|
| Antibodies |
|
|
|
| PE-Cy7 anti-mouse CD4 (clone: GK1.5) |
eBioscience |
Cat# 25-0041-82; RRID:AB_469576 |
| APC anti-mouse CD4 (clone: GK1.5) |
eBioscience |
Cat# 17-0041-82; RRID:AB_469320 |
| PE-Cy5 anti-mouse CD4 (clone: GK1.5) |
eBioscience |
Cat# 15-0041-83; RRID:AB_468696 |
| BV650 anti-mouse CD8 (clone: 53-6.7) |
Biolegend |
Cat# 100742; RRID:AB_2563056 |
| PE-Cy5 anti-mouse CD8 (clone: 53-6.7) |
eBioscience |
Cat# 15-0081-82; RRID:AB_468706 |
| PE-Cy5 anti-mouse CD11b (clone: M1/70) |
Biolegend |
Cat# 101210; RRID:AB_312793 |
| PE-Cy5 anti-mouse CD11c (clone: N418) |
Biolegend |
Cat# 15-0114-82; RRID:AB_468717 |
| PE-Cy5 anti-mouse F4/80 (clone: BM8) |
eBioscience |
Cat# 15-4801-82; RRID:AB_468798 |
| PE-Cy5 anti-mouse B220 (clone: RA3-6B2) |
Biolegend |
Cat# 15-0452-83; RRID:AB_468756 |
| Alexa Fluor 700 anti-mouse CD44 (clone: IM7) |
Biolegend |
Cat# 56-0441-82; RRID:AB_494011 |
| BV421 anti-mouse CD44 (clone: IM7) |
Biolegend |
Cat# 103039; RRID:AB_10895752 |
| APC anti-mouse CD44 (clone: IM7) |
Biolegend |
Cat# 103026; RRID:AB_493713 |
| APC-eFluor780 anti-mouse CD45 (clone: 30F11) |
invitrogen |
Cat# 47-0451-82; RRID:AB_1548781 |
| FITC anti-mouse FOXP3 (clone: FJK-16S) |
eBioscience |
Cat# 11-5773-82; RRID:AB_465243 |
| PE anti-mouse FOXP3 (clone: FJK-16S) |
eBioscience |
Cat# 12-5773-82; RRID:AB_465936 |
| AF647 anti-mouse RORgt (clone: Q31-378) |
BD bioscience |
Cat# 562682; RRID:AB_2687546 |
| PE-Cy7 anti-mouse IL17A (clone: TC 11-18H10.1) |
Biolegend |
Cat# 506922; RRID:AB_2125010 |
| APC anti-mouse Helios (clone: 22F6) |
eBioscience |
Cat# 17-9883-42; RRID:AB_2573322 |
| E450 anti-mouse CD304 (clone: 3DS304M) |
eBioscience |
Cat# 48-3041-82; RRID:AB_2574051 |
| BV605 anti-mouse CD62L (clone: MEL-14) |
Biolegend |
Cat# 104437; RRID:AB_11125577 |
| PE-Cy5 anti-mouse CD25 (clone: PC61) |
Biolegend |
Cat# 102010; RRID:AB_312859 |
| PE-cy7 anti-mouse GITR (clone: DTA-1) |
eBioscience |
Cat# 25-5874-82; RRID:AB_10548516 |
| PE-Cy7 anti-mouse IRF4 (clone: 34E) |
eBioscience |
Cat# 25-9858-82; RRID:AB_2573558 |
| BV650 anti-mouse CD90.1 (clone: OX-7) |
Biolegend |
Cat# 202533; RRID:AB_2562254 |
| Alexa Fluor 700 anti-mouse CD90.2 (clone: 30-H12) |
Biolegend |
Cat# 105320; RRID:AB_493725 |
| PE-Cy7 anti-mouse CXCR5 (clone: L138D7) |
Biolegend |
Cat# 145516; RRID:AB_2562210 |
| BV421 anti-mouse BCL6 (clone: K112-91) |
BD bioscience |
Cat# 561525; RRID:AB_10898007 |
| BV421 anti-mouse T-bet (clone: 4B10) |
Biolegend |
Cat# 644816; RRID:AB_10959653 |
| E605 anti-moues PD-1 (clone: 29F.1A12) |
Biolegend |
Cat# 135220; RRID:AB_2562616 |
| BV605 anti-moues Ki67 (clone: 16A8) |
Biolegend |
Cat# 652413; RRID:AB_2562664 |
| PE-Cy7 anti-mouse CD45.1 (clone: A20) |
eBioscience |
Cat# 25-0453-82; RRID:AB_469629 |
| PE anti-mouse CD45.2 (clone: 104) |
