|
Antibodies
|
| anti-mouse CD45-APC-Cy7 |
Biolegend |
Cat#103116; RRID: AB_312981 |
| anti- mouse CD45-AF700 |
Biolegend |
Cat#103128; RRID: AB_493715 |
| anti- mouse CD45.1-PE-Cy7 |
Biolegend |
Cat#110730; RRID: AB_1134168 |
| anti- mouse CD45.2-APC-Cy7 |
Biolegend |
Cat#109824; RRID: AB_830789 |
| anti- mouse CD3 PACB |
Biolegend |
Cat#100334; RRID: AB_2028475 |
| anti- mouse CD3 PE/Cy7 |
Biolegend |
Cat#100320; RRID: AB_312685 |
| anti- mouse CD3 APC/Cy7 |
Biolegend |
Cat#100222; RRID: AB_2242784 |
| anti- mouse CD4-PerCP-Cy5.5 |
Biolegend |
Cat#100434; RRID: AB_893324 |
| anti- mouse CD4- PE/Cy7 |
Biolegend |
Cat# 100422; RRID: AB_312707 |
| anti-CD8α-APC |
Biolegend |
Cat#100712; RRID: AB_ 312751 |
| anti-CD8β-FITC |
Biolegend |
Cat#126606; RRID: AB_ 961295 |
| anti-CD8β-PerCP-Cy5.5 |
Biolegend |
Cat#126610; RRID: AB_ 2260149 |
| anti-TCR-γδ-PE |
Biolegend |
Cat#118108; RRID: AB_ 313832 |
| anti-TCR-γδ-BV421 |
Biolegend |
Cat#118119; RRID: AB_ 2562566 |
| anti-CD3-PerCP-Cy5.5 |
Biolegend |
Cat#100328; RRID: AB_ 893318 |
| anti-CD5-PerCP-Cy5.5 |
Biolegend |
Cat#100624; RRID: AB_ 2563433 |
| anti-CD19-PerCP-Cy5.5 |
Biolegend |
Cat#115534; RRID: AB_ 2072925 |
| anti-RORγT-APC |
Invitrogen |
Cat#17-6988-82; RRID: AB_10609207 |
| anti-RORγT-PE |
Invitrogen |
Cat#12-6988-82; RRID: AB_1834470 |
| anti-GATA3-AF488 |
BD |
Cat#560077; RRID: AB_1645303 |
| anti-EOMES-PE |
Invitrogen |
Cat#12-4875-82; RRID: AB_1603275 |
| anti-FoxP3-AF647 |
Biolegend |
Cat#124608; RRID: AB_ 1089115 |
| anti-CD69-BV605 |
Biolegend |
Cat#104529; RRID: AB_ 11203710 |
| anti-CCR9- PE/Cy7 |
Biolegend |
Cat#128712; RRID: AB_ 10933082 |
| anti-CD103-Biotin |
Invitrogen |
Cat#13-1031-85; RRID: AB_ 466553 |
| anti-NKp46-Biotin |
Biolegend |
Cat# 137616; RRID: AB_ 11218796 |
| anti-CCR6-BV421 |
Biolegend |
Cat# 129818; RRID: AB_ 11219003 |
| anti-CD90.2-APC |
Biolegend |
Cat# 129818; RRID: AB_ 313183 |
| anti-IL-17A-FITC |
Biolegend |
Cat# 506908; RRID: AB_ 536010 |
| anti-IL-22-PE |
Invitrogen |
Cat# 12-7221-82; RRID: AB_ 10597428 |
| anti-IFN-γ-PE |
Biolegend |
Cat# 505808; RRID: AB_ 315402 |
|
|
|
|
Biological samples
|
| Intestinal tissue from healthy and IBD patients |
Washington University in St. Louis |
N/A |
|
Bacteria
|
|
|
|
C. difficile
|
Colonna Lab |
VPI 10463 |
|
Chemicals, peptides, and recombinant proteins
|
| Mouse IL-23 |
R&D |
Cat#1887-ML |
| Mouse IL-2 supernatant |
Colonna Lab |
N/A |
| Mouse IL-4 supernatant |
Colonna Lab |
N/A |
