REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
H3K27ac (Anti-Histone H3 Acetyl K27)	Abcam	Cat# ab4729; RRID: AB_2118291
Anti-Rad21, Rabbit polyclonal	Abcam	Cat# ab992; RRID: AB_2176601
CTCF (D31H2) XP Rabbit mAb antibody	Cell Signaling Technology	Cat# 3418; RRID: AB_2086791
Bacterial and Virus Strains
Fosmid WIBR1-0075F18: Rcn1 gene FISH probe	BACPAC resource	ID: WIBR1-0075F18
Fosmid WIBR1-0322P22: Pax6 gene FISH probe	BACPAC resource	ID: WIBR1-0322P22
Fosmid WIBR1-1660D19: Elp4 gene FISH probe	BACPAC resource	ID: WIBR1-1660D19
Fosmid WIBR1-2859L14: DRR FISH probe	BACPAC resource	ID: WIBR1-2859L14
Fosmid WIBR1-1230I10: URR FISH probe	BACPAC resource	ID: WIBR1-1230I10
Chemicals, Peptides, and Recombinant Proteins
Formaldehyde solution 37%	Sigma	Cat# 252549
Critical Commercial Assays
NebNext DNA Library Prep Kit	NEB	Cat# E6040
NEBNext mRNA Library Prep Master Mix Set	NEB	Cat# E6110
Protein G Dyna beads	Thermo Fisher Scientific	Cat# 10003D
RiboMinus Eukaryote Kit for RNA-Seq	Thermo Fisher Scientific	Cat# A1083708
SYBR Green I Nucleic Acid Gel Stain	Thermo Fisher Scientific	Cat# S7563
Tapesation D1000 ScreenTapes	Agilent	Cat# 5067-5582
Tapesation D1000 Reagents	Agilent	Cat# 5067-5583
NebNext Multiplex Oligos for Illumina	NEB	Cat# E7335
Nextera DNA Lib prep kit: Tn5 Transposes, TD buffer	Illumina	Cat# FC-121-1030
GenomePlex WGA2 Kit	Sigma	Cat# WGA1-50RXN
GenomePlex WGA2 Reamplification Kit	Sigma	Cat# WGA3-50RXN
CYTAG CGH labeling kit for oligo arrays	Enzo	Cat# ENZ-42671
NimbleGen Dual-Color Labeling Kit	Roche	Cat# 06370250001
NimbleGen Hybridization and Sample Tracking Control Kit	Roche	Cat# 05993776001
NimbleGen Wash Buffer Kit,	Roche	Cat# 0558450700
SeqCap EZ HE-Oligo Kit A	Roche	Cat# 06777287001
SeqCap EZ Hybridization and Wash Kit	Roche	Cat# 05 634 261 001
SeqCap EZ Pure Capture Bead Kit	Roche	Cat# 06 977 952 001
SeqCap EZ Accessory Kit	Roche	Cat# 07145594001
Deposited Data
RNA-seq data: β-TC3, MV+, RAG cells	This paper	GEO: GSE119660
ATAC-seq data: β-TC3, MV+, RAG cells	This paper	GEO: GSE119656
ChIP-Chip Data: Nimblegen 720K, H3K27ac	This paper	GEO: GSE119659
ChIP-Chip Data: Nimblegen 720K, CTCF, Rad21	This paper	GEO: GSE119658
ChIP-Chiip Data: Agilent 180k, Rad21	This paper	GEO: GSE120665
NG-Capture-C Data: β-TC3, MV+, RAG cells	This paper	GEO: GSE120666
The processed simulation and experimental data used to generate all figures. The full set of 200 simulated locus configurations for each cell type used to generate plots and simulation snap-shot images for Figures 4 and 5, and Videos S1, S2, S3, S4, and S5. An input script and python driver script along with example initialization configurations which can be used to run a HiP-HoP simulation of the Pax6-HIGH cells using the LAMMPS software.	This paper	Edinburgh DataShare https://datashare.is.ed.ac.uk/handle/10283/3178
Experimental Models: Cell Lines
MV+, cells, Mus musculus, lens epithelium	Originally supplied by Dr. Alan Prescott. Derived from cultured lens epithelia from a wildtype C57BL6 mouse. McBride et al., 2011	N/A
RAG cells, Mus musculus, kidney carcinoma	ATCC	Cat# CCL-142, RRID: CVCL_3575
β-TC3 cells, Mus musculus, insulinoma	DSMZ	Cat# ACC-324, RRID: CVCL_0172
Oligonucleotides
5′ Biotin Ultramer Capture Oligo	IDT	See Table S1
Software and Algorithms
LAMMPS: Simulations work was performed using the LAMMPS molecular dynamics software	Plimpton, 1995	https://lammps.sandia.gov/
Additional simulation scripts	This paper; Edinburgh DataShare	https://datashare.is.ed.ac.uk/handle/10283/3178
Ringo: Microarray data were processed using the open source R package Ringo, Bioconductor	Toedling et al., 2007	https://doi.org/10.18129/B9.bioc.Ringo
Bowtie2	Langmead and Salzberg, 2012	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
SAMtools	Li et al., 2009	http://samtools.sourceforge.net/
Trim Galore		https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/
BEDtools	Quinlan and Hall, 2010	https://bedtools.readthedocs.io/en/latest/
MACS2	Zhang et al., 2008	https://github.com/taoliu/MACS
STORM	Schones et al., 2007	http://rulai.cshl.edu/storm
Subread feature counts	Liao et al., 2014	http://subread.sourceforge.net/
Other
HEK293T Single-cell transcription data	Darmanis et al., 2015	GEO: GSE67835
H1-hESC Single-cell transcription data	Leng et al., 2015	GEO: GSE64016