REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Antibodies for Cytometry
Amphiregulin (Biot)	R&D system	Cat#BAF989; RRID: AB_2060662
Aqua L/D	ThermoFisher	Cat#L34957
B220 (AF700)	eBioscience	Cat#56-0452-82; RRID: AB_891458
CCR2 (AF700)	R&D system	Cat#FAB5538N; RRID: AB_2725739
CD103 (BV786)	BD	Cat#564322; RRID: AB_2738744
CD103 (PerCP-eF710)	Invitrogen	Cat#46-1031-82; RRID: AB_2573704
CD11b (APC)	eBiosciences	Cat#17-0112-83; RRID: AB_469344
CD11c (PETR)	LifeTechnologies	Cat#MCD11C17; RRID: AB_1464845
CD19 (AF700)	Biolegend	Cat#115528; RRID: AB_493735
CD19 (FITC)	eBioscience	Cat#11-0191-85; RRID: AB_464966
CD44 (BV605)	Biolegend	Cat#103047; RRID: AB_2562451
CD45.1 (PE-Cy7)	Biolegend	Cat#110730; RRID: AB_1134168
CD45.2 (AF700)	Biolegend	Cat#109822; RRID: AB_493731
CD24 (FITC)	Invitrogen	Cat# 11-0242-82; RRID: AB_464988
CD69 (PC7 & PE-Dazzle 594)	Biolegend	Cat#104512; RRID: AB_493564
CXCR6 (PETR)	Biolegend	Cat#151117; RRID: AB_2721700
Ki67 (PE-Cy7)	Biolegend	Cat#652426; RRID: AB_2632694
Ly6C (BV785)	Biolegend	Cat#128041; RRID: AB_2565852
RORgt (BV786)	BD	Cat#564723; RRID: AB_2738916
Tbet (APC)	Invitrogen	Cat#17-5825-82; RRID: AB_2744712
TCRb (APC-Cy7)	Biolegend	Cat#109220; RRID: AB_893626
TCRgd (BV605)	Biolegend	Cat#118129; RRID: AB_2563356
Tet CD1d (BV421)	NIH tetramer core facility	N/A
Tet MR1 (APC)	NIH tetramer core facility	N/A
Tet MR1 (PE)	NIH tetramer core facility	N/A
Antibodies for Immunohistochemistry and Immunofluorescence
DAPI	Sigma	Cat#MBD0015
Donkey anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488	Fisher	Cat#A-21206; RRID: AB_2535792
Goat anti-Chicken IgY (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor Plus 647	Fisher	Cat#A32933; RRID: AB_2762845
Goat anti-Rat IgG (H+L) Cross-Adsorbed Secondary Antibody, Cyanine3	Fisher	Cat#A10522; RRID: AB_1500704
Keratin 14 Polyclonal Chicken Antibody, Purified Antibody	Biolegend	Cat#905301; RRID: AB_2565048
Ki-67 (D3B5) Rabbit mAb	Ozyme	Cat#9129S; RRID: AB_2687446
Purified Chicken IgY Isotype Ctrl Antibody	BIOLEGEND	Cat#402101
Purified Rat Anti-Mouse CD31	BD	Cat#550274; RRID: AB_393571
Purified Rat IgG2a κ Isotype Control	BD	Cat#559073; RRID: AB_479682
Rabbit (DA1E) mAb IgG XP® Isotype Control	Ozyme	Cat#3900S; RRID: AB_1550038
Chemicals, peptides, and recombinant proteins
24G2	Institut Curie, produced in house	N/A
Alt-R S.p. HiFi Cas9 Nuclease V3	IDT	Cat#1081061
Anti-mCXCL16	R&D Systems	Cat#MAB503; RRID: AB_2276752
Anti-PE microbeads	Miltenyi	Cat#130-048-801
Anti-FITC microbeads	Miltenyi	Cat# 130-048-701
B-mercaptoethanol	Sigma	Cat#M3148
BCA Assay	ThermoFisher	Cat#23227
Bovine Serum Albumin	SIGMA	Cat#A7906
Brefeldin A	SIGMA	Cat#B6542
CO2 independent medium	Gibco	Cat#18045088
DAPI	Sigma	Cat#MBD0015
Debris removal solution	Miltenyi	Cat#130-109-398
Dispase	Corning	Cat#354235
DNAse 1	Roche	Cat#5401020001
EDTA	Gibco	Cat#15575-038
Fetal Calf Serum	Eurobio	Cat#CVFSVF00-01
Fluorescent Mounting Medium	Dako	Cat#53023
FTY-720	Sigma	Cat#SML0700-25mg
gelatine from cold water fish skin	Sigma	Cat#67765
GolgiPlug	BD	Cat#555029
GolgiStop	BD	Cat#554724
