KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Syrian Hamster anti-mouse CD3e Biotin | eBioscience | Cat#13003382 RRID:AB_1470754 |
| Rat anti-mouse CD8α Biotin | Biolegend | Cat#100704 RRID:AB_312743 |
| Rat anti-mouse CD11b Biotin | Biolegend | Cat#101204 RRID:AB_312787 |
| Armenian Hamster anti-mouse CD11c Biotin | eBioscience | Cat#13011485 RRID:AB_466363 |
| Rat anti-mouse CD19 Biotin | BD Biosciences | Cat#553784 RRID:AB_395048 |
| Rat anti-mouse Gr-1 Biotin | Biolegend | Cat#108404 RRID:AB_313369 |
| Mouse anti-mouse NK1.1 Biotin | Biolegend | Cat#108704 RRID:AB_313391 |
| Rat anti-mouse Ter-119 Biotin | BD Biosciences | Cat#553672 RRID:AB_394985 |
| Armenian Hamster anti-mouse TCRβ Biotin | eBioscience | Cat#13596185 RRID:AB_466820 |
| Armenian Hamster anti-mouse TCRγ/δ Biotin | Biolegend | Cat#118103 RRID:AB_313827 |
| Rat anti-mouse CD4 Biotin | eBioscience | Cat#13004385 RRID:AB_466334 |
| Armenian Hamster anti-mouse TCRβ BV605 | Biolegend | Cat#109241 RRID:AB_2629563 |
| Armenian Hamster anti-mouse TCRγ/δ PerCP-eFluor 710 | eBioscience | Cat#46571182 RRID:AB_2016707 |
| Armenian Hamster anti-mouse Vγ2 PE-Cy7 | eBioscience | Cat#25582882 RRID:AB_2573474 |
| Armenian Hamster anti-mouse Vγ1.1 BV421 | BD Biosciences | Cat#566308 RRID:AB_2739676 |
| Rat anti-mouse CD24 BV605 | Biolegend | Cat#101827 RRID:AB_2563464 |
| Rat anti-mouse CCR6 Alexa Fluor 647 | BD Biosciences | Cat#557976 RRID:AB_2228793 |
| Armenian Hamster anti-mouse CD27 PE | eBioscience | Cat#12027183 RRID:AB_465615 |
| Rat anti-mouse CD4 BV650 | Biolegend | Cat#100546 RRID:AB_2562098 |
| Rat anti-mouse CD44 BV711 | Biolegend | Cat#103057 RRID:AB_2564214 |
| Rat anti-mouse IL-17A PerCPCy5.5 | eBioscience | Cat#45717782 RRID:AB_925753 |
| Rat anti-mouse IFNγ PE | Biolegend | Cat#505808 RRID:AB_315402 |
| Rat anti-mouse CD8β APC/Cyanine7 | Biolegend | Cat#126620 RRID:AB_2563951 |
| Rat anti-mouse CD45 BV785 | Biolegend | Cat#103149 RRID:AB_2564590 |
| Rat anti-mouse CD49f FITC | Biolegend | Cat#313606 RRID:AB_345300 |
| Rat anti-mouse Sca-1 BV605 | Biolegend | Cat#108134 RRID:AB_2650926 |
| Rat anti-mouse CD71 PE-Cy7 | Biolegend | Cat#113811 RRID:AB_2203383 |
| Rat anti-mouse CD326 PE | Biolegend | Cat#118206 RRID:AB_1134172 |
| Rat anti-mouse CD326 PE-Cy7 | Biolegend | Cat#118216 RRID:AB_1236471 |
| Rat anti-mouse I-A/I-E APC | Biolegend | Cat#107614 RRID:AB_313329 |
| Armenian Hamster anti-mouse CD80 PerCPCy5.5 | Biolegend | Cat#104721 RRID:AB_893406 |
| Rat anti-mouse Ly51 FITC | Biolegend | Cat#108305 RRID:AB_313362 |
| Rat anti-mouse CD104 PE | Biolegend | Cat#123610 RRID:AB_2563544 |
| UEA-1 biotin | Vector Labs | Cat#B1065 RRID:AB_2336766 |
| Rat anti-mouse Scart2 | J. Kisielow | Cloned hybridoma 25A2 |
| Goat anti-Rat IgG PE | Southern Biotech | Cat#305009 RRID:AB_2795834 |
