| Antibodies |
|
|
| Rabbit anti-Human Lysozyme FITC |
Dako |
Cat#: F037201; RRID: AB_578661 |
| Rabbit anti-DCLK1/DCAMKL1 |
Cell Signaling Technology |
Cat#: 62257S; RRID: AB_2799622; Clone: D2U3L |
| Rabbit polyclonal anti-Atoh1 |
Jane E Johnson UT Southwestern |
N/A |
| Rabbit polyclonal anti-Atoh1 |
Proteintech |
Cat#: 212151AP; RRID:AB_10733126 |
| Rabbit anti-Ki-67 |
Biocare Medical |
Cat#: CRM325B; Clone: SP6 |
| Goat anti-E-cadherin |
R & D |
Cat#: AF748; RRID: AB_355568; |
| Goat anti-Lysozyme C |
Santa Cruz Biotechnology |
Cat#: sc-27958; RRID: AB_2138790; Clone: C-19 |
| Mouse anti-Chr-A |
Santa Cruz Biotechnology |
Cat#: sc-393941; RRID: AB_2801371; Clone: C-12 |
| Rabbit anti-Mucin 2 |
Santa Cruz Biotechnology |
Cat#: sc-15334; RRID:AB_2146667; Clone: H-300 |
| Mouse anti-Mucin 2 |
Santa Cruz Biotechnology |
Cat#: sc-515032; RRID: AB_2815005; Clone: F-2 |
| Goat anti-rabbit IgG AF488 |
Jackson ImmunoResearch Labs |
Cat#: 111-545-144; RRID: AB_2338052 |
| F(ab’)2 goat anti-mouse IgG(H+L) AF647 |
Cell Signaling Technology |
Cat#: 4410S; RRID: AB_ 1904023 |
| Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 |
ThermoFisher |
Cat#: A11008; RRID:AB_2536164 |
| Goat anti-Mouse IgG (H+L), Superclonal™ Recombinant Secondary Antibody, Alexa Fluor 555 |
ThermoFisher |
Cat#: A28180; RRID:AB_143165 |
| APC-eFluor 780 anti-mouse CD45 |
eBioscience |
Cat#: 47-0451-82; RRID: AB_1548781 Clone: 30-F11 |
| PE-Cy7 anti-mouse CD3e |
eBioscience |
Cat#: 25-0031-82 RRID: AB_469572 Clone: 145-2C11 |
| PE anti-mouse IL-17A |
eBioscience |
Cat#: 12-7177-81 RRID: AB_763582 Clone: eBio17B7 |
| PE anti-mouse IκBα |
eBioscience |
Cat#: 12-9036-42 RRID: AB_2572683 Clone: MFRDTRK |
| Chemicals, Peptides, and Recombinant Proteins |
| UEA-I Dylight 649 |
Vector Laboratories |
Cat#: DL-1068 |
| VECTASHIELD® HardSet™ Antifade mounting medium with DAPI |
Vector Laboratories |
Cat#: H-1500 |
| ProLong™ Glass Antifade Mountant with NucBlue™ Stain |
ThermoFisher |
Cat#: P36981
|
| Aqua Dead Cell Stain Kit |
Invitrogen |
Cat#: L34957
|
| Recombinant mouse IL-17A |
R&D Systems |
Cat#: 421-ML/CF |
| Recombinant human IL-17A |
R&D Systems |
Cat#: 317-ILB-050 |
| Recombinant mouse IL-25 |
R&D Systems |
Cat#: 1399-IL/CF |
| Recombinant mouse IL-22 |
R&D Systems |
Cat#: 582-ML |
| SsoAdvanced™ Universal Probes Supermix |
Bio-Rad |
Cat#: 1725281 |
| SsoAdvanced™ Universal SYBR® Green Supermix |
Bio-Rad |
Cat#: 1725271 |
| iScript™ Reverse Transcription Supermix |
Bio-Rad |
Cat#: 1708840 |
| High-Capacity cDNA Reverse Transcription Kit |
ThermoFisher |
Cat#: 4368814 |
| Roche Diagnostics LIGHTCYCLER 480 SYBR GREEN |
Roche |
Cat#: 04887352001 |
| Actinomycin D |
Sigma-Aldrich |
Cat#: A9415 |
| Piceatannol |
EMD Millipore |
Cat#: 527948 |
| EDTA |
