REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Goat anti-GFP	Abcam	ab6673, RRID: AB_305643
Rabbit anti-RFP	Rockland	600-401-379, RRID: AB_2209751
Mouse anti-RFP (clone RF5R)	Thermo Fisher Scientific	MA5-15257, RRID: AB_10999796
Mouse anti-E-Cadherin (clone 36/E-Cadherin)	BD Biosciences	610182, RRID: AB_397581
Rabbit anti-Notch1 (clone D1E11)	Cell Signaling	3608, RRID: AB_2153354
Rabbit anti-Cleaved Notch1 (Val1744) (clone D3B8)	Cell Signaling	4147, RRID: AB_2153348
Rabbit anti-Hes1 (clone D6P2U)	Cell signaling	11988
Rabbit anti-Olfm4 (clone D6Y5A)	Cell Signaling	39141, RRID: AB_2650511
Rabbit anti-YAP (clone D8H1X)	Cell Signaling	14074, RRID: AB_2650491
Rabbit anti-Ki67 (clone SP6)	Abcam	ab16667, RRID:AB_302459
Rat anti-Ki67 (clone SolA15)	Thermo Fisher Scientific	14-5698-82, RRID: AB_10854564
Mouse anti-PCNA (clone CP10)	Santa Cruz Biotechnology	sc-56, RRID: AB_628110
Rabbit anti-lysozyme	Biogenex	AR024-10R
Goat anti-Sucrase-Isomaltase	Santa Cruz Biotechnology	sc-27603, RRID: AB_2188721
Goat anti-MMP7	Santa Cruz Biotechnology	sc-8832, RRID: AB_649337
Rabbit anti-Mucin 2	Santa Cruz Biotechnology	sc-15334, RRID: AB_2146667
Rabbit anti-Dclk1/DCAMKL1	Abcam	ab37994, RRID: AB_873538
Rabbit anti-Chromogranin A	ImmunoStar	20085
Rat anti-BrdU (clone BU1/75 [ICR1])	Accurate Chemical	OBT0030G, RRID: AB_609567
Rabbit anti-Phospho-TP53 (S18)	R &D Systems	AF1043-SP
Rabbit anti-Phospho-Stat3 (Y705) (clone D3A7)	Cell Signaling	9145, RRID: AB_2491009
BUV395 Rat anti-mouse CD45 (Clone 30-F11)	BD Biosciences	564279
PerCP/Cy5.5 Rat anti-mouse EpCAM (clone G8.8)	Biolegend	118219
APC/Fire750 Rat anti-mouse CD24 (clone M1/69)	Biolegend	101839
FITC Rat anti-mouse CD24 (clone M1/69)	Biolegend	101805
APC Armenian Hamster anti-mouse Notch1 (clone HMN1-12)	Biolegend	130613
Donkey anti-Rabbit, Alexa Fluor 488	Thermo Fisher Scientific	A-21206
Donkey anti-Rabbit, Alexa Fluor 546	Thermo Fisher Scientific	A10040
Donkey anti-Goat, Alexa Fluor 488	Thermo Fisher Scientific	A-11055
Donkey anti-Goat, Alexa Fluor 555	Thermo Fisher Scientific	A-21432
Donkey anti-Rat, Alexa Fluor 488	Thermo Fisher Scientific	A-21208
Donkey anti-Mouse, Alexa Fluor 555	Thermo Fisher Scientific	A-31570
Donkey anti-Mouse, Alexa Fluor 647	Thermo Fisher Scientific	A-31571
Biotinylated Horse Anti-Rabbit IgG Antibody	Vector Laboratories	BA-1100
Bacterial and Virus Strains
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Biological Samples
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Chemicals, Peptides, and Recombinant Proteins
Tamoxifen	Sigma-Aldrich	T5648
Tamoxifen tablet (21-day release)	Innovative Research of America	E-361
Citric acid	Sigma-Aldrich	251275
Donkey serum	Sigma-Aldrich	D9663
Bovine Serum Albumin	Sigma-Aldrich	A3294
Thiazovivin	Sigma-Aldrich	SML1045
Jagged1	AnaSpec	61298
Recombinant Murine Wnt-3a	Peprotech	315-20
BrdU labeling reagent	Thermo Fisher Scientific	000103
EdU (5-ethynyl-2′-deoxyuridine)	Thermo Fisher Scientific	A10044
