KEY RESOURCES TABLE.

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and Virus Strains
Escherichia coli Rosetta (DE3) pLysS	Novagen	Cat#70956-3
Escherichia coli BL21 (DE3)	Invitrogen	N/A
Chemicals, Peptides, and Recombinant Proteins
Cy3 NHS Ester mono-reactive dye	GE Healthcare	Cat# PA23001
Cy3 maleimide mono-reactive dye	GE Healthcare	Cat# PA23031
Cy5 maleimide mono-reactive dye	GE Healthcare	Cat# PA15131
Alexa Fluor 488 C5 maleimide	Invitrogen	Cat# A10254
Coenzyme A trilithium salt	Sigma-Aldrich	Cat# C3019
(3-Aminopropyl)triethoxysilane	Vector Laboratories	Cat# SP-1800
Trolox	Sigma-Aldrich	Cat# 238813
Glucose oxidase	Sigma-Aldrich	Cat# G2133
Dextrose monohydrate	Sigma-Aldrich	Cat# D9559
Catalase	Sigma-Aldrich	Cat# C100
Bio-PEG-SVA, MW 5,000	Laysan Bio	Cat# 143-117
mPEG-SVA, MW 5,000	Laysan Bio	Cat# 144-136
MS(PEG)4 methyl-PEG4-NHS Ester	Thermo Fisher Scientific	Cat# 22341
Streptavidin	Thermo Fisher Scientific	Cat# 434302
Nanostrip	VWR	Cat# 10135-756
Igepal CA-630	Sigma-Aldrich	Cat# I8896
DNase I	Invitrogen	Cat# 18068015
NEBNext Ultra II DNA Library Prep Kit	New England Biolabs	Cat# E7645
SYBR Gold	Invitrogen	Cat# S11494
Oligonucleotides
See Table S1	This paper	N/A
Recombinant DNA
pEP4 E02S CK2M EN2L	Addgene	Cat# 20924
human Sox2 in pET28B vector	This paper	N/A
human Oct4 with C-terminal Sfp tag in pET28B vector	This paper	N/A
human c-Myc with C-terminal Sfp tag in pET28B vector	This paper	N/A
human Max in pET28B vector	This paper	N/A
Sfp enzyme in pET29B vector	Addgene	Cat# 75015
Xenopus laevis histones	This paper	N/A
601 plasmid in pBluescript II SK vector	(Lietal., 2010)	N/A
mutant 601 plasmids	This paper	N/A
Software and Algorithms
SPARTAN	(Juette et al., 2016)	https://www.scottcblanchardlab.com/software
ORIGIN	OriginLab	https://www.originlab.com
MATLAB	MathWorks	https://www.mathworks.com/products/matlab.html
PRISM	GraphPad	https://www.graphpad.com/scientific-software/prism
PYMOL	Schrödinger, LLC	http://www.pymol.org
Custom analysis scripts	This paper	https://www.github.com/LiZhaoLab/Oct4Sox2_nuclpos/