| Collagenase from Clostridium histolyticum |
Sigma |
Cat#C5138 |
|
|
|
|
Critical commercial assays
|
| Foxp3 transcription factor staining Buffer set |
eBioscience |
Cat#00-5523-00 |
| BD Cytofix/Cytoperm Plus |
BD Biosciences |
Cat#555028 |
| LS Columns |
Miltenyi Biotec |
Cat#130-042-401 |
| CD45 MicroBeads, mouse |
Miltenyi Biotec |
Cat#130-052-301 |
| Pan T Cell Isolation Kit II, mouse |
Miltenyi Biotec |
Cat#130-095-130 |
| RNeasy Plus Micro Kit |
QIAGEN |
Cat#74034 |
|
Deposited data
|
| Single cell RNAseq data |
This paper |
GSE199960 |
|
Experimental models: Organisms/strains
|
| Mouse: Ahrrfl/fl, Ahrr−/−
|
This study |
N/A |
| Mouse: Rorccre
|
Tumanov lab |
N/A |
| Mouse:CD45.1 |
Jackson lab |
JAX:002014 |
| Mouse: CD45.1/2 |
This study |
N/A |
|
|
|
|
Oligonucleotides
|
|
Sequence
|
|
Reg-IIIb-Fwd
|
Integrated DNA Technologies |
TCCCAGGCTTATGGCTCCTA |
|
Reg-IIIb-Rev |
Integrated DNA Technologies |
GCAGGCCAGTTCTGCATCA |
|
Reg-IIIg-Fwd |
Integrated DNA Technologies |
CATCAACTGGGAGACGAATCC |
|
Reg-IIIg-Rev |
Integrated DNA Technologies |
CAGAAATCCTGAGGCTCTTGACA |
|
Ahrr-Fwd |
Integrated DNA Technologies |
CTGCCCCGGGATCAAAGATG |
|
Ahrr-Rev |
Integrated DNA Technologies |
CTCTGTATTGAGGCGGTCCC |
|
Cyp1a1- Fwd |
Integrated DNA Technologies |
GACATTTGAGAAGGGCCACAT |
|
Cyp1a1-Rev |
Integrated DNA Technologies |
TCCTGGATCTTTCTCTGTACCC |
|
Il6- Fwd |
Integrated DNA Technologies |
GAGGATACCACTCCCAACAGACC |
|
Il6- Rev |
Integrated DNA Technologies |
AAGTGCATCATCGTTGTTCATACA |
|
Ifng- Fwd |
Integrated DNA Technologies |
AGGAACTGGCAAAAGGATGGT |
|
Ifng- Rev |
Integrated DNA Technologies |
ACCTGTGGGTTGTTGACCTC |
|
Tnfa- Fwd |
Integrated DNA Technologies |
CATCTTCTCAAAATTCGAGTGACAA |
|
Tnfα- Rev |
Integrated DNA Technologies |
TGGGAGTAGACAAGGTACAACCC |
|
Hsph1 -Fwd |
Integrated DNA Technologies |
TGCAGCACTATGCCAAGATTG |
|
Hsph1 -Rev |
Integrated DNA Technologies |
TTCTCAACCTTCTTCATTTCTGATTC |
|
Dnajb1-Fwd |
Integrated DNA Technologies |
TTCGACCGCTATGGAGAGGAA |
|
Dnajb1-Rev |
Integrated DNA Technologies |
CACCGAAGAACTCAGCAAACA |
|
Hspa1a-Fwd |
Integrated DNA Technologies |
ATGGACAAGGCGCAGATCC |
|
Hspa1a-Rev |
Integrated DNA Technologies |
CTCCGACTTGTCCCCCAT |
|
Software and algorithms
|
| FlowJo |
Tree Star |
https://www.flowjo.com/
|
| Prism |
Graphpad |
https://www.graphpad.com/
|
| Endnote |
Endnote |
https://endnote.com/
|
| Seurat |
R |
https://satijalab.org/seurat/
|
| Biorender |
Biorender |
https://biorender.com/
|
