| Antibodies |
| cleaved caspase-3 |
Cell Signaling Technology |
Cat# 9661 |
| lysozyme |
BioGenex |
Cat# AR024-10R |
| Donkey anti-Goat IgG (H+L) Alexa Fluor 546 |
Thermo Fisher Scientific |
Cat# A-11056 |
| AnnexinV-FITC |
Biolegend |
Cat# 640905 |
| Chemicals, Peptides, and Recombinant Proteins |
| 5-ethynyl-2′-deoxyuridine (EDU) |
GeneCopoeia |
Cat# A003 |
| Diphtheria Toxin (DT) |
Sigma Aldrich |
Cat# 322326-1MG |
| Cytofix/Cytoperm |
BD Biosciences |
Cat# 554722 |
| ProLong Gold antifade reagent |
Thermo Fisher Scientific |
Cat# P36934
|
| 20% Paraformaldehyde |
Electron Microscopy Sciences |
Cat# 15713 |
| Antigen Unmasking Solution, Citrate-Based |
Vector Laboratories |
Cat# H-3300 |
| Staurosporine |
Millipore Sigma |
Cat# S5921 |
| 0.25% trypsin |
Corning |
Cat# 25-053Cl |
| Hoechst 33342 |
Thermo Fisher Scientific |
Catt# H3570 |
| propidium iodide |
Thermo Fisher Scientific |
Cat# P1304MP |
| 7-AAD |
Biolegend |
Cat# 420403 |
| TO-PRO-3 |
Thermo Fisher Scientific |
Cat# T3605 |
| CellMask Green |
Thermo Fisher Scientific |
Cat# C37608
|
| Cell trace violet |
Thermo Fisher Scientific |
Cat# C34571
|
| CypHer5E NHS Ester |
GEHealhcare |
Cat# PA15401 |
| EDTA (0.5 M), pH 8.0, RNase-free |
Invitrogen |
Cat# AM9260G |
| Critical Commercial Assays |
| CF640R TUNEL Assay |
Biotium |
Cat# 30074 |
| iClick EdU Andy Fluor 488 Imaging Kit |
GeneCopoeia |
Cat# A003 |
| ApopTag ISOL Dual Fluorescence Apoptosis Detection Kit |
Milipore |
Cat# APT1000 |
| Experimental Models: Cell Lines |
| HCT116 human colon cells (ATCC CCL-247) |
American Type Culture Collection |
https://www.atcc.org/products/all/CCL-247.aspx |
| Experimental Models: Organisms/Strains |
| Mouse: JAX C57BL/6J Mice |
Jackson Laboratory |
https://www.jax.org/strain/000664 |
| Mouse: Gt(ROSA)26Sortm4(ACTB-tdTomato,-EGFP)Luo/J
|
Jackson Laboratory |
https://www.jax.org/strain/007676 |
| Mouse: C57BL/6-Gt(ROSA)26Sortm1(HBEGF)Awai/J
|
Jackson Laboratory |
https://www.jax.org/strain/007900 |
| Mouse: Defensin-6-cre (Defa6-cre) |
Blumberg Laboratory |
https://www.hms.harvard.edu/dms/immunology/fac/Blumberg.php |
| Software and Algorithms |
| CellProfiler v2.2 |
Broad Institute of Harvard and MIT |
https://cellprofiler.org/previous-releases |
| FIJI |
Laboratory for Optical and Computation Instrumentation |
https://imagej.net/Downloads |
| R |
R Foundation |
https://www.r-project.org/ |
| Prism 9 |
GraphPad Software |
www.graphpad.com |
| Enteroid Analysis Pipeline |
This Paper |
https://github.com/lsshankman/Paneth-Cells-as-novel-efferocytic-phagocytes-within-the-intestine |
| Other |
| MACS dead cell removal kit |
Miltenyi Biotec |
Cat# 130-090-101 |
| McCoy’s 5A Modified Medium |
Thermo Fisher Scientific |
Cat# 12330031 |
| intesticult media |
Stem Cell Technologies |
Cat# 06005 |
| Matrigel GFR Basement Membrane Matrix |
Corning |
Cat# 354230 |
| CellBIND 96-well Clear Flat Bottom Polystyrene Microplate |
Corning |
Cat# 3300 |
| L-Glutamine:Penicillin:Streptomycin (PSQ) |
Thermo Fisher Scientific |
Cat# 50-753-3016 |
| 70μm nylon filter |
Corning |
Cat# CLS431751 |
| 8 well glass chambered slides |
Thermo Fisher Scientific |
Cat# 154534 |
| 4 well coverslip bottom slides |
Thermo Fisher Scientific |
Cat# 155382 |
| pluriStrainer® 20 μm |
pluriSelect |
Cat# 43-50020-03 |
