REAGENT or RESOURCE	SOURCE	IDENTIFIER
Chemicals, peptides, and recombinant proteins
Hypothermosol FRS	Stemcell Technologies	Cat# 07935;
Hanks' Balanced Salt Solution	Millipore Sigma	Cat# 55021C
Collagenase NB4	Nordmark Biochemicals	Cat# S1745402
Trypsin/EDTA	Sigma	Cat# T3924
DNase I	Sigma	Cat# D4263
Fetal bovine serum	Gibco	Cat# 12483-020
Trypan Blue Dye	Bio-Rad	Cat# 1450013
Bovin serum albumin	Miltenyi Biotec	Cat# 130-091-376
Nuclease-free water	Thermofisher Scientific	Cat# AM9937
10% Tween 20	Bio-Rad	Cat# 1662404
Glycerin, 50% (v/v) aqueous solution	Ricca Chemical Company	Cat# 3290-32
Qiagen Buffer EB	Qiagen	Cat# 19086
Critical commercial assays
Dead cell removal kit with MS Columns	Miltenyi Biotec	Cat#s 130-090-101 (kit) and 130-042-201 (MS columns)
10X Genomics Chromium Single Cell 3' GEM, Library & Gel Bead Kit V3	10x Genomics	Cat# PN-1000092
High sensitivity D1000 ScreenTape/Reagents	Agilent	Cat# 5067-5592/5067-5593
Qubit dsDNA HS Assay Kit	Thermofisher Scientific	Q32854
KAPA library quantification kit	KAPA Biosystems	KK4824
Deposited data
Simulated datasets	Figshare data: 10.6084/m9.figshare.19740475.v1
Real datasets (trimmed)	Figshare data: 10.6084/m9.figshare.19735678.v1
Software and algorithms
scTagger (commit #19d2be5)	This manuscript	https://github.com/vpc-ccg/scTagger/
FLAMES (commit #18fb83c)	Tian et al 2021	https://github.com/LuyiTian/FLAMES
edlib (v1.3.9)	Šošić and Šikić, 2017	https://github.com/Martinsos/edlib
Minnow (v1.2)	Sarkar et al 2019	https://github.com/COMBINE-lab/minnow
Badread (v0.1.5)	Wick 2019	https://github.com/rrwick/Badread