| Antibodies |
| Mouse anti FOXA1 (IHC) |
Millipore Sigma |
05-1466 |
| Rabbit anti FOXA2 (IHC) |
Millipore Sigma |
07-633 |
| Mouse anti E-Cadherin |
BD Biosciences |
610181 |
| Rabbit anti Epcam |
Abcam |
ab71916 |
| Rat anti CD45R |
BD Biosciences |
550286 |
| Rabbit anti CD3 (SP7) |
Novus Biologicals |
NB600-1441 |
| Rat anti Ki67 |
Invitrogen |
50-245-563 |
| Rabbit anti MUC2 (for immunostaining) |
Santa Cruz |
sc-15334 |
| Rabbit anti MUC2 (for western blot) |
Abcam |
ab272692 |
| Mouse anti Tubulin |
Sigma |
T9026 |
| Mouse anti FOXA1 (ChIP) |
Abcam |
ab23738 |
| Rabbit anti FOXA2 (ChIP) |
Santa Cruz Biotechnology |
sc-6554 |
| Rabbit anti CD45 (D3F8Q) |
Cell Signaling |
70257 |
| Monoamine Oxidase A (MAO-A) |
|
|
| Cy2 AffiniPure Donkey Anti-Rabbit IgG |
Jackson ImmunoResearch |
711-225-152 |
| Cy5 AffiniPure Donkey Anti-Mouse IgG |
Jackson ImmunoResearch |
715-175-151 |
| Cy3 AffiniPure Donkey Anti-Rabbit IgG |
Jackson ImmunoResearch |
711-165-152 |
| Cy5 AffiniPure Donkey Anti-Rabbit IgG |
Jackson ImmunoResearch |
711-175-152 |
| Cy3 AffiniPure Donkey Anti-Mouse IgG |
Jackson ImmunoResearch |
715-165-151 |
| Chemicals, peptides, and recombinant proteins |
| R-buffer A |
Electron Microscopy Sciences |
62706-10 |
| Cas-block |
Thermo Fisher Scientific |
008120 |
| Hoechst 33342 |
Thermo Fisher Scientific |
H3570 |
| HRP |
Vector laboratories |
PK-7100 |
| DAB substrate |
Vector laboratories |
SK-4100 |
| Ulex Europaeus Agglutinin I (UEA I), Fluorescein |
Vector laboratories |
FL-1061 |
| Maackia Amurensis Lectin II (MAL II), Cy3 |
GlycoMatrix |
21511109-1 |
| Wheat Germ Agglutinin (WGA), Rhodamine |
Vector laboratories |
RL-1022 |
| Carbo-Free Blocking Solution |
Vector laboratories |
SP-5040-125 |
| TrueBlack® Lipofuscin Autofluorescence Quencher |
Biotium |
23007 |
| ProLong™ Gold Antifade Mounting medium |
Thermofischer |
P36930 |
| FITC-dextran, 3–5 kDa |
Sigma-Aldrich |
FD4 |
| 5-ethynyl-2’-deoxyuridine (EdU) |
Invitrogen |
E10187 |
| TRIzol reagent |
Invitrogen |
15596026 |
| T4 DNA polymerase |
NEB |
M0203 |
| Klenow DNA polymerase |
NEB |
M0210 |
| T4 polynucleotide kinase |
NEB |
M0201 |
| Klenow Fragment (3’→5’ exo-) |
NEB |
M0212 |
| Nuclei EZ Lysis Buffer |
Sigma |
NUC-101 |
| TAQMAN Fast Gene Expression Universal PCR Master Mix |
Thermo Fisher Scientific |
4352042 |
| Q5 High-Fidelity DNA Polymerase |
NEB |
M0491 |
| Critical commercial assays |
| Lipocalin-2 DuoSet mouse ELISA kit |
R&D systems |
DY1857 |
| Click-iT™ EdU Cell Proliferation Kit for Imaging, Alexa Fluor™ 555 dye |
Thermo Fisher Scientific |
C10338 |
| RNeasy Micro Kit |
Qiagen |
74004 |
| High-Capacity cDNA Reverse Transcription Kit |
