hydrochloride	Sigma-Aldrich	Cat # V4629-1G
RNasin® Plus RNase Inhibitor, 2500u	Promega	Cat # N2611
Dimethoate Standard	FUJIFILM WAKO	Cat # 041-15843
Arsenic (III) oxide	Sigma-Aldrich	Cat # 311383-125G
Quinidine hydrochloride monohydrate technical grade	Sigma-Aldrich	Cat # Q0750-5G
Critical commercial assays
CellTiter-Glo® Luminescent Cell Viability Assay	Promega	Cat # G7571
RNeasy Mini Kit	QIAGEN	Cat # 74106
RNase-Free DNase Set (50)	QIAGEN	Cat # 79254
TruSeq Stranded mRNA Library Prep (48 Samples)	Illumina	Cat # 2020594
TruSeq RNA Single Indexes Set A (12 Indexes, 48 Samples)	Illumina	Cat # 20020492
TruSeq RNA Single Indexes Set B (12 Indexes, 48 Samples)	illumina	Cat # 20020493
HiSeq 3000/4000 SR Cluster Kit	illumina	Cat # GD-410-1001
HiSeq 3000/4000 SBS Kit (50 Cycles)	illumina	Cat # FC-410-1001
PrimeScript™ RT Reagent Kit (Perfect Real Time)	TAKARA BIO	Cat # RR037B
KAPA SYBR Fast qPCR Kit (Universal qPCR kit)	KAPA BIOSYSTEMS	Cat # KK4602
Deposited data
RNA-seq	This study	GEO: GSE188203
Experimental models: Cell lines
KhES-3 cell line (XY)	(Nakatsuji, 2005)	NA
HPS4138 cell line (XY)	RIKEN BRC	NA
HPS4234 cell line (XY)	RIKEN BRC	NA
HPS4046 cell line (XY)	RIKEN BRC	NA
Oligonucleotides
Primers for qRT-PCR	This study	https://www.stemcellinformatics.org/toxicology/
Software and algorithms
alvaDesc	Affinity Science	https://www.alvascience.com/alvadesc/
CORINA Classic	mn-am.com	https://www.mn-am.com/online_demos/corina_demo/
Other
The source code of R analysis script and the data supporting the findings of this study	This study	https://www.stemcellinformatics.org/toxicology/