REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Goat Anti-Human KLF4 affinity-purified polyclonal antibody	R&D	Cat#AF3640, RRID:AB_2130224
RNA pol II mouse monoclonal antibody	Active Motif	Cat#39097, RRID:AB_2732926
Alexa Fluor 488 Mouse anti-Human TRA-1-60 Antigen	BD Pharmingen	Cat#560173, RRID:AB_1645379
Human TRA-1-85/CD147 APC-conjugated Antibody	R&D	Cat#FAB3195A, RRID:AB_663789
Monoclonal ANTI-FLAG M2 antibody produced in mouse	Sigma	Cat#F1804, RRID:AB_262044
Mouse Anti-Human/Mouse/Rat GAPDH/G3PDH Monoclonal Antibody	R&D	Cat#MAB5718, RRID:AB_10892505
Anti-KLF4 polyclonal Rabbit Ig Antibodies	MBL	Cat#PM057, RRID:AB_10598180
Ubiquitin (P4D1) Mouse mAb	Cell Signaling Technology	Cat#3936, RRID:AB_331292
Anti-SOX2 antibody, Polyclonal Goat IgG	R&D systems	Cat#AF2018, RRID:AB_355110
Normal Goat IgG Control	R&D systems	Cat#AB-108-C, RRID:AB_354267
Chemicals, peptides, and recombinant proteins
ChIP-IT Protein G Magnetic Beads	Active Motif	Cat#53014
Polybrene Solution	Nacalai Tesque	Cat#12996-81
Blasticidin S Hydrochloride	Wako	Cat#029-18701
FuGENE 6 Transfection Reagent	Promega	Cat#E2692
Shield1	Takara Bio	Cat#632189
Fibroblast Growth Factor (basic)	Wako	Cat#060-04543
CultureSure Y-27632	Wako	Cat#034-24024
iMatrix-511, silk (Laminin-511)	Nippi	Cat# 892021
STEM-CELLBANKER GMP Grade	Takara Bio	Cat# CB045
FuGENE6 Transfection Reagent	Promega	Cat#E2691
SDS-PAGE Sample Buffer Solution without 2-ME(2x) for SDS-PAGE	Nacalai Tesque	Cat#30567-12
1mol/l-Dithiothreitol Solution (DTT)	Nacalai Tesque	Cat#14130-41
Critical commercial assays
PrimeSTAR Mutagenesis Basal Kit	Takara Bio	Cat#R046A
ChIP-IT Express	Active Motif	Cat# 53008
Chromatin IP DNA Purification Kit	Active Motif	Cat# 58002
ChIP-IT Control qPCR Kit – Mouse	Active Motif	Cat# 53027
Universal Magnetic Co-IP Kit	Active Motif	Cat# 54002
Anti-Mouse Detection Module for Jess, Wes, Peggy Sue or Sally Sue	ProteinSimple	Cat#DM-002
Monarch Total RNA Miniprep Kit	New England BioLabs	Cat#T2010S
FastGene Premium RNA extractioni Kit	Nippon Genetics Co. Ltd.	Cat#FG-81250
Retrovirus Titer Set (for Real Time PCR)	Takara Bio	Cat#6166
One Step TB Green PrimeScript RT-PCR Kit (Perfect Real Time)	Takara Bio	Cat#RR066A
Retro-X Concentrator	Takara Bio	Cat#Z1455N
Recombinant DNase I (RNase-free)	Takara Bio	Cat#2270A
Recombinant RNase Inhibitor	Takara Bio	Cat#2313A
12-230 kDa Jess or Wes Separation Module, 8 x 25 capillary cartridges	Protein Simple	Cat#SM-W004
Anti-Mouse Detection Module for Jess, Wes, Peggy Sue or Sally Sue	Protein Simple	Cat#DM-002
Anti-Goat Detection Module for Jess, Wes, Peggy Sue or Sally Sue	Protein Simple	Cat#DM-006
Deposited data
Crystal Data (KLF4 zinc finger)	www.rcsb.org	PDB ID: 2WBU
Crystal Data (Klf4 zinc finger)	www.rcsb.org	PDB ID: 4M9E
Raw and analyzed data of ChIP-seq	This paper	GEO: GSE157762
Raw and analyzed data of RNA-seq	This paper	GEO: GSE184449
Experimental models: Cell lines
Mouse embryonic fibroblasts isolated from Tg(Nanog-GFP,Puro)1Yam mice featuring transgenic GFP driven by Nanog promoter	This study	NA
Platinum-E (Plat-E) Retroviral Packaging Cell Line	Cell Biolabs, Inc.	Cat#RV-101
Platinum-GP (Plat-GP) Retroviral Packaging Cell Line	Cell Biolabs, Inc.	Cat#RV-103
Normal human skin fibroblast (NB1RGB)	RIKEN BRC Cell Bank	Cat#RCB0222
SL10 feeder cells	Reprocell	Cat#RCHEFC001
Experimental models: Organisms/strains
Mouse: STOCK Tg(Nanog-GFP,Puro)1Yam	RIKEN BRC (Okita et al., 2007)	RBRC 02290
Oligonucleotides
Primers for plasmid construction, see Table S2 (KLF4 alanine mutants)	This paper
Recombinant DNA
Plasmids made in this study, see Table S3	This paper
pMXs-hKLF4	Laboratory of Plath (Lowry et al., 2008)	Addgene plasmid Cat#17967
pMXs-hOCT3/4	Laboratory of S. Yamanaka (Takahashi et al., 2007)	Addgene plasmid Cat#17217
pMXs-hSOX2	Laboratory of S. Yamanaka (Takahashi et al., 2007)	Addgene plasmid Cat#17218
pMXs-Hu-L-Myc	Laboratory of S. Yamanaka (Nakagawa et al., 2008)	Addgene plasmid #26022
pMXs-mRFP1	Laboratory of J. Ellis (Hotta et al., 2009)	Addgene plasmid Cat#21315
pMXs-p53DD	Laboratory of S. Yamanaka (Hong et al., 2009)	Addgene plasmid Cat#22729
pCMV-VSV-G	Laboratory of H. Miyoshi, RIKEN BRC DNA Bank	Cat#RDB04392
pMXs-hFOXH1	Laboratory of S. Yamanaka (Takahashi et al., 2014)	Addgene plasmid Cat#59183
pMXs-GLIS1	Laboratory of S. Yamanaka (Maekawa et al., 2011; Worringer et al., 2014)	Addgene plasmid Cat#30166
pMXs-ms-Klf5	Laboratory of S. Yamanaka (Nakagawa et al., 2008)	Addgene plasmid Cat#50787
pMXs-MC	Laboratory of D. Pei (Liao et al., 2011)	Addgene plasmid Cat#31704
pMXs-MB	Laboratory of D. Pei (Liao et al., 2011)	Addgene plasmid Cat#31703
pMXs-hNANOG (Plath)	Laboratory of K. Plath (Lowry et al., 2008)	Addgene plasmid Cat#18115
SeVdp(fKgOSMaB)	This paper	NA
SeVdp(fK[507]gOSMaB)	This paper	NA
Software and algorithms
Bowtie2	(Langmead and Salzberg, 2012)	http://bowtie-bio.sourceforge.net/index.shtml
MACS2	(Zhang et al., 2008)	https://github.com/taoliu/MACS
CLC genomics workbench	Qiagen	https://digitalinsights.qiagen.com/ja/qiagen-clc-genomics-workbench/