REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
anti-Phospho-c-Jun (Ser73) (D47G9) (Dilution 1:500)	Cell Signaling TECHNOLOGY	3270; RRID:AB_2129575
anti-Cleaved Caspase-3 (Asp175) (Dilution 1:400)	Cell Signaling TECHNOLOGY	9661; RRID:AB_2341188 06-570
anti-Aldolase B + Aldolase C antibody [EPR3138Y] (Dilution 1:300)	Abcam	ab75751; RRID:AB_2226682
anti-Lysozyme (EC 3.2.1.17) (Dilution 1:500)	Agilent	A0099; RRID:AB_2341230
anti-Olfm4 (D6Y5A) (1:100)	Cell Signaling TECHNOLOGY	39141; RRID:AB_2650511
Chicken anti-Rabbit, Alexa Fluor 647 (Dilution 1:500)	Thermo Fisher Scientific	A21443; RRID:AB_2535861
Chemicals, peptides, and recombinant proteins
Cultrex PathClear Reduced Growth Factor Basement Membrane Extract Type 2	R&D Systems	3533-005-02
Advanced DMEM F/12	Thermo Fisher Scientific	12634-010
HEPES	Thermo Fisher Scientific	15630-056
Penicillin/streptomycin	Thermo Fisher Scientific	15140-122
GlutaMAX	Thermo Fisher Scientific	35050-068
R-spondin1	prepared in house	n/a
Noggin	prepared in house	n/a
B-27	Thermo Fisher Scientific	17504-044
hEGF	PeproTech	AF-100-15
N-acetylcysteine	Sigma-Aldrich	A9165
Y-27632	AbMole BioScience	M1817
CHIR-99021	Tocris Bioscience	4423
TryplE	Thermo Fisher Scientific	12605-010
DPBS, no calcium, no magnesium	Thermo Fisher Scientific	14190144
PBS tablets	Gibco	18912014
Paraformaldehyde 16% (w/v) in aqueous solution methanol-free	Alfa Aesar	43368.9M; CAS RN:50-00-0
BSA	Roche	10735094001
4′,6-Diamidino-2-phenylindole Dihydrochloride (DAPI)	Toronto Research Chemicals	D416050; CAS RN: 28718-90-3
TX-100	Sigma-Aldrich	X-100; CAS RN: 9036-19-5
Deposited data
RNA-seq data	Krotenberg Garcia et al., 2021	NCBI GEO:GSE176027
Experimental models: Cell lines
Murine WT small intestine organoids Gt(ROSA) 26Sortm4(ACTB-tdTomato,-EGFP)Luo/J Mus	Krotenberg Garcia et al., 2021	n/a
Murine CRC organoids Villin-CreERT2Apcfl/flKrasG12D/WTTr53fl/R1	Fumagalli et al., 2017	n/a
Software and algorithms
FIJI	https://imagej.net/	2.1.0/1.53h 9.0.0
FlowJo 10.6.1	BD Biosciences	https://www.flowjo.com/
Imaris	Oxford Instruments	9.3.1
Other
Cooled centrifuge	Eppendorf	Eppendorf Centrifuge 5702 R Serienr: 5703II619246
Eppendorf centrifuge	Eppendorf	Eppendorf AG 5424 Serienr: 5424FR273064
Tissue culture microscope equipped with fluorescent light source	Thermo Fisher Scientific	EVOS FL
Inverted confocal microscope	Leica Microsystems	TCS SP8
Spinning disk confocal microscope	Andor	Dragonfly
Cell counter	Westburg	Model: LUNA II Serienr: LUC-04-00126
Pasteur Capillary Pipette, short size 150mm	VWR	612-1798
5 mL Polystyrene Round-Bottom Tube with 35 μm Cell-Strainer Cap	Falcon	352235
5 mL Polystyrene Round-Bottom Tube	Falcon	352063
15 mL tubes	Sarstedt	62554502
1.5 mL Safe-Lock Tubes	Eppendorf	0030120.086
24 well CELLSTAR® plate, polystyrene	Greiner Bio-One	662165
12 well CELLSTAR® plate, polystyrene	Greiner Bio-One	665165
6 well CELLSTAR® plate, polystyrene	Greiner Bio-One	657165
8 well chambered μ-Slide, glass-bottom	IBIDI	80827
96 well μ-Plate, ibiTreat #1.5 polymer coverslip	IBIDI	89626
96 well SensoPlate, glass-bottom	Greiner Bio-One	655892
384 well microplate, tissue culture treated	Greiner Bio-One	781091