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 |
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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 |
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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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