Reagent/Resource	Reference/ Source	Identifier/Catalog number
Experimental models
HEK293 Flp‐In T‐Rex cells	Thermo Fisher Scientific	Cat # R78007
Oligonucleotides
Read1CustSeqB	Macosko et al (2015)	GCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGTAC
TSO	Macosko et al (2015)	AAGCAGTGGTATCAACGCAGAGTGAATrGrGrG
SMART PCR oligo	Picelli et al (2014)	AAGCAGTGGTATCAACGCAGAGT
New‐P5‐SMART PCR hybrid oligo	Macosko et al (2015)	AATGATACGGCGACCACCGAGATCTACACGCCTGTCCGCGGAAGCAGTGGTATCAACGCAGAGT*A*C
Chemicals, enzymes and other reagents
Dulbecco's modified Eagle medium	Gibco	Cat # 41965039
AMPure XP beads	Beckman Coulter	Cat # A63881
Bovine serum albumin (BSA)	Sigma‐Aldrich	Cat # A8806
Dithiothreitol (DTT)	Sigma‐Aldrich	Cat # D9779
DPBS	Gibco	Cat # 14190250
ECL detection reagent	GE Healthcare	Cat # RPN2209
Exonuclease I	New England Biolabs	Cat # M0293
Fetal bovine serum	Gibco	Cat # 10270106
Ficoll PM 400	Sigma‐Aldrich	Cat # F4375
l‐Glutamine	Gibco	Cat # 25030081
Iodoacetamide	Sigma‐Aldrich	Cat # I6125‐5G
Maxima H‐ RT enzyme	Thermo Fisher	Cat # EP0753
Methanol z. A. (min. 99.8%)	Th. Geyer	Cat # 11646935
MTSEA‐XX‐biotin	Biotium	Cat # 90066
Nylon membrane	Amersham Hybond‐N+	Cat # RPN203B
N‐Lauroylsarcosine (Sarkosyl)	Sigma‐Aldrich	Cat # L7414
Phase Lock Gel Heavy tubes	QuantaBio	Cat # 2302830
Phenol/Chloroform/Isoamylalkohol	Carl Roth	Cat # A156.1
QX200 Droplet Generation Oil	Bio‐Rad	Cat #1864006
SDS 20%	Carl Roth	Cat # 1057.1
Streptavidin‐HRP	Pierce	Cat # 21130
Superase•In RNAse Inhibitor	Thermo Fisher	Cat # AM2694
4‐Thio uridine	ChemGem	Cat # RP‐2304
Trizol	Thermo Fisher	Cat # 15‐596‐018
TrypLE express enzyme	Gibco	Cat # 12605036
Software
bcl2fastq v2.20.0
STAR v2.6.0a	Dobin et al (2013)
bcftools v1.9	Li (2011)
Drop‐seq tools v2.2.0	Macosko et al (2015)
Revelio	Schwabe et al (2020)
GATK toolkit	McKenna et al (2010)
Seurat	Macosko et al (2015)
DropletUtils	Griffiths et al (2018) and Lun et al (2019)
FastQC v0.11.5
Samtools v1.6
Bedtools v2.30.0
Pysam v 0.15.4
VarScan v2.3.9
sam2tsv.jar
Python 2.7.18 & python 3.9.0
R ‘mgcv’ packages	Wood (2017)
R 3.6.0
Other
Nadia instrument	Dolomite Bio
TC20 cell counter	Bio‐Rad
Bio‐Dot apparatus	Bio‐Rad
Direct‐zol RNA Miniprep	Zymo Research
QuBit 2.0 Fluorometer	Thermo Fisher
UV Stratalinker Ultraviolet Crosslinker	Stratagene
Imager AI680	GE Amersham
2100 Bioanalyzer Instrument	Agilent
Nextera XT DNA Library Preparation Kit	Illumina
Nextseq 500/550 HO v2 kit	Illumina
Illumina Nextseq 500	Illumina
Illumina NovaSeq 6000	Illumina