HEPES	Gibco	Cat#15630-056
Liberase TL	Sigma	Cat#10104159001
Live and Dead AQUA	Thermo Fischer Scientific	Cat#L34957
LS columns	Miltenyi	Cat#130-042-401
Maristamat	Sigma	Cat#M2699
Monensin	Invitrogen	Cat#00-4505-51
Non-essential amino acid	ThermoFisher	Cat#11140050
OCT	Tissue-Tek	Cat#16-004004
Paraformaldehyde	EMS	Cat#15710
PBS	Eurobio scientific	Cat#CS1PB501-01
Penicillin/Streptomycin	Gibco	Cat#15140-122
Pertussis Toxin	Gibco	Cat#PHZ1174
Protease inhibitors	Roche	Cat#11697498001
Rat IgG2A Isotype Control	R&D Systems	Cat#MAB006; RRID: AB_357349
RBC lysis buffer	Biolegend	Cat#420302
RPMI 1640 GlutaMAX	Gibco	Cat#61870036
skim milk powder	Régilait	Cat#B0110287
Sodium Chloride	VWR Chemicals	Cat#27810-295
Sodium Pyruvate (NaPyr)	ThermoFisher	Cat#11360070
Triton X-100	Sigma	Cat#11332481001
Tween	Sigma	Cat#P9416
5-OP-RU	Curie Institute	Soudais et al., 2015
Critical commercial assays
Cytofix/Cytoperm Solution Kit	BD	Cat#554714
FoxP3 Transcription factor Permeabilization buffer	Thermofischer	Cat#00-5523-00
mrmIL-2	Peprotech	Cat#212-12
rmIL-18	R&D	Cat# 9139-IL
Proteome array	R&D	Cat#ARY028
Solution P3 Primary Cell 4DNucleofector X kit S	Lonza	Cat#VAXP-3032
Deposited data
Skin single cell datasets	This paper	GSE20734869
Thymic single cell dataset	Legoux et al.24	E-MTAB-7704
Experimental models: Organisms/strains
B6 Aregflox/flox (Aregtm2a(EUCOMM)Hmgu)	Bred in Institut Curie - provided by D. Zaiss	Minutti et al.70
Zbtb16-GFPcre	Institut Curie	Constantinides et al.54
Cd3e-/-Mr1+/+ and Mr1-/-	Institut Curie	Malissen et al.71
CD45.1/1 and CD45.1/2 B6-MAITCAST	Institut Curie	N/A
CD45.2/2 B6-MAITCASTMr1+/+ or Mr1-/-	Institut Curie	Cui et al.20 and Treiner et al.22
Kaede B6	Rachel Golub, Institut Pasteur	Tomura et al.40
Nr4a1-GFP B6-MAITCAST	Institut Curie	Zikherman et al.72
Rorc-GFP B6-MAITCAST	Institut Curie	Lochner et al.73
Oligonucleotides
Alt-R CRISPR-Cas9 crRNA: Mm_CXCR6.1_AA: /AltR1/rCrU rGrUrA rCrGrA rUrGrG rGrCrA rCrUrA rCrGrA rGrUrU rUrUrA rGrArG rCrUrA rUrGrC rU/AltR2/	IDT	N/A
Alt-R® CRISPR-Cas9 tracrRNA	IDT	Cat#1072534
Software and algorithms
Astrios software (Summit)	BECKMAN COULTER (Summit v62)	https://www.beckman.fr/flow-cytometry/cell-sorters/moflo-astrios-eq
Cytoflex software (CytExpert)	BECKMAN COULTER (V2.4)	https://www.beckman.fr/flow-cytometry/research-flow-cytometers/cytoflex/software
FlowJo	BD (V10.8.0)	https://www.flowjo.com/
Fortessa software (BD FACSDiva software)	BD (V6)	https://www.bdbiosciences.com/en-eu/products/software/instrument-software/bd-facsdiva-software
Image J Software	Schneider et al., 2012	https://imagej.nih.gov/ij/
Prism	GraphPad (V8)	https://www.graphpad.com/scientific-software/prism/
Other
Astrio	BECKMAN COULTER	Cat#B25982
Biopsy punch (4Ø)	Stiefel	Cat#600210
ChemiDoc Imaging System	BIORAD	Cat#17001402
Chromium 3’ Chip	10X Genomics	N/A
Cryostat	LEICA	Cat#CM1950
Cytoflex LX	BECKMAN COULTER	Cat#C00445
Fortessa LSR	BD	Cat#23-11617-01
Hair removal cream	Veet	Cat#EA_3108955
Microscope pour immunostaining	ThermoFischer	Cat#EVOS_M500
Silicone sheet (5mm thick)	Grace Bio-Labs	Cat#GBL664581-5EA