REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-CTCF	Millipore	Cat# 07-729; RRID:AB_441965
Anti-SMC1	Bethyl	Cat# A300-055A; RRID:AB_2192467
Normal Rabbit IgG	CST	Cat# #2729; RRID:AB_1031062
Anti-TCF-1	CST	Cat# 2206S; RRID:AB_2199300
Biotin anti-mouse CD8a (53-6.7)	BioLegend	Cat# 100703, RRID:AB_312742
Anti-NIPBL	Bethyl	A301-779A; RRID:AB_1211232
Histone H3 (acetyl K27) antibody	Abcam	ab4729; RRID:AB_2118291
Anti-Histone H3 Antibody, Unconjugated	CST	Cat# 9715, RRID:AB_331563
PE anti-mouse CD4 (RM4-4)	BioLegend	Cat# 116005; RRID:AB_313690
APC anti-mouse CD8 (53-6.7)	BioLegend	Cat# 100711; RRID:AB_312750
PeCy7 anti-mouse CD25 (PC61)	BioLegend	Cat# 102015; RRID:AB_312864
Brilliant Violet 785™ anti-mouse/human CD44 (IM7)	BioLegend	Cat# 103041; RRID:AB_11218802
APC Streptavidin	BioLegend	Cat# 405207
Biotin anti-mouse Ly-6G/Ly-6C (Gr-1) (RB6-8C5)	BioLegend	Cat# 108403; RRID:AB_313368
Biotin anti-mouse NK1.1 (PK136)	BioLegend	Cat# 108703; RRID:AB_313390
Biotin anti-mouse CD11b (M1/70)	BioLegend	Cat# 101203, RRID:AB_312786
Biotin anti-mouse Ter119 (TER-119)	BioLegend	Cat# 116203, RRID:AB_313704
Biotin anti-mouse B220 (RA3-6B2)	BioLegend	Cat# 103203, RRID:AB_312988
Anti-rabbit IgG, HRP-linked Antibody	CST	Cat# 7074, RRID:AB_2099233
Bacterial and Virus Strains
One Shot Stbl3 Chemically Competent E. coli	Thermo	Cat# C737303
Chemicals, peptides, and recombinant proteins
Dulbecco’s Modified Eagle Medium (DMEM)	Thermo	Cat# 11965084
FBS (HyClone)	Cytiva	Cat# SH30910.03
Bovine Serum, heat inactivated	Thermo	Cat# 26170035
RPMI 1640 medium	Invitrogen	Cat# 11875085
L-Glutamine 200 mM	Lonza	Cat# 17-605E
MEM Non-Essential Amino Acids Solution (100X)	Invitrogen	Cat# 11140050
Sodium Pyruvate (100 mM)	Invitrogen	Cat# 11360070
Penicillin-Streptomycin	Gibco	Cat# 15140122
Gateway Clonase II LR	Thermo	Cat# 11791020
Gateway Clonase II BP	Thermo	Cat# 11789020
Polybrene	Sigma	Cat# TR-1003-G
Lipofectamine 3000	Thermo	Cat# L3000008
Fugene HD	Promega	Cat# E2311
Chloroquine	Sigma	Cat# C6628-25G
G418	GIBCO	Cat# 11811-023
Doxycycline	Sigma	Cat# D9891
Dimethylformamide	Sigma-Aldrich	Cat# D4551
Puromycin	Takara	Cat# 631305
Ethylene glycol bis(succinic acid N hydroxysuccinimideester) (EGS)	Thermo	Cat# 21565
DMSO	Fisher	Cat# BP231-1
Formaldehyde solution 16%	Thermo	Cat# PI28908
Glycine	Thermo	Cat# 15527013
cOmplete, Mini, EDTA-free Protease Inhibitor Cocktail	Roche	Cat# 11836170001
MboI	NEB	Cat# R0147
Biotin-14-dATP	Invitrogen	Biotin-14-dATP
dCTP	Invitrogen	Cat# 18253-013
dTTP	Invitrogen	Cat# 18255-018
dGTP	Invitrogen	Cat# 18254-011
Tris HCl, pH 7.5, 1M	Thermo	Cat# 15567027
NaCl, 5M	Thermo	Cat# AM9759
MgCl2 1M	Thermo	Cat# AM9530G
IGEPAL CA-630	Sigma	Cat# I8896-50ML
EDTA	Invitrogen	Cat# 15575-038
Protein A Magnetic beads	Pierce	Cat# 88846
Lithium Chloride, 8M	Sigma-Aldrich	Cat# L7026
Sodium bicarbonate	Sigma-Aldrich	Cat#144-55-8
T4 DNA Ligase	NEB	Cat# M0202L
BSA, 50mg/mL	Invitrogen	Cat# AM2616
Tween 20	BIO-RAD	Cat# 170-6531
DNA Polymerase I, Large (Klenow) Fragment	NEB	Cat# M0210S
Qubit dsDNA HS Assay Kit	Invitrogen	Cat# Q32851
