| Antibodies |
| Anti-Ki67 Antibody |
Abcam |
Cat#: ab16667 RRID: AB_302459 |
| Anti-GFP Antibody |
Abcam |
Cat#: ab13970 RRID: AB_300798 |
| RFP Antibody Pre-adsorbed |
Rockland Immunochemicals |
Cat#: 600-401-379 RRID: AB_2209751 |
| H+/K+ ATPase Antibody (C-4) |
Santa Cruz Biotechnology Biotechnology |
Cat#: sc-374094, RRID:AB_10917224 |
| Mucin 5AC Antibody (K-20) |
Santa Cruz Biotechnology |
Cat# sc-16903, RRID:AB_649616 |
| Somatostatin Antibody |
Abcam |
Cat# ab30788, RRID:AB_778010 |
| Gastrin Antibody (C-20) |
Santa Cruz Biotechnology |
Cat# sc-7783, RRID:AB_2108261 |
| Anti-DLL1 Antibody |
Abcam |
Cat# ab10554, RRID:AB_2092808 |
| Anti-NUMB Antibody |
Abcam |
Cat# ab14140, RRID:AB_443023 |
| Trefoil Factor 2 (TFF2) Antibody |
Antibodies-online |
Cat# ABIN351426, RRID:AB_10826089 |
| Human Gastrin Antibody |
Abcam |
Cat#: ab22622, RRID:AB_447203 |
| CCK-BR Antibody (C-18) |
Santa Cruz Biotechnology |
Cat# sc-16177, RRID:AB_2070493 |
| Rat anti-E-Cadherin (Mouse) |
Innovative Research |
Cat# 13-1900, RRID:AB_86571 |
| Intrinsic Factor Antibody |
Santa Cruz Biotechnology |
Cat# sc-161643, RRID:AB_10839153 |
| DCKL1 Antibody (C-term) |
Abgent |
Cat# AP7219b, RRID:AB_2090081 |
| BrdU Antibody |
Abcam |
Cat# ab6326, RRID:AB_305426 |
| Rabbit Anti-activated Notch1 Polyclonal Antibody |
Abcam |
Cat# ab8925, RRID:AB_306863 |
| E-cadherin Antibody |
Cell Signaling Technology |
Cat# 3195, RRID:AB_2291471 |
| β-Catenin Antibody |
BD Bioscience |
Cat# 610153, RRID:AB_397554 |
| EnVision+ System-HRP (DAB) |
DAKO |
Cat#: K4011 |
| Anti-Chromogranin A Antibody (ab15160) |
Abcam |
Cat# ab15160, RRID:AB_301704 |
| Anti-Hes1 Antibody (ab71559) |
Abcam |
Cat# ab71559, RRID:AB_1209570 |
| Alexa Fluor 647 Donkey Anti-Rabbit |
Abcam |
Cat# ab150075, RRID:AB_2752244 |
| Alexa Flour 488 Chichen Anti-Goat |
Life technologies |
Cat#: A-21467 |
| Alexa Fluor 488 Goat Anti-Chicken |
Thermo Fisher Scientific |
Cat# A-11039, RRID:AB_2534096 |
| Alexa Fluor 594 Goat Anti-Rabbit |
Thermo Fisher Scientific |
Cat# R37117, RRID:AB_2556545 |
| Alexa Fluor 488 Chicken Anti-Rabbit |
Thermo Fisher Scientific |
Cat# A-21441, RRID:AB_2535859 |
| Alexa Fluor 594 Chicken Anti-Goat |
Thermo Fisher Scientific |
Cat# A-21468, RRID:AB_2535871 |
| Alexa Fluor 647 Phalloidin |
Thermo Fisher Scientific |
Cat# A22287, RRID:AB_2620155 |
| Alexa Fluor 555 Goat Anti-Chicken |
Thermo Fisher Scientific |
Cat# A-21437, RRID:AB_2535858 |
| Alexa Fluor 555 Goat Anti-Mouse |
Thermo Fisher Scientific |
Cat# A-21422, RRID:AB_2535844 |
| Bacterial and Virus Strains |
| Bacterial: Helicobacter felis |
N/A |
Strains: ATCC 49179 |
| Biological Samples |
|
|
| Human Blood Samples |
Zhongshan Hospital |
N/A |
| Human Gastric Samples |
Zhongshan Hospital |
N/A |
| Chemicals, Peptides, and Recombinant Proteins |
| HBSS – Hank’s Balanced Salt Solution |
Gibco |
