REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit anti-Cleaved caspase-3	Cell Signalling Technology	9661; RRID:AB_2341188
Rabbit anit-MCL-1	Cell Signalling Technology	5453; RRID:AB_10694494
Rabbit anti-BCL-XL	Cell Signalling Technology	2764; RRID:AB_2228008
Rabbit anti-BCL2	Cell Signalling Technology	2870; RRID:AB_2290370
Mouse anti-β-ACTIN	Proteintech	66009-1-Ig; RRID:AB_2687938
Mouse anti-YAP	Santa Cruz Biotechnology	sc-101199; RRID:AB_1131430
Rabbit anti-Phospho-YAP (Ser127)	Cell Signalling Technology	4911; RRID:AB_2218913
Mouse anti-non-muscle Myosin IIB/MYH10	Abcam	ab684; RRID:AB_305661
Rabbit anti-α-tubulin	Cell Signalling Technology	2144; RRID:AB_2210548
Mouse anti-TRA-1-81 monoclonal	In-house	N/A
Mouse anti-TRA-1-85 monoclonal	In-house	N/A
Rat anti-SSEA3 monoclonal	In-house	N/A
Mouse anti-THY1(CD90)	In-house	N/A
Mouse anti-P3X	In-house	N/A
Goat anti-Mouse AffiniPure IgG+IgM H+L (Alexa Fluor® 647)	Stratech	115-605-044-JIR; RRID:AB_2338906
Goat anti-Rabbit AffiniPure IgG+IgM H+L (Alexa Fluor® 647)	Stratech	111-605-003-JIR; RRID:AB_2338072
Goat anti-Mouse AffiniPure IgG, Fcγ Fragment Specific (Alexa Fluor® 594)	Stratech	115-585-008-JIR;RRID:AB_2338873
Goat anti-Rabbit AffiniPure IgG H+L (Alexa Fluor® 594)	Stratech	111-585-003-JIR;RRID:AB_2338871
Anti-Mouse IgG H+L (HRP)	Promega	W4021; RRID:AB_430834
Anti-Rabbit IgG H+L (HRP)	Promega	W4011; RRID:AB_430833
Chemicals, peptides, and recombinant proteins
Y-27632	Generon	A11001-10
Latrunculin A	Cambridge Bioscience	10010630-25ug-CAY
Cytochalasin B	Sigma-Aldrich	C2743-200UL
Nocodazole	VWR	487928
Z-VAD-FMK	Stratech	A1902-APE-10mg
(R)-PFI 2 hydrochloride	Bio-Techne	4892/10
Hoechst 33342, trihydrochide	Fisher Scientific	11534886
Incucyte® Caspase-3/7 Red Dye for Apoptosis	Sartorius	4704
Vitronectin (VTN-N)	Life Technologies	A14700
Sodium selenium	Sigma-Aldrich	S5261
Insulin	Thermo Fisher Scientific	A11382IJ
NaHCO3	Sigma-Aldrich	S5761
Transferrin	Sigma-Aldrich	T0665
Glutamax	Thermo Fisher Scientific	35050038
FGF2	Peprotech	100-18B
Heat Stable Recombinant bFGF	Thermo Fisher Scientific	PHG0367
TGFβ1	Peprotech	100-21
Vectashield Mounting Medium	Vector Laboratories	H-1000
Phalloidin (Alexa Fluor® 647)	Cell Signalling Technology	8940
TrypLE Express enzyme	Thermo Fisher Scientific	11528856
ReLeSR	STEMCELL Technologies	05873
DMEM/F12	Sigma-Aldrich	D6421
DMEM/F12 without phenol red	Sigma-Aldrich	D6434
Dulbecco’s phosphate buffered saline (PBS)	Sigma-Aldrich	D1408
FastDigest EcoRI	Thermo Fisher Scientific	FD0275
Critical commercial assays
DNeasy Blood & Tissue Kit	QIAGEN	69504
RNAeasy Plus Mini Kit	QIAGEN	74134
Qubit RNA HS Assay Kit	Thermo Fisher Scientific	Q32855
Silicone culture-inserts 2 well	Ibidi	80209
Transwell 8.0μm PET membrane inserts	Millipore	PIEP12R48
TaqMan Fast Universal Master Mix	Thermo Fisher Scientific	4352042
Deposited data
RNA-Seq	This paper	ArrayExpress: EMBLE-MTAB-10193
Experimental models: Cell lines
H7 (WA07) hPSC line	Thomson et al., 1998	RRID:CVCL_9772
H7-H2B-RFP; H7 hPSCs constitutively expressing H2B-RFP (in this study referred to as wild-type-RFP cells)	This paper	RRID:CVCL_A5NJ
H7-YAP; H7 hPSCs overexpressing YAP (in this study referred to as wild-type-YAP)	This paper	RRID:CVCL_A5LL
H7v1q; H7 hPSCs with a gain of chromosome 1q (in this study referred to as v1q)	This paper	RRID:CVCL_A5KR
H7v17q; H7 hPSCs with a gain of chromosome 17q (in this study referred to as v17q)	This paper	RRID:CVCL_A5KS
H7v20q; H7 hPSCs with a gain of chromosome 20q (in this study referred to as v20q)	This paper	RRID:CVCL_A5KT
H7v1,17q,i20; H7 hPSCs with a gain of chromosomes 1, 17q and isochromosome 20 (in this study referred to as v1,17q,i20)	This paper	RRID:CVCL_A5LK