Applied Biosystems |
4374966 |
| Pierce™ BCA Protein Assay Kits |
ThermoFisher |
23225 |
| Immobilon Crescendo Western HRP substrate |
Millipore |
WBLUR0100 |
| RNAscope® Multiplex Fluorescent Detection Reagents V2 |
ACD |
323110 |
| HybEZ oven |
ACD |
PN 321710/321720 |
| RNAscope® Probe Diluent |
ACD |
300041 |
| TSA Vivid fluorophore 650 |
ACD |
323273 |
| TSA Vivid fluorophore 570 |
ACD |
323272 |
| TSA Vivid fluorophore 520 |
ACD |
323271 |
| NEBNext Ultra RNA Library Prep Kit for Illumina |
NEB |
E7530 |
| NEBNext Poly(A) mRNA Magnetic Isolation Module |
NEB |
E7490 |
| QIAquick PCR Purification Kit |
Qiagen |
28104 |
| Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 |
10X genomics |
PN-1000121 PN-1000122 |
| DNeasy PowerSoil Pro kit |
Qiagen |
47016 |
| Nextera XT DNA Library Preparation Kit |
Illumina |
FC-131-1096 |
| Deposited data |
| Glycan analysis MS raw files at GlycoPOST database: https://glycopost.glycosmos.org/preview/7094574161e18019e3f37
|
This paper |
GlycoPOST ID: GPST000248 password: 6868 |
| Micrbial 16S sequencing |
This paper |
PRJNA1091956 |
| Metagenomic sequencing |
This paper |
PRJNA1091956 |
| RNA sequencing of proximal and distal colon |
This paper |
PRJNA1091956 and GEO: GSE263630
|
| ChIP sequencing of FOXA1 and FOXA2 |
This paper |
PRJNA1091956 and GEO: GSE263629
|
| Single nuclei RNA sequencing of distal colon |
This paper |
PRJNA1091956 and GEO: GSE263631
|
| Unprocessed Western blots |
This paper |
Mendeley data: http://dx.doi.org/DOI:10.17632/r2h76p84r4.1
|
| Experimental models: Organisms/strains |
|
Foxa1lox/lox mice |
Kaestner lab, University of Pennsylvania |
N.A. |
|
Foxa2lox/lox mice |
Kaestner lab, University of Pennsylvania |
N.A. |
|
Villin1-Cre mice |
Jackson Laboratory |
033019 |
| Oligonucleotides |
| EUB338 FISH probe, Cy3-conjugated: 5′-GCTGCCTCCCGTAGGAGT-3′ |
IDT |
N.A. |
| Nonsense FISH probe, Cy3-conjugated: 5′-CGACGGAGGGCATCCTCA-3′ |
IDT |
N.A. |
| RNAscope™ Probe- Mm-Foxa2-C2 |
ACD |
409111-C2 |
| RNAscope™ Probe- Mm-Muc2-C3 |
ACD |
315451-C3 |
| RNAscope™ Probe- Mm-Gcnt3 |
ACD |
553881 |
| RNAscope™ Probe- Mm-Fut2 |
ACD |
811421 |
| 16s qPCR BSF8 primer: AGAGTTTGATCCTGGCTCAG |
IDT |
N.A. |
| 16s qPCR BSR357 primer: CTGCTGCCTYCCGTA |
IDT |
N.A. |
| 16s qPCR Taqman probe: /56-FAM/TAA +CA+C ATG +CA+A GT+C GA/3BHQ 1/ |
IDT |
N.A. |
| Lcn2 forward primer: CAATGTCACCTCCATCCTGG |
IDT |
N.A. |
| Lcn2 reverse primer: CCTGGAGCTTGGAACAAATG |
IDT |
N.A. |
| Tnf forward primer: ACTCCAGGCGGTGCCTATGT |
IDT |
N.A. |
| Tnf reverse primer: AGTGTGAGGGTCTGGGCCAT |
IDT |
N.A. |
| Actb forward primer: CACAGCTTCTTTGCAGCTCCT |
IDT |
N.A. |
| Actb reverse primer: GTCATCCATGGCGAACTGG |
IDT |
N.A. |