14175079 |
| DPBS, no calcium, no magnesium |
Gibco |
14190250 |
| Advanced DMEM/F12 |
Gibco |
12634010 |
| Fetal Bovine Serum |
Gibco |
16140071 |
| Collagenase, Type 4 |
Worthington Biochemical Corporation |
LS004186 |
| DNase I |
Thermo Fisher Scientific |
3724778103 |
| BD Horizon BrilliantTM Stain Buffer |
BD Biosciences |
563794 |
| DAPI Solution |
BD Pharmingen |
564907 |
| B-27® Supplement (50X), serum free |
Thermo Fisher Scientific |
17504-044 |
| N-2 Supplement (100X) |
Thermo Fisher Scientific |
17502-048 |
| Matrigel® Growth Factor Reduced (GFR) Basement Membrane Matrix |
Corning |
356231 |
| Gastrin |
Sigma-Aldrich |
G9145 |
| IntestiCult™ Organoid Growth Medium (Mouse) |
STEMCELL Technologies |
6005 |
| RNAlater® Stabilization Solution |
Thermo Fisher Scientific |
AM7020 |
| Mouse Gastrin EIA |
RayBiotech |
EIAM-GAS-1 |
| Insulin growth factors |
STEMCELL Technologies |
2742 |
| BIRB-796 (p38 MAPK inhibitor) |
STEMCELL Technologies |
72682 |
| IntestiCult™ Organoid Growth Medium (Mouse) |
STEMCELL Technologies |
6005 |
| Gamma-secretase inhibitor (DBZ) |
RD Systems |
4489/10 |
| Diphtheria Toxin |
Sigma-Aldrich |
D0564-1MG |
| BrdU (5-Bromo-2’-deoxyuridine) |
Sigma-Aldrich |
B5002-5G |
| EdU (5-ethynyl-2’-deoxyuridine) |
Life Technologies |
A10044 |
| HEPES |
Thermo Fisher Scientific |
15630-080 |
| TrypLE™ Express Enzyme (1X), phenol red |
Thermo Fisher Scientific |
12605-028 |
| MNU (N-methyl-N-nitrosourea) |
Gojira Fine Chemicals |
NM1003 |
| Tamoxifen |
Sigma-Aldrich |
T5648-5G |
| GlutaMAX™ Supplement |
Thermo Fisher Scientific |
35050-079 |
| Gentamicin |
Thermo Fisher Scientific |
SR0185E |
| Penicillin-Streptomycin (10,000 U/mL) |
Thermo Fisher Scientific |
15140-122 |
| N-acetylcysteine |
Sigma-Aldrich |
A9165-5G |
| EDTA |
Sigma-Aldrich |
431788-25G |
| A83-01 |
Sigma-Aldrich |
909910-43-6 |
| Poly-L-lysine |
Sigma-Aldrich |
25988-63-0 |
| Y-27632 |
Sigma-Aldrich |
Y0503-1MG |
| Nicotinamide |
Sigma-Aldrich |
N0636-100G |
| Recombinant Murine Noggin |
Peprotech |
250-38 |
| Recombinant Human FGF-10 |
Peprotech |
100-26 |
| Recombinant Human R-Spondin-1 |
Peprotech |
120-38 |
| Recombinant Murine WNT-3a |
Peprotech |
315-20B |
| Recombinant Murine EGF |
Peprotech |
315-09 |
| UltraPure™ DNase/RNase-Free Distilled Water |
Thermo Fisher Scientific |
10977-023 |
| Hydrogen peroxide solution 30 % (w/w) in H2O, contains stabilizer |
Sigma-Aldrich |
H1009-500ML |
| Collagenase type I (0.25%) |
STEMCELL Technologies |
07902 |
| Acta lube |
Pharmacy |
NDC 198-50 |
| Diphtheria Toxin |
Sigma-Aldrich |
D0564-1MG |
| Falcon Yellow Nylon Mesh Cell Strainer, 70 Micron |
BD Biosciences |
352350 |
| Falcon Blue Nylon Mesh Cell Strainer, 40 Micron |
BD Biosciences |
352340 |
| Alzet pump Model 2006 (0.15 μl/hr, 6 weeks) |
Alzet |
7223 |
| Alzet pump Model 1002 (0.25 μl/hr, 2 weeks) |