eBioscience |
Cat# 12-0454-82 RRID:AB_465678 |
| E450 anti-mouse LAG3 (clone: C9B7W) |
eBioscience |
Cat# 48-2231-82; RRID:AB_11149866 |
| APC anti-mouse CTLA4 (clone: UC10-4B9) |
eBioscience |
Cat# 17-1522-82; RRID:AB_2016700 |
| PE-Cy7 anti-mouse CD39 (clone: 24DMS1) |
eBioscience |
Cat# 25-0391-82; RRID:AB_1210766 |
| Alexa Fluor 700 anti-mouse CD49b (clone: DX5) |
eBioscience |
Cat# 56-5971-82; RRID:AB_2574507 |
| APC anti-CD226 (clone: 10E5) |
Biolegend |
Cat# 128810; RRID:AB_2566627 |
| Rat IgG2a (clone: 2A3) |
BioXcell |
Cat# BE0089; RRID:AB_1107769 |
| Rat IgG2b (clone: LTF-2) |
BioXcell |
Cat# BE0090; RRID:AB_1107780 |
| Mouse IgG1 (clone: MOPC-21) |
BioXcell |
Cat# BE0083; RRID:AB_1107784 |
| Hamster IgG (polyclonal) |
BioXcell |
Cat# BP0091; RRID:AB_1107773 |
| Rat IgG1 к (clone: HRPN) |
BioXcell |
Cat# BE0088; RRID:AB_1107775 |
| anti-mouse CD3 (clone: 145-2C11) |
BioXcell |
Cat# BP0001-1; RRID:AB_1107634 |
| anti-mouse CD28 (clone: 37.51) |
BioXcell |
Cat# BE0015-1; RRID:AB_1107624 |
| anti-mouse IL10 (clone: JES5-2A5) |
BioXcell |
Cat# BE0049; RRID:AB_1107696 |
| anti-mouse IL10R (clone: 1B1.3A) |
BioXcell |
Cat# BE0050; RRID:AB_1107611 |
| anti-mouse TGFβ (clone: 1D11.16.8) |
BioXcell |
Cat# BE0057; RRID:AB_1107757 |
| anti-mouse CTLA4 (clone: UC10-4F10-11) |
BioXcell |
Cat# BE0032; RRID:AB_1107598 |
| anti-mouse LAG3 (clone: C9B7W) |
BioXcell |
Cat# BE0174; RRID:AB_10949602 |
| anti-mouse OX-40L (clone: RM134L) |
BioXcell |
Cat# BE0033-1; RRID:AB_1107594 |
| anti-mouse ICOSL (clone: HK5.3) |
BioXcell |
Cat# BE0028; RRID:AB_1107566 |
|
| Bacterial and virus strains |
|
|
|
|
Listeria monocytogenes-2W1S |
Ertelt et al.30
|
Derived from WT strain 10403s |
|
Salmonella typhimurium-2W1S |
McSorley Lab, University of California, Davis; Benoun et al.31
|
SL1344 ΔAroA |
|
| Biological samples |
|
|
Candida albicans-2W1S |
Kaplan Lab, University of Pittsburg; Igyarto et al.25
|
CaURA3/CaURA3 pENO1-ENO1-GFP-2W1S-OVA323-339-OVA257-264-I-Eα50-66
|
|
| Chemicals, peptides, and recombinant proteins |
|
| Ampicillin |
Sigma-Aldrich |
Catalog# A0166 |
| Gentamicin |
Sigma-Aldrich |
Catalog# G3632 |
| Metronidazole |
Sigma-Aldrich |
Catalog# M3761 |
| Neomycin |
Sigma-Aldrich |
Catalog# N6386 |
| Vancomycin |
MP Biomedical |
Catalog# 0219554005 |
| Sucralose |
Sigma-Aldrich |
Catalog# 69293-100G |
| Dehydrated Culture Media: Brain Heart Infusion |
Thermo Fisher Scientific |
Catalog# B11060
|
| Yeast extract |
Boston Bio Product |
Catalog# P-950 |
| Bactopeptone BD |
Bioscience |
Catalog# DF0118170 |
| Uridine |
Alfa-Aesar |
Catalog# A15227 |
| D-(+)-Glucose |
Sigma-Aldrich |
Catalog# G5767 |
| Agar |
Bio Express |
Catalog# J637 |
| DMEM |
Gibco |
Catalog# 10313-21 |
| Fetal bovine serum |
GeneMate |
Catalog# S-1200-500 |
| Glutamine (100X) |
