REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit monoclonal anti-SOX2	BioGenex	Cat# NU579-UC
Mouse anti-HuNu (Clone 235-1)	Millipore	Cat# MAB1281; RRID: AB_11212527
Rabbit anti-monomeric Kusabira-Orange 2	MBL	Code# PM051M
Rabbit anti-GFP	MBL	Code# 598
Rat monoclonal anti-cytokeratin 8/18 (TROMA-I)	DSHB	RRID: AB_531826
Mouse monoclonal anti-epithelial antigen	DAKO	Cat# M0804; RRID: AB_2335685
Mouse monoclonal anti-Ep-CAM	Santa Cruz	Cat# sc-25308; RRID: AB_627531
Mouse monoclonal anti-actin α-smooth muscle (Clone 1A4)	Sigma-Aldrich	Cat# A5228; RRID: AB_262054
Rabbit polyclonal anti-Histone H3 (tri methyl K9)	Abcam	Cat# ab8898; RRID: AB_306848
Rabbit polyclonal anti-Histone H4 (tri methyl K20)	Abcam	Cat# ab9053; RRID: AB_306969
Rat anti-Mouse CD31 (Clone MEC13.3)	BD PharMingen	Cat# 553370; RRID: AB_394816
Mouse monoclonal anti-Oct3/4 (C-10)	Santa Cruz	Cat# sc-5279; RRID: AB_628051
Mouse anti-Tubulin β3 (Clone TUJ1)	BioLegend	Cat# 801202; RRID: AB_10063408
Chemicals, Peptides, and Recombinant Proteins
Y-27632 dihydrochloride	Torcris	Cat# 1254
Recombinant human FGF-basic (FGF2)	Peprotech	Cat# 100-18B
Recombinant human LIF	Peprotech	Cat# 300-05
CHIR99021	Selleckchem	Cat# S2924
PD035901	Selleckchem	Cat# S1036
L-ascorbic acid 2-phosphate	Sigma-Aldrich	Cat# A8960
Recombinant human IGF-I LR3	Peprotech	Cat# 100-11R3
Recombinant human TGF-β1	Peprotech	Cat# 100-21C
SB203580	Selleckchem	Cat# S1076
SP600125	Selleckchem	Cat# S1460
LDN193189	Selleckchem	Cat# S2618
Recombinant human/murine/rat Activin A	Peprotech	Cat# 120-14P
Doxycycline hyclate (dox)	Stemgent	Cat# 04-0016
Critical Commercial Assays
MEGAshortscript T7 Transcription Kit	Invitrogen	Cat# AM1354
MEGAclear Transcription Clean-up Kit	Ambion	Cat# AM1908
Cas9 mRNA	Sigma-Aldrich	Cat# CAS9MRNA-1EA
P2 Primary Cell 4D-Nucleofector kit	Lonza	Cat# V4XP-2024
NucleoSpin Gel and PCR Clean-up	MACHEREY-NAGEL	Cat# 740609
DNeasy Blood and Tissue kit	QIAGEN	Cat# 69506
PicoPure DNA Extraction Kit	Thermo Fisher Scientific	Cat# KIT0103
SYBR Green PCR Master Mix	Thermo Fisher Scientific	SKU# 4309155
Experimental Models: Cell Lines
DAC2	Li et al., 2008	N/A
DAC8	Li et al., 2008	N/A
SDFE	This paper	N/A
SDFF	This paper	N/A
iPS-MEF-Ng-20D-17	RIKEN BRC	Cat# APS001
HFF hiPSCs	This paper	N/A
NHSM-hiPSCs	This paper	N/A
2iLD-hiPSCs	This paper	N/A
4i-hiPSCs	This paper	N/A
FAC-hiPSCs	This paper	N/A
Human foreskin fibroblast (HFF)	ATCC	CRL-2429
Experimental Models: Organisms/Strains
Mouse: C57BL/6J	The Jackson Laboratory	Stock No: 000664
Mouse: B6D2F1/J	The Jackson Laboratory	Stock No: 100006
Mouse: ICR (CD1)	Envigo	Order code: 030
Mouse: NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ	The Jackson Laboratory	Stock No: 005557
Rat: Sprague Dawley	Envigo	Order code: 002
Pig: Large-White × Landrace	Murcia, Spain	N/A
Pig: Pietrain	Murcia, Spain	N/A
Pig: Yorkshire	University of California Davis	N/A
Pig: Yorkshire cross	University of California Davis	N/A
Recombinant DNA
pCXLE-hOCT3.4-shp53-F	Okita et al., 2011	Addgene Plasmid #27077
pCXLE-EGFP	Okita et al., 2011	Addgene Plasmid #27082
pCXLE-hSK	Okita et al., 2011	Addgene Plasmid #27078
pCXLE-hUL	Okita et al., 2011	Addgene Plasmid #27080
pFUW-tetO-hKlf2	This paper	N/A
pFUW-tetO-hNanog	This paper	N/A
pCAG-IP-humanized Kusabira Orange	This paper	N/A
pmKO1-MC1	MBL	Code No. AM-V0052M
LV-tetO-FU-Oct3/4	Hockemeyer et al., 2008	Addgene Plasmid #20726
LV-tetO-FU-Sox2	Hockemeyer et al., 2008	Addgene Plasmid #20724
LV-tetO-FU-KLF4	Hockemeyer et al., 2008	Addgene Plasmid #20725
LV-tetO-FU-Myc	Hockemeyer et al., 2008	Addgene Plasmid #20723
LV-FUW-M2rtTA	Hockemeyer et al., 2008	Addgene Plasmid #20342
pEGIP	Zou et al., 2009	Addgene Plasmid#26777
pMDLg/pRRE	Dull et al., 1998	Addgene Plasmid #12251
pRSV-Rev	Dull et al., 1998	Addgene Plasmid #12253
pMD2.G	pMD2.G was a gift from Didler Trono	Addgene Plasmid #12259
Sequence-Based Reagents
sgRNA sequences, see Table S2	This paper	N/A
Genomic PCR primers, see Table S2	This paper	N/A
DNA sequencing primers, see Table S2	This paper	N/A
Genomic qPCR primers, see Table S2	This paper	N/A
Software and Algorithms
CRISPR Design	MIT	http://crispr.mit.edu