REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, peptides, and recombinant proteins
1M Tris HCl, pH 8.0	Thermo Fisher	Cat#15568025
1M Tris HCl, pH 7.5	Thermo Fisher	Cat#15567027
1M MgCl2	Quality Biological	Cat#351-033-721
BSA, lyophilized powder	Millipore Sigma	Cat#A9418
100 mM dATP	Thermo Fisher	Cat#10216018
100 mM dGTP	Thermo Fisher	Cat#10218014
100 mM dCTP	Thermo Fisher	Cat#10217016
1 mM DY488-dUTP (listed as fluorescent nucleotide stock within the protocol)	Dyomics	Cat#488-34
1 mM DY549P1-dUTP (listed as fluorescent nucleotide stock within the protocol)	Dyomics	Cat#549P1-34
1 mM DY647P1-dUTP (listed as fluorescent nucleotide stock within the protocol)	Dyomics	Cat#647P1-34
β-Mercaptoethanol	Bio-Rad	Cat#1610710
DNAse I grade II, lyophilized powder	Roche	Cat#11284932001
E. Coli DNA Polymerase I	NEB	Cat#M0209S
3M Sodium Acetate (NaOAc)	Thermo Fisher	Cat#R1181
0.5M EDTA	Thermo Fisher	Cat#15575020
1 mg/mL Human Cot-1 DNA	Thermo Fisher	Cat#15279011
10 mg/mL Yeast tRNA	Thermo Fisher	Cat#AM7119
50% w/v Dextran sulfate	Millipore Sigma	Cat#S4030
Deionized formamide, pH 7.0	Ambion	Cat#AM9344
20× Saline sodium citrate (SSC)	Corning	Cat#46-020-CM
10% Tween-20	Millipore Sigma	Cat#P9416
16% Paraformaldehyde (PFA)	Electron Microscopy Sciences	Cat#15710
10% Triton X-100	Millipore Sigma	Cat#X100
Saponin from Quillaja bark, powder	Millipore Sigma	Cat#S7900
1N HCl	Fisher Scientific	Cat#SA48
4′6-Diamidino-2-phenylindole (DAPI)	Millipore Sigma	Cat#9542
Glycerol	Millipore Sigma	Cat#G5516
100% Ethanol	Millipore Sigma	Cat#E7023
Phosphate Buffered Saline (PBS)	Millipore Sigma	Cat#D8537
Critical commercial assays
Nucleobond BAC 100 Maxiprep	Takara	Cat#740579
Deposited data
DNA FISH raw images	4D Nucleome	4DNFI2VH2VA2
FISH Spot positions	4D Nucleome	4DNFID78GRES
SpotLearn pipeline	GitHub	https://github.com/CBIIT/Misteli-Lab-CCR-NCI/tree/master/Gudla_CSH_2017
Experimental models: cell lines
HFF c6 hTERT immortalized human foreskin fibroblasts	4DN	4DNINE5V67ON
Other
1.5 mL DNA LoBind Tube	Eppendorf	Cat#022431021
1.5 mL LightSafe microcentrifuge tube	Millipore Sigma	Cat#Z688312
CellCarrier-384 Ultra Microplates	PerkinElmer	Cat#6007550
Aluminum foil plate seal	Greiner	Cat#676090
Water bath set to 16°C	N/A	N/A
Water bath set to 37°C–45°C	N/A	N/A
Benchtop microcentrifuge for 1.5–2.0 mL tubes	N/A	N/A
Vortex	N/A	N/A
Cooled microcentrifuge for 1.5–2.0 mL tubes	N/A	N/A
Tabletop plate centrifuge	N/A	N/A
Humidified incubator for cell culture	N/A	N/A
Humidified incubator for hybridization	Fisher Scientific	15-015-2632
Utility sponge (optional)	N/A	N/A
Slide moat (preferred) or heat block	Daigger	EF14654
Thermoshaker (preferred) or heat block	N/A	N/A
500 nm Tetraspeck fluorescent beads	Thermo Fisher	Cat#T281