REAGENT or RESOURCES	SOURCE	IDENTIFIER
Chemicals, peptides, and recombinant proteins
Ethylenediaminetetraacetic acid (EDTA) 0.5M	Corning	46-034-CI
Dithiothreitol (DTT) 1M	Teknova	D9750
Deoxyribonuclease I (Dnase I)	Sigma-Aldrich	DN25
Protease from Bacillus licheniformis	Sigma-Aldrich	P5380
Collagenase type 1	Calbiochem	234153
TrypLE™ Express Enzyme (1X), no phenol red	Gibco	12604-013
Paraformaldehye (PFA) 4% in PBS	Thermo Scientific	AAJ19943K2
Dimethyl sulfoxide (DMSO)	Sigma-Aldrich	D8418
dithiobis(succinimidyl propionate) (DSP)	Thermo Scientific	22585
Optiprep Density Gradient Medium	Sigma-Aldrich	D1556
Y-27632	Sigma-Aldrich	Y0503
Mineral Oil	Sigma-Aldrich	M5310
Barcoded Gel Beads - inDrops V2 capture sequence: CGATGACGTAATACGACTCACTATAGGGATACCA CCATGGCTCTTTCCCTACACGACGCTCTTCCGATCT [Barcode 1] GAGTGATTGCTTGTGACGCCTT [Barcode 2] [6bp UMI] T19V	1CellBio	10070
Oil Red O	Alfa Aesar	A12989
Deposited data
Optimization datasets	This study	GEO: GSE234620
K562	Klein et al.9	GEO: GSE65525
Fresh and Frozen Human Tumor sc-, sn-RNA-Seq Datasets	Slyper et al.14	GEO: GSE140819
Critical commercial assays
MACS® Tumor Dissociation Kit, Mouse	Miltenyi Biotech	130-096-730
MACS® Dead Cell Removal Kit	Miltenyi Biotech	130-090-101
Experimental models: Organisms/strains
C57BL/6J	The Jackson Laboratory	664
Software and algorithms
CellBender	Fleming et al.22	https://github.com/broadinstitute/CellBender.git
dropkick	Heiser et al.18	https://github.com/Ken-Lau-Lab/dropkick
QCPipe	Chen et al.42	https://github.com/Ken-Lau-Lab/STAR_Protocol.git
Scanpy	Wolf et al.43	https://github.com/theislab/scanpy
Anndata	Virshup et al.44	https://github.com/scverse/anndata.git
Seaborn	Seaborn	https://github.com/mwaskom/seaborn
Matplotlib	Matplotlib	https://github.com/matplotlib/matplotlib
Scipy	Virtanen et al.45	https://scipy.org/
Numpy	Harris et al.46	https://numpy.org/
Pandas	Pandas	https://pandas.pydata.org/
Scikit-learn	Pedregosa et al.47	https://github.com/scikit-learn/scikit-learn.git
AmbiQuant	This study	https://github.com/Ken-Lau-Lab/AmbiQuant
Other
UV Crosslinking oven	Stratagene	Stratalinker 1800
AccuSpin Micro 17R	FisherBrand	13-100-675
Syringe pump	New Era Pump Systems	NE-300
Masterflex tubing	Cole Parmer	MFLX0640660
luer lock connectors	Qosina	80410
Male luer adapter	Idex	P-836
Female luer adapter	Idex	P-835
Primer	Loctite	SF 770
Glue	Loctite	4310
p200 Non-Filter Pipette tips	Biotix	M-0200-9TS
Cell Barcoding Chip	Droplet Genomics	DG-CBC2-80
Droplet Stabilization Oil	Droplet Genomics	DG-DSO-15
100ft Micro medical Tubing .015”I.D. x 0.043”O.D.	Scientific Commodities	BB31695-PE/2
100ft Micro medical Tubing .030”I.D. x 0.048”O.D.	Scientific Commodities	BB31695-PE/4
70μm PluriStrainer Mini Cell Strainers	PluriSelect	43-10070-40
2mL Round bottom tubes	FisherBrand	14-666-315
27G x 0.5" Hypodermic Needles	BD	305109
20G x 1" Hypodermic Needles	BD	305175
Gyromax Orbital Incubator Shaker	Amerex	703
Nexcelom Cellometer Auto 2000	Nexcelom Bioscience	8001334, Rev E
ViaStain™ AO/PI Staining Solutions	Nexcelom Bioscience	CS2-0106-5mL
Cellometer SD100 Counting Chambers	Nexcelom Bioscience	CHT4-SD100-014