TrypLE Express Enzyme (1X), phenol red	Thermo Fisher Scientific	12605010
Deoxyribonuclease I from bovine pancreas (DNase I)	Sigma-Aldrich	DN25
Advanced DMEM/F12 medium	Thermo Fisher Scientific	12634028
IntestiCult™ Organoid Growth Medium	STEMCELL Technologies	06005
Fluorescein labeled Ulex Europaeus Agglutinin I (UEA)	Vector Laboratories	FL-1061
Rhodamine labeled Ulex Europaeus Agglutinin I	Vector Laboratories	RL-1062
TO-PRO-3 Iodide (642/661)	Thermo Fisher Scientific	T3605
4′,6-Diamidino-2-Phenylindole (DAPI)	Thermo Fisher Scientific	D1306
SignalStain EDTA Unmasking Solution (10X)	Cell Signaling	14747
Dako Target Retrieval Solution, pH 6.1 (10×)	Agilent	S1699
Prolong Gold antifade medium	Thermo Fisher Scientific	P36930
Critical Commercial Assays
VECTASTAIN Elite ABC HRP Kit (Peroxidase, Standard)	Vector Laboratories	PK-6100
DAB Peroxidase (HRP) Substrate Kit (with Nickel), 3,3′-diaminobenzidine	Vector Laboratories	SK-4100
Click-iT™ EdU Alexa Fluor™ 555 Imaging Kit	Thermo Fisher Scientific	C10338
Alexa Fluor™ 488 Tyramide SuperBoost™ Kit, goat anti-rabbit IgG	Thermo Fisher	B40922
Alexa Fluor™ 488 Tyramide Reagent	Thermo Fisher	B40953
RNeasy Plus Micro kit	Qiagen	74034
Deposited Data
Raw and analyzed data	This paper	GEO: GSE113536
Experimental Models: Cell Lines
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Experimental Models: Organisms/Strains
Mouse: Lyz1mCherry-IRES-CreER	This paper	In-house
Mouse: B6.129X1-Gt(ROSA)26Sortm1(EYFP)Cos/J	Jackson Laboratory	https://www.jax.org/strain/006148
Mouse: B6. Cg-Gt(ROSA)26Sortm14(CAG-tdTomato) Hze/J	Jackson Laboratory	https://www.jax.org/strain/007914
Mouse: Gt(ROSA)26Sortm1(Notch1)Dam/J	Jackson Laboratory	https://www.jax.org/strain/008159
Mouse: Villin-CreER	Robine, S.	(el Marjou et al., 2004)
Mouse: β-Catenin flox (exon3)	Taketo, M. M.	(Harada et al., 1999)
Oligonucleotides
tdT primers: Forward, 5′-GCCCGGCTACTACTACGTGG-3′ and reverse, 5′-TACAGGAACAGGTGGTGGCG-3′	This Paper	N/A
Hprt primers: Forward, 5′-TCCCTGGTTAAGCAGTACAGC-3′ and reverse, 5′-TCCAACAAAGTCTGGCCTGT-3′	This Paper	N/A
Primers for β-Catenin exon 3 detection: F, 5′-CTGCGTGGACAATGGCTAC-3′, R1, 5′-CAGGGAAGGAGCTGTGGTGG-3′; and R2, 5′-TCGGACCCTCTGAGCCCTAG-3′	This Paper	N/A
Primers for Internal control detection: oIMR8744, 5′-CAAATGTTGCTTGTCTGGTG-3′ and oIMR8745, 5′-GTCAGTCGAGTGCACAGTTT-3′	This Paper	N/A
Recombinant DNA
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Software and Algorithms
AIM 4.2 Service Pack 1	Zeiss	https://www.zeiss.com/microscopy/us/downloads/lsm-5-series.html
Fiji software		https://fiji.sc
Flowjo software 10.2	TreeStar-BD	https://www.flowjo.com/solutions/flowjo/downloads
IDEAS software version 6.2	Millipore	http://www.emdmillipore.com/US/en/life-science-research/cell-analysis-flow-cytometry/amnis-imaging-flow-cytometers/analysis-acquisition-software/ideas-software/qe2b.qB.Oq8AAAFLQM8Jx34R,nav
GSEA	Broad Institute	http://software.broadinstitute.org/gsea/index.jsp
Other
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