REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse Anti-α-Tubulin (DM1A)	Sigma	Cat# T9026; RRID:AB_477593
Rabbit polyclonal anti-CTCF	Millipore	Cat# 07-729; RRID:AB_441965
Goat polyclonal Anti-Rabbit HRP	DAKO	P0448; RRID:AB_2617138
Goat polyclonal Anti-Mouse HRP	DAKO	P0447; RRID:AB_2617137
Rabbit polyclonal anti-CTCF	Diagenode	Cat# C15410210-50; RRID:AB_2753160
Rat anti-CD43 MicroBeads	Miltenyi Biotec	Cat# 130-049-801; RRID:AB_2861373
Chemicals, peptides, and recombinant proteins
ACK Lysing Buffer	Lonza	Cat# BP10-548E
Critical commercial assays
RNeasy Mini Kit	Qiagen	Cat# 74104
Power SYBR Green PCR Master Mix	Applied Biosystems	Cat# 4367659
iDeal ChIP-seq Kit for Transcription Factors	Diagenode	Cat# C01010055
Deposited data
Raw and analyzed data	This paper	GEO: GSE207640
ChIP-seq, ChIA-PET and Hi-C	Kieffer-Kwon et al.36 and Vian et al.38	GEO: GSE82144 GEO: GSE98119
Hi-C	Rao et al.4	4D nucleome: 4DNESK95HVFB
TAD and intra-TAD loop anchors	Matthews and Waxman9	GEO: GSE102999
CTCF binding sites	Luan et al.25	GEO: GSE150415
Experimental models: Organisms/strains
Mouse: CTCFfl/fl	Heath et al.27	N/A
Mouse: B6.129P2(C)-Cd19tm1(cre)Cgn/J	Jackson laboratories	Cat# 006785; RRID:IMSR_JAX:006785
Oligonucleotides
CTCF deletion Fwd GGGCATCAGATCTCATTAAGGA	Perez-Garcia et al.31	N/A
CTCF deletion Rv ACTCCATCTCTAGCCTCTCTATT	Perez-Garcia et al.31	N/A
Software and algorithms
Loop prediction algorithm	This paper, GitHub	https://github.com/ARRlab/Loop_prediction_algorithm
Prism – version 6	GraphPad	https://www.graphpad.com/scientificsoftware/prism
R	RCoreTeam	http://www.R-project.org/
MACS2	Zhang et al.48	https://github.com/macs3-project/MACS/
BedTools	Quinlan and Hall49	https://bedtools.readthedocs.io/en/latest/
DESeq2	Love et al.50	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
HOMER	Heinz et al.51	http://homer.ucsd.edu/
deeptools	Ramírez et al.52	https://deeptools.readthedocs.io/en/develop/
FastQC	Krueger et al.53	http://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Cutadapt	Criscuolo and Brisse54	http://code.google.com/p/cutadapt/
BWA	Li and Durbin55	http://bio-bwa.sourceforge.net/
Picard	Broad Institute	http://broadinstitute.github.io/picard
bamtools	Barnett et al.56	https://github.com/pezmaster31/bamtools/wiki
ChIPQC	Carroll et al.57	https://doi.org/10.18129/B9.bioc.ChIPQC
DiffBind	Ross-Innes et al.58	http://bioconductor.org/packages/release/bioc/html/DiffBind.html
samtools	Li et al.59	http://htslib.org/
IGV	Robinson et al.60	http://www.broadinstitute.org/igv/
ChIPseeker	Yu et al.61	https://bioconductor.org/packages/ChIPseeker/
Spamo - MEMEsuite	Whitington et al.62	http://meme-suite.org/
Other
CTCF signal visualization	This paper, UCSC genome browser	https://genome.ucsc.edu/s/lab_arr/mm10