Invitrogen |
Cat#: AM9260G |
| DSS |
MP Biomedicals |
Cat#: 160110 |
| Alcian blue |
Alfa Aesar |
Cat#: J60122 |
| Tamoxifen |
Sigma-Aldrich |
Cat#: T5648 |
| DMSO |
ThermoFisher |
Cat#: BP231 |
| Percoll |
Cytiva |
Cat#: 17089101 |
| RPMI-1640 |
Hyclone |
Cat#: SH30255.01 |
| DMEM/F12 |
Gibco |
Cat#: 12634-010 |
| PBS |
Corning |
Cat#: 21040CV |
| DNase I |
Roche |
Cat#: 11284932001 |
| Fetal bovine serum |
Gibco |
Cat#: SH30071.03HI |
| Bovine serum albumin |
ThermoFisher |
Cat#: BP1600-100 |
| 1x Hank’s Balanced Salt Solution (HBSS) |
ThermoFisher |
Cat#: 14170112 |
| Liberase TL |
Roche |
Cat#: 5401020001 |
| Nuclear Fast Red |
Electron Microscopy Sciences |
Cat#: 26078-05 |
| Hematoxylin |
VWR |
Cat#: 95057-844 |
| Eosin |
VWR |
Cat#: 95057-848 |
| Thiazolyl Blue Tetrazolium Bromide (MTT) |
Sigma |
Cat#: M2128 |
| NEG-50™ Frozen Section Medium |
Epredia |
Cat#: 6502 |
| Matrigel Matrix |
Corning |
Cat#: 356231 |
| IntestiCult™ Organoid Growth Medium (Human) |
Stemcell |
Cat#: 06010 |
| 100x penicillin-streptomycin-glutamine |
Gibco |
Cat#: 10378016 |
| Penicillin-Streptomycin solution, 100X |
Corning |
Cat#: 30-002-CI |
| Gentamicin |
Gibco |
Cat#: 15750060 |
| L-Glutamine |
Corning |
Cat#: 25-005-CI |
| N2 |
Gibco |
Cat#: 17502048 |
| B27 |
Gibco |
Cat#: 17504044 |
| Human R-Spondin-1 |
R&D Systems |
Cat#: 4645-RS |
| Mouse Wnt-3a |
R&D Systems |
Cat#: 1324-WN |
| Mouse Noggin |
R&D Systems |
Cat#: 1967-NG |
| Human EGF |
R&D Systems |
Cat#: 236-EG |
| Mouse EGF |
Peprotech |
Cat#: 315-09 |
| Human IGF-1 |
BioLegend |
Cat#: 590908 |
| Human FGF-basic |
Peprotech |
Cat#: 100-18B |
| N-acetylcysteine |
Sigma-Aldrich |
Cat#: A9165 |
| Gastrin-Leu15 |
Sigma-Aldrich |
Cat#: G9145 |
| A83-01 |
Torics |
Cat#: 2939 |
| Y-27632 |
Sigma-Aldrich |
Cat#: Y05030 |
| Cell Recovery Medium |
Corning |
Cat#: 354253 |
| Gentle Cell Dissociation Reagent |
Stemcell |
Cat#: 100-0485 |
| TrypLE express |
Gibco |
Cat#: 12605010 |
| Leukocyte Activation Cocktail, with BD GolgiPlug |
BD Biosciences |
Cat#: 550583 |
| IC Fixation Buffer |
eBioscience |
Cat#: 00-8222-49 |
| 10x Permeabilization Buffer |
eBioscience |
Cat#: 00-8333-56 |
| RNA Clean & Concentrator -5 kit |
Zymo Research |
Cat#: R1015 |
| NEBNext rRNA Depletion Kit |
NEB |
Cat#: 6310 |
| NEBNext Ultra II Directional RNA Library Prep Kit |
NEB |
Cat#: 7760 |
| Bioanalyzer High Sensitivity DNA Analysis |
Agilent |
Cat#: 5067-4626 |
| 2-mercaptoethanol |
Sigma-Aldrich |
Cat#: M6250 |
| Sodium dodecyl sulfate (SDS) |
Sigma-Aldrich |
Cat#: 436143 |
| 16% paraformaldehyde |
Electron Microscopy Sciences |
Cat#: 15710-S |
| Sucrose |
Sigma-Aldrich |
Cat#: S0389 |
| Triton X-100 |
Sigma-Aldrich |
Cat#: T8787 |
| Tween-20 |
VWR |
Cat#: 0777 |
| 2-methylbutane |
Sigma-Aldrich |
Cat#: M32631