H7v1,12,17q,20q-GFP; H7.s6-GFP (in this study referred to as variant-GFP)	Baker et al., 2016	RRID:CVCL_A5KW
H14 (WA14) hPSC line	Thomson et al., 1998	RRID:CVCL_9775
H14-H2B-RFP; H14 hPSCs constitutively expressing H2B-RFP (in this study referred to as H14 wild-type-RFP)	This paper	RRID:CVCL_A5NK
H14-YAP; H14 hPSCs overexpressing YAP (in this study referred to as H14 wild-type-YAP)	This paper	RRID:CVCL_A5LM
H14.BJ1-GFP; H14 hPSCs with a gain of chromosomes 12 and 17 and stably expressing GFP (in this study referred to as H14 variant-BJ1)	Baker et al., 2016	RRID:CVCL_A5KX
HUES 17 hPSC line	Cowan et al., 2004	RRID:CVCL_B147
HUES 17-H2B-RFP; HUES 17 hPSCs constitutively expressing H2B-RFP (in this study referred to as HUES-17 wild-type-RFP)	This paper	RRID:CVCL_A5NL
HUES 17v12,17; HUES 17 hPSCs with a gain of chromosomes 12 and 17 (in this study referred to as HUES-17v12,17)	This paper	RRID:CVCL_A5KC
Oligonucleotides
PrimeTime qPCR Assay: TERT	Integrated DNA Technologies	Hs.PT.58.27489922
PrimeTime qPCR Assay: KLF5	Integrated DNA Technologies	Hs.PT.56a.40282397
PrimeTime qPCR Assay: KLF4	Integrated DNA Technologies	Hs.PT.58.45542593
PrimeTime qPCR Assay: KLF2	Integrated DNA Technologies	Hs.PT.58.39339409
PrimeTime qPCR Assay: GBX2	Integrated DNA Technologies	Hs.PT.58.803756
PrimeTime qPCR Assay: POU5F1	Integrated DNA Technologies	Hs.PT.58.14648152.g
PrimeTime qPCR Assay: SOX2	Integrated DNA Technologies	Hs.PT.58.237897.g
PrimeTime qPCR Assay: ACTB	Integrated DNA Technologies	Hs.PT.39a.22214847
PrimeTime qPCR Assay: YAP1	Integrated DNA Technologies	Hs.PT.58.14881945
PrimeTime qPCR Assay: TFCP2L1	Integrated DNA Technologies	Hs.PT.58.26495531
PrimeTime qPCR Assay: NANOG	Integrated DNA Technologies	Hs.PT.58.21480849
PrimeTime qPCR Assay: OTX2	Integrated DNA Technologies	Hs.PT.58.46695245
PrimeTime qPCR Assay: DPPA3	Integrated DNA Technologies	Hs.PT.58.2165190
PrimeTime qPCR Assay: TBX3	Integrated DNA Technologies	Hs.PT.58.3646164
PrimeTime qPCR Assay: DNMT3B	Integrated DNA Technologies	Hs.PT.58.5075361
PrimeTime qPCR Assay: GATA6	Integrated DNA Technologies	Hs.PT.58.38396504
PrimeTime qPCR Assay: Lin28A	Integrated DNA Technologies	Hs.PT.58.24268123
PrimeTime qPCR Assay: ZFP42	Integrated DNA Technologies	Hs.PT.58.23001209
TaqMan® Gene Expression Assay: ACTB	ThermoFisher Scientific	Hs99999903_m1
TaqMan® Gene Expression Assay: YAP1	ThermoFisher Scientific	Hs00902712_g1
TaqMan® Gene Expression Assay: CTGF	ThermoFisher Scientific	Hs00170014_m1
TaqMan® Gene Expression Assay: CYR61	ThermoFisher Scientific	Hs00155479_m1
ESIRNA HUMAN YAP1	Sigma-Aldrich	EHU113021-20UG
ESIRNA RLUC	Sigma-Aldrich	EHURLUC-20UG
Recombinant DNA
pGAMA-YAP	Qin et al., 2016	RRID:Addgene_74942
pCAGeGFP	Liew et al., 2007	N/A
pCAG-YAP	This paper	N/A
pCAG-H2B-RFP	A kind gift from Dr Jie Na, Tsinghua University, Beijing	N/A
Software and algorithms
Cell Profiler	Carpenter et al., 2006	RRID:SCR_007358
R	R Core Team	RRID:SCR_001905
FlowJo Software v10	FlowJo	RRID:SCR_008520
FIJI	Schindelin et al., 2012	RRID:SCR_002285
DESeq2	Love et al., 2014	RRID:SCR_015687
PANTHER v14	Mi et al., 2019	RRID:SCR_004869
ReViGO	Supek et al., 2011	RRID: SCR_005825
GraphPad Prism 9.0.2	Prism	RRID:SCR_002798
Developer Toolbox 1.7	GE Healthcare	RRID:SCR_015790
QuantStudio 12K Flex Software	Applied Biosystems	N/A
Sortware	BD	N/A
TreeGraph 2	Stöver and Müller, 2010	N/A
Interactive Tree of Life (iTOL)	Letunic and Bork, 2007	N/A
arivis Vision4D	arivis AG	RRID:SCR_018000
ZEN Digital Imaging for Light Microscopy	ZEISS	RRID:SCR_013672
Other
Manual Cell Stretching System	STREX Inc.	STB-100-10
4-well PDMS Stretch Chamber	STREX Inc.	STB-CH-4W