Gibco |
Catalog# 25030-081 |
| HEPES 1M |
Gibco |
Catalog# 15630-080 |
| Penicillin-streptomycin solution (100X) |
Gibco |
Catalog# 15140-122 |
| BD Golgi Plug (Brefeldin A solution) |
BD Bioscience |
Catalog# 555029 |
| 10% normal formalin |
Sigma-Aldrich |
Catalog# HT501128-4L |
| Percoll |
Sigma |
Catalog# P4937 |
| Dnase I |
Roche |
Catalog# 10104159001 |
| CollagenaseA |
Roche |
Catalog# 11088793001 |
| DL-Dithiothreitol |
Sigma |
Catalog# D9779 |
| EDTA |
Amresco |
Catalog# E177 |
| β-galactosidase peptide |
|
NLSVTLPAASHAIPH |
| Tamoxifen chow 400 mg/kg |
Envigo |
Catalog# 130860 |
| CFSE |
Thermo Fisher Scientific |
Catalog#65-0850-84 |
| Cell stimulation cocktail (500X) |
Thermo Fisher Scientific |
Catalog#00-4975-03 |
| FTY720 |
Sigma |
Catalog# SML0700-25MG |
| BrdU |
BD Pharmigen |
Catalog# 550891 |
|
| Critical commercial assays |
|
| Mouse Lipocalin-2 Quantikine ELISA |
R&D |
Catalog# MLCN20 |
| Milliplex (Mouse cytokine/chemokine panel 1) |
Sigma-Aldrich |
Catalog# MCYTOMAG-70K-PMX |
| LIVE/DEAD Near-IR staining Kit |
ThermoFisher |
Catalog# L34976
|
| LIVE/DEAD Blue staining Kit |
ThermoFisher |
Catalog# L34962
|
| Fixation/Permeabilization solution kit |
BD Bioscience |
Catalog# 554722 |
| Foxp3/Transcription factor staining buffer set |
eBioscience |
Catalog# 00-5523-00 |
| Anti-PE Microbeads |
Miltenyi |
Catalog# 130-048-801 |
| Anti-APC Microbeads |
Miltenyi |
Catalog# 30-090-855 |
| APC BrdU Kit |
BD Pharmingen |
Catalog# 552598 |
| SMARTer® Stranded Total RNA-Seq Pico Input Mammalian Kit v3 |
Takara |
Catalog# 634485 |
|
| Deposited data |
|
|
|
| Code for analysis single cell RNAseq and open access human IBD cohort |
This paper |
https://github.com/Deshmukh-Lab/KLF2_WayLab
|
|
| Experimental models: Organisms/strains |
|
|
|
| CD45.1 |
Jackson Laboratory |
Strain Code: 002014 |
| CD90.1 |
Jackson Laboratory |
Strain Code: 000406 |
| FOXP3RFP
|
Jackson Laboratory |
Strain Code: 008374 |
| CD4Cre
|
Jackson Laboratory |
Strain Code: 017336 |
| CD4CreER(T2)
|
Jackson Laboratory |
Strain Code: 022356 |
| IL10−/− |
Jackson Laboratory |
Strain Code:002251 |
| Rag1 −/− |
Jackson Laboratory |
Strain Code:002216 |
| 10BiT |
Dr. Casey T. Weaver |
Maynard et al.55
|
| BG-2 TCR |
Dr. Dale S. Gregerson |
McPherson et al.51
|
| KLF2GFP
|
Dr. George Deepe |
Lingrel et al.42
|
| KLF2f/f
|
Dr. Stephen Jameson |
Weinreich et al.34
|
|
| Software and algorithms |
|
|
|
| Prism 6.0h |
GraphPad |
N/A |
| Flow Jo 9.9.6 |
Treestar |
N/A |
| Seurat 4.3.0 |
Satija Lab |
N/A |
| Sickle 1.33 |
https://github.com/najoshi/sickle
|
N/A |
| Subread |
N/A |
Liao et al.82
|
| DESeq2 |
N/A |
Love et al.83
|
|
| Other |
|
|
|
| I-Ab:2W1S55-68 Tetramer |
NIH Tetramer Core |
Moon et al.27
|
| I-Ab:CBir1464-472 Tetramer |
NIH Tetramer Core |
Eshleman et al.84
|