Dynabeads MyOne Streptavidin C-1	Invitrogen	Cat# 65001
Phusion PCR Master Mix	NEB	Cat# M0531
Nextera XT Index Kit	Illumina	Cat# FC-131-1001
SPRIselect	Beckman Coulter	Cat# B23318
MinElute Reaction Cleanup Kit	QIAGEN	Cat# 28204
QIAQuick PCR Purification Kit	QIAGEN	Cat# 28104
Phosphate-Buffered Saline, 1X	Thermo	Cat# 10010031
RNase	Thermo	Cat# EN0531
Proteinase K	Thermo	Cat# AM2546
Protein G Dynabeads	Thermo	Cat# 10003D
2-Mercaptoethanol	Thermo	Cat# 21985023
Buffer RLT Plus	QIAGEN	Cat# 1053393
RNeasy Plus Micro Kit	QIAGEN	Cat# 74034
Trypsin-EDTA (0.05%)	Gibco	Cat# 25300054
RIPA Buffer (10X)	CST	Cat# 9806
NuPAGE LDS Sample Buffer (4X)	Thermo	Cat# NP0007
NuPAGE™ 4 to 12%, Bis-Tris, 1.0 mm, Mini Protein Gel, 10-well	Thermo	Cat# NP0321BOX
iBlot™ 2 Transfer Stacks, nitrocellulose, mini	Thermo	Cat# IB23002
Tris Buffered Saline with Tween® 20	CST	Cat# 9997S
SuperSignal™ West Femto Maximum Sensitivity Substrate	Thermo	Cat# 34095
Polysine adhesion glass slides	Electron Microscopy Sciences	Cat# 63412-01
Silicone Isolators	Electron Microscopy Sciences	Cat# 70339-05
Ethanol	Decon Laboratories	2716
Dimethylformamide	Sigma-Aldrich	Cat# D4551
Triton X-100	Sigma-Aldrich	Cat# T8787-250ML
Polyvinylsulfonic acid (PVSA)	Sigma-Aldrich	Cat# 278424
Fisherbrand™ Premium Cover Glasses	Fisher Scientific	Cat# 12-548-5M
Nowrinkle rubber cement	Elmer’s	Cat# 34633
Slowfade Gold Antifade Reagent	Invitrogen by Thermo Fisher Scientific	Cat# S36936
Secondary Oligopaint probe NDB_1279_Atto565: /5ATTO565N/ AGC GAA TCC GAC GCA CCG CTA /3ATTO565N/
Secondary Oligopaint probe NDB_1281_Alexa647: /5Alex647N/ AGG ACC CTG TTC GGC TAA CCA /3AlexF647N/
Dextran sulfate	Sigma Aldrich	Cat# D8906-50G
20X SSC buffer	Corning	Cat# 46-020-CM
Phosphate-Buffered Saline, 10X	Stemcell Technologies	Cat# 37354
Formamide, molecular grade	Promega	Cat# H5052
Formamide, > 99.5% (4 × 4L)	Sigma Aldrich	Cat# 221198-4X4L
dNTP mixture, 100mM (25mM of each)	Thomas Scientific	Cat# C788T68
RNase A, DNase and protease-free (10 mg/mL)	Thermo Fisher	Cat# EN0531
Defy & Inspire™ clear nail polish	Target Corporation	Cat# 052-06-3573
Critical commercial assays
Illumina Tagment DNA Enzyme and Buffer Large Kit	Illumina	Cat# 20034198
SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian	Takara	Cat# 634413
NEBNext Ultra II DNA Library Prep Kit for Illumina	NEB	Cat# E7645S
Arima HiC+ kit	Arima Genomics
Accel-NGS 2S Plus DNA Library Kit	Swift Biosciences	Cat# 21024
2S SET A INDEXING KIT	Swift Biosciences	Cat# 26148
KAPA Library Amplification Kit with Primer Mix	Roche	KK2620
Kapa library Quantification kit	Roche	7960140001
D1000 ScreenTape	Agilent	Cat# 5067-5582
D1000 Reagents	Agilent	Cat# 5067-5583
High Sensitivity D1000 ScreenTape	Agilent	Cat# 5067-5584
High Sensitivity D1000 Reagents	Agilent	Cat# 5067-5585
Genomic DNA ScreenTape	Agilent	Cat# 5067-5365
Genomic DNA Reagents	Agilent	Cat# 5067-5366
RNA ScreenTape	Agilent	Cat# 5067-5576
RNA ScreenTape Ladder	Agilent	Cat# 5067-5578
RNA ScreenTape Sample Buffer	Agilent	Cat# 5067-5577
