REAGENT or RESOURCE	SOURCE	IDENTIFIER
Biological samples
Human breast tissue samples	Netherlands Cancer Institute, Duke University Hospital and Baylor College of Medicine	N/A
Human lung cancer samples	MD Anderson Cancer Center	N/A
Human prostate cancer samples	MD Anderson Cancer Center	N/A
Chemicals, peptides, and recombinant proteins
Formalin solution, neutral buffered, 10%	Millipore Sigma	HT5012–1CS
DMEM	Millipore Sigma	D5796
FBS	Millipore Sigma	F0926
Penicillin-streptomycin	Corning	30–002-Cl
L-glutamine Solution	Corning	25005CI
Trypsin-EDTA	Corning	25053CI
DPBS	Millipore Sigma	D8537
Tris-HCl (pH7.4)	Millipore Sigma	T2194
Tween-20	Andwin Scientific	NC9022994
Nonidet P40 Substitute	Millipore Sigma	74385
NaCl	Invitrogen	AM9760G
MgCl2	Invitrogen	AM9530G
Dimethyl sulfoxide (DMSO)	Millipore Sigma	D2650
Triton™ X-100	Fisher scientific	ICN19485483
QIAGEN Protease (30 AU)	Qiagen	19157
0.5 M EDTA	Thermo Scientific	R1021
Critical commercial assays
Illumina Tagment DNA Enzyme and Buffer Large Kit	Illumina	20034198
KAPA HotStart PCR Kit, with dNTPs	Roche	KK2502
FFPE Tissue Dissociation Kit	Miltenyi Biotec	130–118-052
Deposited data
Raw data files and processed data files	This manuscript	SRA: PRJNA799605 and https://github.com/navinlabcode/Arc-well
Experimental models: Cell lines
Human: MDA-MB-231	MD Anderson Characterized Cell Line Core Facility	N/A
Human: 315A	Cold Spring Harbor Laboratory	N/A
Human: GM12878	Coriell Institute for medical research	GM12878
Mouse: A20	ATCC	ATCC: TIB-208
Oligonucleotides
See Table S6	IDT	N/A
Software and algorithms
bcl2fastq (v2.20.0.422)	Illumina	https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html
bowtie2	Langmead et.al52	https://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Sambamba (v0.8.0)	Tarasov et.al53	https://lomereiter.github.io/sambamba/
DNACopy	Seshan et.al	10.18129/B9.bioc.DNAcopy
CNV pipeline	Minussi et.al26	https://github.com/navinlabcode/CNV_pipeline
CopyKit (V0.1.0)	Minussi et.al54	https://github.com/navinlabcode/copykit
bedtools (v2.26.0)	Quinlan et.al55	https://bedtools.readthedocs.io/en/latest/
mixtools (v1.2.0)	Benaglia et.al56	https://cran.r-project.org/web/packages/mixtools/index.html
uwot (v0.1.11)	Melville et.al	https://github.com/jlmelville/uwot
dbscan (v1.1.10)	Hahsler et.al	https://github.com/mhahsler/dbscan
ComplexHeatmap (v2.2.0)	Gu et.al57	10.1093/bioinformatics/btw313
MEDICC2	Kaufmann et.al40	https://bitbucket.org/schwarzlab/medicc2/src/master/
ggtree	Yu et.al58	https://github.com/YuLab-SMU/ggtree