REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, peptides, and recombinant proteins
Bromodeoxyuridine (BrdU, 5-bromo-2′-deoxyuridine)	Sigma-Aldrich	Cat. #: B5002
5-fluorodeoxyuridine (5-FdU, floxuridine, 5-fluoro-2′-deoxyuridine)	Sigma-Aldrich	Cat. #: F0503
Micrococcal nuclease (MNase)	New England Biolabs	Cat. #: M0247
Qiagen protease	Qiagen	Cat. #: 19155
Hoechst 33258 (Hoechst)	ThermoFisher Scientific	Cat. #: H3569
Propidium iodide (PI)	Sigma-Aldrich	Cat. #: P4864
Deposited data
FASTQ files	This paper	SRA: SRP326369; BioProject: PRJNA742746
Experimental models: Cell lines
Human: EBV-transformed B cells for NA12878	Coriell	RRID: CVCL_7526
Oligonucleotides
Sequencing adapters and index primers; see Table S1	This paper	N/A
Software and algorithms
Preseq gc_extrap and bam2mr	(Daley and Smith, 2014)	RRID: SCR_018664
AneuFinder	(Bakker et al., 2016)	N/A
BreakpointR	(Porubsky et al., 2020b)	N/A
ASHLEYS quality control	(Gros et al., 2021)	N/A
Bowtie2	(Langmead and Salzberg, 2012)	RRID:SCR_016368
Picard Tools	Broad Institute	RRID: SCR_006525
Other
cellenONE X1i	SCIENION, Cellenion	N/A
Bespoke nanoarrays; see Figure S1B and Data S1 (or use ICELL8 chips, below)	This paper	N/A
Parylene-C coating services	Plasma Ruggedized Solutions	N/A
ICELL8 150V chips	Takara Bio	Cat. #: 640013
Bespoke primer transfer device	This paper	N/A
Microseal ‘A’ Sealing Film	Bio-Rad	Cat. #: MSA5001
BlueWave MX-250 Emitter, RediCure (365 nm)	Dymax	Cat. #: C-42806, FR0045