|
| CHIR99021 |
Tocris Bioscience |
Cat#: 4423 |
| Deposited data |
|
|
| ScRNA-seq data: C57BL/6J mouse-derived small intestinal organoids |
Gene Expression Omnibus |
Accession#: GSE159423
|
| RNA-seq data: terminal ileum of Il17rafl/fl;Atoh1-cre mice at 6 days post 2.5% DSS treatment |
Gene Expression Omnibus |
Accession#: GSE189219
|
| Experimental Models: Cell lines |
|
|
| L-WRN cells |
Dr. Thaddeus Stappenbeck Washington University in St. Louis |
N/A |
| Experimental Models: Organisms/Strains |
|
|
| Mouse: Villin-cre
|
Jackson Laboratory |
Cat#: 004586 |
| Mouse: Villin-creERT2
|
Dr. Sylvie Robine, Institut Curie-CNRS |
Cat#: 020282 |
| Mouse: ROSA-CAG-LSL-tdTomato
|
Jackson Laboratory |
Cat#: 007905 |
| Mouse: Atoh1-cre
|
Jackson Laboratory |
Cat#: 011104 |
| Mouse: Atoh1-creER-T2/flox;RosaTdtomato
|
Dr. Steve Maricich University of Pittsburgh |
N/A |
| Mouse: Atoh1-EGFP |
Jackson Laboratory |
Cat#: 013593 |
| Mouse: Defa6-cre
|
Dr. Rich Blumberg Harvard University |
N/A |
| Mouse: Lgr5-EGFP-creERT2
|
Jackson Laboratory |
Cat#: 008875 |
| Mouse: Il17rafl/fl
|
Dr. Jay Kolls, Tulane University |
N/A |
| Mouse: Il17ra−/−
|
Amgen Dr. Jay K. Kolls, Tulane University |
N/A |
| Mouse: Il17c−/−
|
Dr. Sarah Gaffen, University of Pittsburgh |
N/A |
| Mouse: Il17re−/−
|
Dr. Sarah Gaffen, University of Pittsburgh |
N/A |
| Mouse: Myd88fl/fl;Villin-cre
|
Dr. Jeremy McAleer, Marshall University |
N/A |
| Mouse: Lgr5-EGFP-creERT2; ROSA-CAG-LSL-tdTomato
|
Dr. Vincent Yang, Stony Brook University |
N/A |
| Mouse: Rorc−/−
|
Dr. Jay K. Kolls, Tulane University |
N/A |
| Oligonucleotides |
|
|
| Primer Sequences for qPCR-See table 2 |
This paper |
N/A |
|
Mki67 (Mm_Mki67_1_SG) |
Qiagen |
Cat#: QT00247667 |
|
Il17a (Mm00439618_m1) |
Applied Biosystems |
Cat#: 4331182 |
|
Il22 (Mm00444241_m1) |
Applied Biosystems |
Cat#: 4331182 |
|
Hprt (Mm00446968_m1) |
Applied Biosystems |
Cat#: 4331182 |
|
Atoh1 (Mm00476035_s1) |
Applied Biosystems |
Cat#: 4331182 |
|
Chga (Mm0051431_m1) |
Applied Biosystems |
Cat#: 4331182 |
|
Dclk1 (Mm00444950_m1) |
Applied Biosystems |
Cat#: 4331182 |
|
Lgr5 (Mm00438890_m1) |
Applied Biosystems |
Cat#: 4331182 |
|
Muc2 (Mm.PT.58.53535475.g) |
IDT |
N/A |
|
Tnfa (Mm.PT.58.12575861) |
IDT |
N/A |
|
Lyz1 (Mm.PT.58.7374112) |
IDT |
N/A |
|
Clca1 (Mm.PT.58.41915855) |
IDT |
N/A |
|
Il17ra (Mm.PT.58.17281196) |
IDT |
N/A |
|
Il17rc (Mm.PT.58.29101252) |
IDT |
N/A |
| Software and Algorithms |
|
|
| Prism 7 |
GraphPad Software |
https://www.graphpad.com/scientificsoftware/prism/
|
| ImageJ |
NIH |
https://imagej.nih.gov/ij/index.html
|
| cellSens Standard |
Olympus |
https://www.olympus-lifescience.com/en/software/cellsens/
|
| LSM Image Browser |
Zeiss |
https://www.embl.de/eamnet/html/body_image_browser.html
|