Alzet |
4317 |
| Alzet pump Model 1007D (0.5 μl/hr, 7 days) |
Alzet |
290 |
| 48-well Uncoated glass dish |
MatTek |
P48G-1.5-6-F Case |
| 35 mm Collagen Coated dish |
MatTek |
P35GCOL-0-10-C Case |
| ImmEdge Hydrophobic Barrier Pen |
Vector |
H-4000 |
| Critical Commercial Assays |
| NucleoSpin tissue kit (Macherey-Nagel) |
Macherey-Nagel |
740952 |
| Nucleospin RNA II kit |
Clontech Laboratories |
740468.4 |
| Human Gastrin ELISA Kit |
Abcam |
ab133033 |
| Click-iT® EdU Imaging Kit with Alexa Fluor® 488, 594, and 647 Azides |
Life Technologies |
C10086 |
| Click-iT® EdU Alexa Fluor® 488 Imaging Kit |
life technologies |
C10337 |
| MTT assay Kit |
Thermo Fisher Scientific |
V13154 |
| Nextera XT DNA Library Preparation Kit |
Illumina |
FC-131-1024 |
| SuperScript III First-Strand Synthesis System |
Thermo Fisher Scientific |
18080051 |
| PrimeTime qPCR Assays |
Integrated DNA Technologies |
N/A |
| FastStart Universal SYBR Green Master (Rox) |
Roche Molecular Systems |
4913850001 |
| MethoCult™ GF M3434 |
STEMCELL Technologies |
3444 |
| MethoCult™ GF M3534 |
STEMCELL Technologies |
3534 |
| MethoCult™ M3630 |
STEMCELL Technologies |
3630 |
| Deposited Data |
| Raw and analyzed sequencing data |
This paper |
NCBI SRA database with number: PRJNA599415 |
| Experimental Models: Cell Lines |
| Cell: AGS Cell Line |
Sigma-Aldrich |
Strains:89090402 |
| Cell: AGS-E Cell Line |
Our lab (J Biol Chem. 2004 Mar 5;279(10):8684-93) |
N/A |
| Experimental Models: Organisms/Strains |
| Mouse: C57BL/6J |
The Jackson Laboratory |
Stock No: 000664 |
| Mouse: R26-tdTomato |
The Jackson Laboratory |
Stock No: 007914 |
| Mouse: GAS-KO |
The Jackson Laboratory |
Stock No: 031681 |
| Mouse: Cck2r −/−
|
The Jackson Laboratory |
Stock No:006369 |
| Mouse: Cck2r-CreERT |
This paper |
N/A |
| Mouse: C57BL/6J |
The Jackson Laboratory |
Stock No: 000664 |
| Mouse: Eef1a1-LSL-Notch1(IC) mice |
Dr. Kenneth Olive (Columbia University) |
N/A |
| Mouse: LSL-Trp53R172H mice |
Dr. Kenneth Olive (Columbia University) |
N/A |
| Mouse: Apc flox/flox mice |
the National Cancer Institute (NCI) |
N/A |
| Mouse: Lgr5-DTR-GFP mice |
Genentech |
N/A |
| Mouse: Lgr5-GFP-IRES-CreERT2 mice |
Dr. Hans Clevers |
N/A |
| Software and Algorithms |
| ImageJ version1.51h |
N/A |
http://imagej.net |
| Fiji version 2.0.0-rc54 |
N/A |
http://imagej.net |
| FlowJo |
FlowJo |
https://www.flowjo.com |
| GraphPad Software |
GraphPad Software |
http://graphpad.com |
| Broad FireCloud computing system |
N/A |
https://software.broadinstitute.org/firecloud/ |
| Picard Tools at Broad Institute |
N/A |
http://broadinstitute.github.io/picard/ |
| Other |
|
|
| Whole exome sequencing: Pair-end (PE) libraries were prepared and sequenced on the Illumina HiSeq instruments |
Broad Institute, Columbia University Medical Center and Beijing Genomic Institute (BGI) |
N/A |
