REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit polyclonal anti-SA1 (for ChIP and IP)	Remeseiro et al., 2012	N/A
Rat monoclonal anti-SA1 (for western blot)	Kojic et al., 2018	N/A
Rabbit polyclonal anti-SA2	Remeseiro et al., 2012	N/A
Rabbit polyclonal anti-SMC1	Remeseiro et al., 2012	N/A
Rabbit polyclonal anti-Rad21	Carretero et al., 2013	N/A
Rabbit polyclonal anti-Wapl	Kojic et al., 2018	N/A
Rabbit polyclonal anti-Ring1B	Luciano di Croce (CRG, Barcelona); Richly et al., 2010	N/A
Rabbit polyclonal anti-Suz12	Abcam	Cat#ab12073; RRID:AB_442939
Rabbit polyclonal anti-Nanog	Millipore	Cat# AB5731; RRID:AB_2267042
Mouse monoclonal anti-alpha-tubulin	Sigma	Cat#DM1A; RRID:AB_521686
Rabbit polyclonal anti-H3K27me3	Abcam	Cat#6002; RRID:AB_305237
Chemicals, Peptides, and Recombinant Proteins
PD0325901 (MEK inhibitor)	Sigma-Aldrich	Cat#PZ0162
CHIR99021 (GSK3 inhibitor)	Sigma-Aldrich	Cat#SML1046
Critical Commercial Assays
Dharmafect reagent 1	Dharmacon	Cat#T-2001-1
SYBR Green PCR Master Mix	Life Technologies	Cat#4367659
Dynabeads mRNA purification kit	Invitrogen	Cat#61006
Deposited Data
Raw and analyzed data ChIP-seq, RNA-seq, Hi-C	This paper	GSE126659
Experimental Models: Cell Lines
R1 129 murine male embryonic stem cells with 129/Sv background, passage 15-16	CNIO Transgenic mice Unit	N/A
Oligonucleotides
Stag1 siGENOME SMARTpool siRNA	Dharmacon	M-041989
Stag2 siGENOME SMARTpool siRNA	Dharmacon	M-049483
Primers for qRT-PCR, see Table S6	Life Technologies	N/A
Software and Algorithms
FlowJo software (version 9.3.1).	FlowJo	N/A
OligoPerfect Designer™	Invitrogen	https://www.thermofisher.com/es/es/home/life-science/oligonucleotides-primers-probes-genes/custom-dna-oligos/oligo-design-tools/oligoperfect.html
Nextpresso	Graña et al., 2018	http://bioinfo.cnio.es/nextpresso/
Samtools 0.1.16	Li et al., 2009	http://samtools.sourceforge.net/
‘Bowtie2′ (version 2.3.3.1)	Langmead and Salzberg, 2012	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
MACS2 (version 2.1.1.20160309)	Zhang et al., 2008	https://github.com/taoliu/MACS
BEDtools (version 2.27.1),	Quinlan and Hall, 2010	https://bedtools.readthedocs.io/en/latest/
deepTools 2.5.4	Ramírez et al., 2016	https://deeptools.readthedocs.io/en/develop/
TADbit	Serra et al., 2017	https://github.com/3DGenomes/tadbit.