REAGENT or RESOURCE	SOURCE	IDENTIFIER
Bacterial and virus strains
pCDH lentivector	System Bioscience	CD811A-1
Stable Competent E. Coli cells	NEB	Cat# C3040
pPACKH1 Lentivector Packaging Kit	System Bioscience	Cat# LV500A-1
Chemicals, peptides, and recombinant proteins
NsiI-HF	NEB	Cat# R3127S
Asc1-HF	NEB	Cat# R0558S
T4 DNA Ligase	NEB	Cat# M0202T
QIAGEN Protease	QIAGEN	Cat# 19157
ExoSap	Thermo fisher scientific	Cat# 78205.10.ML
NlaIII	NEB	Cat# R0125S
B27	Thermo fisher scientific	Cat# 17504044
DMEM/F12 medium	Thermo fisher scientific	Cat# 12634010
nicotinamide	Sigma Aldrich	Cat# 72340
N-acetylcysteine	Sigma Aldrich	Cat# A0737
A83-01	Tocris	Cat# 2939
SB202190	Sigma Aldrich	Cat# 7067
Gefitinib	Selleck Chemicals	Cat# ZD1839
Matrigel	Corning	Cat# 354234
Polybrene	Sigma Aldrich	Cat# TR-1003
PEI transfection reagen	Polysciences	Cat# 26406
Puromycin	Sigma Aldrich	Cat# P9620
Critical commercial assays
NEBNext High fidelity PCR mix	NEB	Cat# M0544
AMPure DNA beads	Beckman	Product # A63881
Deposited data
MSKCC dataset	European variation archive	PRJEB23844
Single cell whole genome data, generated in this study	This study	Sequence read archive PRJNA645018
Experimental models: Cell lines
Organoid lines	Drost et al. (2015)22; Clevers group, Hubrecht institue	N/A
Oligonucleotides
Viral library barcode PCR primers	This study	Table S1
Truseq small RNA library PCR primers	Illumina	RS-200-0012
Software and algorithms
Burrows Wheeler Aligner	Li and Durbin, 200935	http://bio-bwa.sourceforge.net/
GATKBaseRecalibrator	Van der Auwera et al., 201336	https://gatk.broadinstitute.org/
Mutect	Cibulskis et al., 201337	https://gatk.broadinstitute.org/
Single cell whole genome data processing	This paper	https://doi.org/10.5281/zenodo.5844399
Cutadapt	Martin, 201138	https://github.com/marcelm/cutadapt
ToverBoom	This paper	https://doi.org/10.5281/zenodo.5844342
SciCloneFitIO	This paper	https://github.com/zztin/siCloneFitIO