REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse monoclonal anti-H3	Active motif	Cat# 39763; RRID:AB_2650522
Rabbit monoclonal anti-H3K4me3	Millipore	Cat# 04-745; RRID:AB_1163444
Rabbit polyclonal anti-H3K27me3	Millipore	Cat# 07-449; RRID:AB_310624
Rabbit monoclonal anti-H3K27me3	Cell Signaling Technology	Cat# 9733; RRID:AB_2616029
Rabbit polyclonal anti-H3K27me3	Diagenode	Cat# C15410195; RRID:AB_2753161
Rabbit monoclonal anti-H3K27me2	Cell Signaling Technology	Cat# 9728; RRID:AB_1281338
Rabbit monoclonal anti-H3K27me1	Cell Signaling Technology	Cat# 5326; RRID:AB_10695148
IRDye 800CW Donkey anti-Mouse IgG (H + L)	LI-COR Bio-sciences	Cat# 926-32210; RRID:AB_621842
IRDye 680RD Donkey anti-Rabbit IgG (H + L)	LI-COR Bio-sciences	Cat# 926-68073; RRID:AB_10954442
Chemicals, Peptides, and Recombinant Proteins
Micrococcal Nuclease	NEB	Cat# M0247S
Proteinase K	Life technologies	Cat# 25530015
RNase A	Life technologies	Cat# EN0531
RNase H	NEB	Cat# M0297S
GSK-J4	Sigma	Cat# SML0701
Zebularin	Sigma	Cat# Z4775
EZSolution EPZ-6438	BioVision	Cat# 2428
Accutase solution	Sigma	Cat# A6964
PD0325901	Sigma	Cat# PZ0162
CHIR99021	Sigma	Cat# SML1046
Critical Commercial Assays
End-It DNA End-Repair kit	Lucigen	Cat# ER81050
Fast-Link DNA Ligation kit	Lucigen	Cat# LK6201H
SureBeads Protein A/G Magnetic beads	Biorad	Cat# 161-4013/4023
Silane beads	Life technologies	Cat# 37002D
Agencourt AMPure XP	Beckman Coulter	Cat# A63881
High Sensitivity DNA Kit for Bioanalyzer	Agilent	Cat# 5067-4626
Qubit DSDNA HS Assay Kit	Life technologies	Cat# Q32854
Qubit RNA HS Assay Kit	Life technologies	Cat# Q32855
HiScribe T7 Quick High Yield RNA Synthesis kit	NEB	Cat# E2050S
T4 RNA Ligase 2, truncated	NEB	Cat# M0242L
SuperScript III First-Strand Synthesis SuperMix	Life technologies	Cat# 18080-400
NEBNext® High-Fidelity 2X PCR Master Mix	NEB	Cat# M0541L
NextSeq® 500/550 High Output Kit v2 (75 cycles)	Illumina	Cat# 20024906
Deposited Data
All NGS data	This study	GEO: GSE126252
Genomic files and Pseudocode	This study, Mendeley Data	https://doi.org/10.17632/s23bhg4xjv.1
Experimental Models: Cell Lines
Mouse ESC: RW.4 (129/SvJ)	Karolinska Center for Transgene Technologies	N/A
Oligonucleotides
Primers	This study	See Table S1
Software and Algorithms
bcl2fastq (v2.20)	Illumina	http://emea.support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html
Bowtie 2 (v2.3.4.3)	Langmead and Salzberg, 2012	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
SAMtools (v1.9)	Li et al., 2009	http://www.htslib.org/
BEDtools (v2.27.1)	Quinlan, 2014	https://bedtools.readthedocs.io/en/latest/
Je	Girardot et al., 2016	https://gbcs.embl.de/portal/tiki-index.php?page=Je
deepTools (v3.1.0)	Ramírez et al., 2014	https://deeptools.readthedocs.io/en/develop/
Picard (v2.10.3)		https://broadinstitute.github.io/picard/
bwtool	Pohl and Beato, 2014	https://github.com/CRG-Barcelona/bwtool/
ngsplot	Shen et. al., 2014	https://github.com/shenlab-sinai/ngsplot
SeqPlots	Stempor and Ahringer, 2016	http://seqplots.ga
DESeq	Anders and Huber, 2010	http://bioconductor.org/packages/release/bioc/html/DESeq.html
R (v)	R core team	https://www.r-project.org/
Image Studio	LI-COR Bio-sciences	N/A
Other
Mod Spec® Service	Active Motif	Cat# 25085