EasySep™ Release Mouse Biotin Positive Selection Kit	Stemcell	Cat# 17655
EasySep™ Mouse CD4 Positive Selection Kit II	Stemcell	Cat# 18952
Recombinant DNA
Plasmid: pInducer20	Addgene	Cat# 44012; RRID:Addgene_44012
Plasmid: pSL21-vex	Addgene	Cat# 158230
Plasmid: MSCV-Cas9_Puro	Addgene	Cat# 65655
Plasmid: pCL-Eco	(Naviaux et al., 1996)
Deposited data
HiC, HiChIP, ChIPseq, RNAseq	This study	GSE178348
Publicly accessible data
TCF-1 ChIPseq in thymus	24	GSE46662
CTCF ChIPseq in DP T cells	27	GSE141853
SMC1 HiChIP in DP T cells	27	GSE141853
3e Hi-C during T cell development	25	GSE79422
Histone modifications during T cell development	29	GSE31235
ATAC-seq during T cell development	49	GSE100738
RNA-seq during T cell development	25	GSE79422
Mouse B cell hic	42	4DNFISA93XFU
Mouse cardiomyocyte hic	(Rosa-Garrido et al., 2017)	GSE96693
Mouse mESC hic	(Bonev et al., 2017)	4DNFIC21MG3U
Human hESC hic	(Oksuz et al., 2020)	4DNFI7JNCNFB
Human IMR90 hic	45	4DNFIJTOIGOI
Human olfactory sensory neurons hic	(Zazhytska et al., 2021)	4DNFI7V61PXA
Human HCT116 hic	42	4DNFIV3PIEQJ
Human K562 hic	(Ray et al., 2019)	4DNFI244AS29
Human HFF hic	(Oksuz et al., 2020)	4DNFIWMLVHWX
Experimental models: Cell lines
NIH 3T3	ATCC	Cat# CRL-1658 RRID:CVCL_0594
HEK293T	ATCC	Cat# CRL-3216 RRID:CVCL_0063
Scid.adh	Warren Pear lab at UPENN
Experimental models: Organisms and Strains
Mouse: C57BL/6J	Jackson Laboratory	RRID:IMSR_JAX:000664
Mouse: B6(Cg)-Tcf7tm1Hhx/J	Jackson Laboratory	RRID:IMSR_JAX:030909
Mouse: B6.Cg-Commd10Tg(Vav1-icre)A2Kio/J	Jackson Laboratory	RRID:IMSR_JAX:008610
Software and algorithms
FastQC		https://www.bioinformatics.babraham.ac.uk/projects/fastqc/; RRID:SCR_014583
Trim Galore		https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/; RRID:SCR_011847
Bowtie2	50	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
STAR	51	https://github.com/alexdobin/STAR
Picard		https://broadinstitute.github.io/picard/
HTSeq	52	https://htseq.readthedocs.io/en/master/; RRID:SCR_005514
DESeq2	53	https://github.com/Bioconductor-mirror/DESeq2; RRID:SCR_015687
R		https://cran.r-project.org; RRID:SCR_001905
MACS2	54	https://github.com/taoliu/MACS
Homer	55	http://homer.ucsd.edu/homer; RRID:SCR_010881
bedtools		https://bedtools.readthedocs.io/en/latest/#; RRID:SCR_006646
wigToBigWig		http://hgdownload.cse.ucsc.edu/admin/exe/
HiC-Pro	56	https://github.com/nservant/HiC-Pro; RRID:SCR_017643
ggplot2		https://ggplot2.tidvverse.org/
Metascape	57	https://metascape.org/gp/index.html#/main/step1; RRID:SCR_016620
Juicer	58	https://github.com/aidenlab/juicer
Cooler		https://github.com/open2c/cooler
cooltools		https://github.com/open2c/cooltools
HiCExplorer	59	https://hicexplorer.readthedocs.io/en/latest/
UpSetR	60	https://cran.r-project.org/web/packages/UpSetR/index.html
deeptools	61	https://deeptools.readthedocs.io/en/develop/
dekker-cworld		https://github.com/dekkerlab/cworld-dekker
hichipper	62	https://github.com/aryeelab/hichipper
Coolpup.py	63	https://github.com/open2c/coolpuppy
TANGO
Fiji
IMARIS
Sushi
OligoMiner
Flowjo v.10.6.1