REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and virus strains
e. cloni 10G supreme electrocompetent E. coli	Lucigen	Cat# 60081-1
5-alpha competent bacteria	NEB	Cat# C2987
Chemicals, peptides, and recombinant proteins
My-Taq Red mix	Bioline	Cat# BIO-25044
Fast-link ligase	Lucigen	Cat# LK0750H
Klenow HC 3′→5′exo−	NEB	Cat# M0212L
CleanPCR magnetic beads	CleanNA	Cat# CPCR-0050
Gibson Assembly® Master Mix	NEB	Cat# E2611S
XmaJI (AvrII) restriction enzyme	Thermo Fischer	Cat# ER1561
XcmI restriction enzyme	NEB	Cat# R0533
NheI restriction enzyme	NEB	Cat# R0533
T4 DNA ligase	Roche	Cat# 10799009001
I-CeuI restriction enzyme	NEB	Cat# R0699S
I-SceI restriction enzyme	NEB	Cat# R0694S
TRIsure	Bioline	Cat# BIO-38032
DNase I recombinant, RNase-free	Roche	Cat# 04716728001
Maxima reverse transcriptase	Thermo Fischer	Cat# EP0743
Neurobasal medium	Gibco	Cat# 21103-049
DMEM-F12 medium	Gibco	Cat# 11320-033
N27	Gibco	Cat# 17504-044
B2	Gibco	Cat# 17502-048
LIF	Sigma-Aldrich	Cat# ESG1107
CHIR-99021	MedChemExpress	Cat# HY-10182
PD0325901	MedChemExpress	Cat# HY-10254
monothioglycerol	Sigma	Cat# M6145-25ML
Critical commercial assays
ISOLATE II PCR and Gel Kit	Bioline	Cat# BIO-52059
End-It DNA End-Repair Kit	Epicentre	Cat# ER0720
Takara ligation kit version 2.1	Takara	Cat# 6022
PureLink HiPure Plasmid Filter Maxiprep Kit	Invitrogen	Cat# K210016
Mouse Embryonic Stem Cell Nucleofector Kit	Lonza	Cat# VPH-1001
GeneJET RNA Purification Kit	Thermo Fischer	Cat# K0732
MycoAlert Mycoplasma Detection Kit	Lonza	Cat# LT07-318
Deposited data
Raw and Processed data	This study	GEO: GSE186265
Code	This Study	GitHub: https://github.com/vansteensellab/EPCombinations https://doi.org/10.5281/zenodo.6406791
Annotated mouse TSSs	GENCODE	Release vM16: https://www.gencodegenes.org/mouse/release_M16.html
mESC TAD coordinates	Bonev et al., 2017	Supplementary Table: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5651218/bin/mmc2.xlsx
Mouse reference genome mm10 genome build (GRCm38)	Genome Reference Consortium	https://www.ncbi.nlm.nih.gov/grc/mouse
DNAse Hypersensitivity mESCs 2i+lif	Joshi et al., 2015	GEO: GSE72164
DNAse Hypersensitivity mESCs serum	ENCODE	GEO: GSE37074
TF motif database	Diaferia et al., 2016	GitHub: https://github.com/vansteensellab/EPCombinations https://doi.org/10.5281/zenodo.6406791
RNA-seq mESCs 2i+lif	Joshi et al., 2015	GEO: GSE72164
ExP K562 count data	Bergman et al., 2022	GEO: GSE184426
MicroC mESCs	Hsieh et al., 2020	GEO: GSE130275
Experimental models: Cell lines
E14TG2a mESCs	ATCC	Cat# CRL-1821
Oligonucleotides
Table S3	This Study	N/A
Recombinant DNA
SuRE vector (JvAp101)	van Arensbergen et al., 2017	N/A
Downstream Assay vector (JvAp102)	This Study	N/A
Software and algorithms
Homer v4.10	Heinz et al., 2010	http://homer.ucsd.edu/homer/data/software/homer.v4.10.zip
BatchPrimer3 v1.0	You et al., 2008	https://wheat.pw.usda.gov/demos/BatchPrimer3/
R version 4.0.5 (2021-03-31)	R Core Team, 2021	https://www.r-project.org/
ggplot2	Wickham, 2016	https://ggplot2.tidyverse.org/
Bowtie2 version 2.3.4	Langmead and Salzberg, 2012	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Python version 3.6.2	Rossum and Drake, 2009	https://www.python.org/downloads/release/python-362/
Snakemake version 4.4.0	Köster and Rahmann, 2012	https://anaconda.org/bioconda/snakemake/files?version=4.4.0
Starcode version 1.1	Zorita et al., 2015	https://github.com/gui11aume/starcode
MEME suite version 5.0.2	Bailey et al., 2009	https://meme-suite.org/meme/doc/download.html
HRT Atlas v1.0	Hounkpe et al., 2021	www.housekeeping.unicamp.br
Other
Hamilton Microlab® STAR	Hamilton	https://www.hamiltoncompany.com/automated-liquid-handling/platforms/microlab-star