REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
anti-H3K9me3 - Rabbit Polyclonal	Diagenode	Diagenode Cat# pAb-056-050; RRID:AB_2616051
anti-H3K27ac - Rabbit Polyclonal	Abcam	Abcam Cat# ab4729; RRID:AB_2118291
anti-KLF4 - Goat Polyclonal Goat	R&D Systems	RRID:AB_2130224
anti-OCT4 - Rabbit polyclonal	Abcam	Abcam Cat# ab19857; RRID:AB_445175)
Bacterial and Virus Strains
CRISPRi - pLV hU6-sgRNA hUbC-dCas9-KRAB-T2a-Puro	Addgene	#71236; RRID:Addgene_71236
lenti sgRNA(MS2)_zeo backbone	Addgene	#62205; RRID:Addgene_61427
CRISPRa - EF1a-NLS-dCas9(N863)-VP64-2A-Blast-WPRE	Addgene	#61425; RRID:Addgene_61425
CRISPRa - EF1a-MS2-p65-HSF1-2A-Hygro-WPRE	Addgene	#61426; RRID:Addgene_61426
FpG5 - Enhancer reporter vector	Addgene	#69443; RRID:Addgene_69443
pAIB-GFP-IRES-BSD	De Iaco et al., 2017	N/A
pAIB-KLF4-IRES-BSD	This paper	N/A
pAIB-KLF17-IRES-BSD	This paper	N/A
pRLL-GFP-IRES-BSD	This paper	N/A
pRLL-ZNF611-IRES-BSD	This paper	N/A
Chemicals, Peptides, and Recombinant Proteins
N2	Thermo Fisher Scientific	#17502048
B27	Thermo Fisher Scientific	#17504044
hLIF	Peprotech	#300-05
Activin A	Peprotech	#120-1
WH-4-023	SelleckChem	#S7565
PD0325901	Stemgent	#04-0006
CHIR99021	Stemgent	#04-0004
SB590885	R&D system	# 2650
Doxycycline	Sigma-Aldrich	#D9891
IM-12	Enzo life Sciences	#BML-WN102-0005
Y-27632	Abcam	# ab120129
Deposited Data
ATAC-seq - naive/primed hESC	This paper	GEO: GSE117395
ATAC-seq -naive hESC ± CRISPRi against SVA/LTR5Hs	This paper	GEO: GSE117395
ChIP-seq - KLF4 in naive hESC	This paper	GEO: GSE117395
ChIP-seq - H3K27ac in naive/primed hESC	This paper	GEO: GSE117395
ChIP-seq - KLF4 in HAP1 + OKS	This paper	GEO: GSE117395
ChIP-seq - H3K27ac in induced neurons	This paper	GEO: GSE117395
ChIP-seq - H3K9me3/H3K27ac in primed hESC + GFP, KLF4 or KLF17	This paper	GEO: GSE117395
ChIP-seq - H3K9me3/H3K27ac in naive hESC ± CRISPRi against SVA/LTR5Hs	This paper	GEO: GSE117395
ChIP-seq - H3K9me3/H3K27ac in naive hESC + GFP or ZNF611	This paper	GEO: GSE117395
RNA-seq - primed hESC + GFP, KLF4 or KLF17	This paper	GEO: GSE117395
RNA-seq - naive hESC ± CRISPRi against SVA/LTR5Hs	This paper	GEO: GSE117395
RNA-seq - induced neurons ± CRISPRi against SVA/LTR5Hs	This paper	GEO: GSE117395
RNA-seq - naive hESC ± CRISPRi against LTR7YB	This paper	GEO: GSE117395
RNA-seq - naive hESC + GFP or ZNF611	This paper	GEO: GSE117395
Experimental Models: Cell Lines
H1 - Human Embryonic Stem Cells	Male - Human Embryo - From Krause lab	N/A
WIBR3 - Human Embryonic Stem Cells	Female - Human Embryo - From Jaenisch lab	N/A
HEK293T	Female - Embryonic Kidney	N/A
HAP1	Male - derived from KBM-7 (chronic myeloid leukemia) - From Horizon discovery	N/A
Primary Dermal Fibroblast Normal; Human, Neonatal (HDFn)	Male - Neonatal - From ATCC	PCS-201-010
Oligonucleotides
See Table S3.	This paper	N/A
Software and Algorithms
FlowJo - FACS analysis	FlowJo, LLC	v8.8.7
Bowtie2 - Mapping DNA-sequencing	Langmead and Salzberg, 2012	v2.2
MarkDuplicates - Remove PCR duplicates	Picard tools	v1.1
Seqminer - Data visualiztation	Ye et al., 2014	v1.4
IGV - Data visualiztation	Robinson et al., 2011	v2.3
Samtools - Processing post-mapping	Li et al., 2009	v1.7
Homer - Enrichment analysis	Heinz et al., 2010	v3
Intervene - Intersection analysis	Khan and Mathelier, 2017	v0.6
MACS1.4 & MACS2 - Peak calling	Zhang et al., 2008	N/A
hg19 & RheMac8 - Genome Assembly		N/A
TopHat - Mapping RNA-sequencing	Kim et al., 2013	2.0.11
HTSeq-count - RNA-seq reads counting	Anders et al., 2015	0.6.1
multiBamCov - Bedtools	Quinlan and Hall, 2010	v2.27.1
limma - Bioconductor	Gentleman et al., 2004	Bioconductor version 3.7
UCSC liftOver tool	Karolchik et al., 2012	N/A
Shuffle - Bedtools	Quinlan and Hall, 2010	v2.27.1
getfasta tool - Bedtools	Quinlan and Hall, 2010	v2.27.1
MAFFT	Katoh et al., 2002	7.310
HISAT2 - Mapping RNA-sequencing	Kim et al., 2015	2.1.0
ETE toolkit	Huerta-Cepas et al., 2016	v3
Other
DNase-seq - pre-implantation embryo	Gao et al., 2018	GSA: CRA000297
DNase-seq - Roadmap tissues	Roadmap consortium	GEO: GSE18927
ChIA-PET - SMC1 in naive/primed hESC	Ji et al., 2016	GEO: GSE69643
ChIP-seq - OCT4 in naive/primed hESC	Ji et al., 2016	GEO: GSE69646
ChIP-seq - OCT4/KLF4 + OKSM in Human dermal fibroblast	Ohnuki et al., 2014	GEO: GSE56569
ChIP-seq - H3K27ac in fetal brain/liver	Yan et al., 2016	GEO: GSE63634
ChIP-seq - H3K27ac in adult liver	Trizzino et al., 2017	SRA: SRP091949
ChIP-seq - H3K27ac in adult brain	Vermunt et al., 2014	GEO: GSE40465
RNA-seq - Human Primordial Germ Cells	Tang et al., 2015	SRA: SRP057098
RNA-seq - Human dermal fibroblast reprogrammation by OKSM	Ohnuki et al., 2014	GEO: GSE56569
RNA-seq - single-cell Human embryo	Yan et al., 2013	GEO: GSE36552
RNA-seq - single-cell Rhesus Macaque embryo	Wang et al., 2017	GEO: GSE86938
RNA-seq - primed Rhesus Macaque and Human ESC	Fang et al., 2014	GEO: GSE61420