| Rat anti-mouse Anti-CD16/32 | Biolegend | Cat#101330 RRID:AB_2561482 |
| Rabbit anti-GFP | Invitrogen | Cat#A11122 |
| Rabbit anti-RFP | Rockland | Cat#600401379 RRID:AB_11182807 |
| Rat anti-mouse SCART2 Alexa Fluor 647 | Muzaki et al.74 | Cloned hybridoma 41G1 |
| Rat anti-mouse AIRE Alexa Fluor 488 | eBioscience | Cat#53593480 RRID:AB_10852560 |
| Cy3-conjugated donkey anti-rabbit | Jackson ImmunoResearch Laboratories | Cat#711165152 RRID:AB_2307443 |
| Streptavidin Alexa Fluor 450 | eBioscience | Cat#48431782 RRID:AB_10359737 |
| Chemicals, peptides, and recombinant proteins | ||
| Fetal Bovine Serum | Sigma-Aldrich | Cat#F0926 |
| Phorbol 12-myristate 13-acetate (PMA) | LC Laboratories | Cat#P-1680 |
| Ionomycin Calcium Salt | Sigma-Aldrich | Cat#I3909 |
| GolgiStop (Monensin) | BD Biosciences | Cat#512301KZ |
| GolgiPlug (Brefeldin A) | BD Biosciences | Cat#512092KZ |
| DNase I, grade II | Roche | Cat#10104159001 |
| Liberase TL | Roche | Cat#05401020001 |
| Liberase TM | Roche | Cat#05401119001 |
| Hylauronidase | Sigma-Aldrich | Cat#H3506 |
| Trizol | Ambion Life Technologies | Cat#15596018 |
| Tamoxifen | Sigma-Aldrich | Cat#T5648 |
| Peanut Oil | Sigma-Aldrich | Cat#P2144 |
| Hepes (1 M) | Gibco | Cat#15630080 |
| 0.25% Trypsin in HBSS w/o Calcium and Magnesium | Corning | Cat#25050CI |
| EDTA 500mM, pH 8.0 | Teknova | Cat#E036 |
| RLT buffer (RNeasy Lysis Buffer) | Qiagen | Cat#79216 |
| 2-mercaptoethanol | Sigma-Aldrich | Cat#6250 |
| Percoll | GE Healthcare | Cat#17089101 |
| DAPI | Sigma Aldrich | Cat#D9542 |
| 7α,25-dihydroxycholesterol | Avanti Polar Lipids | Cat#700080P |
| 25-hydroxycholesterol | Avanti Polar Lipids | Cat#700019P |
| Imiquimod Cream 5% | Perrigo | Cat#45802036862 NDC#45802036862 |
| Critical commercial assays | ||
| Cytofix/Cytoperm Fixation/Permeabilization Kit | BD Biosciences | Cat#554714 |
| Fixable Viability Dye eFluor 780 | eBioscience | Cat#65086514 |
| Fixable Viability Dye eFluor 506 | eBioscience | Cat#65086618 |
| RNeasy Micro kit | Qiagen | Cat#74004 |
| RNeasy Mini kit | Qiagen | Cat#74104 |
| SuperScript First-Strand Synthesis System for RT-PCR | Invitrogen | Cat#11904018 |
| iQ SYBR green Supermix | Bio-Rad | Cat#1725270 |
| Fluoromount-G | SouthernBiotech | Cat#0100–01 |
| Deposited data | ||
| Single-cell RNA Sequencing of γδ thymocytes | This Paper | GEO: GSE221488 |
| Single-cell RNA Sequencing of TEC subsets | Cowan et al.75 | GEO: GSE131368 |
| Experimental models: Cell Lines | ||
| M12-EBI2-GFP | Gift from J. Cyster | Kelly et al.30 |
| Human Embryonic Kidney Cells (HEK293T) | ATCC | Cat#CRL-3216 |
| Experimental models: Organisms/strains | ||
| Mouse: C57BL/6J | The Jackson Laboratory | 000664 |
| Mouse: Ccr6−/− | The Jackson Laboratory | 005793 |
| Mouse: Ch25h−/− | The Jackson Laboratory | 016263 |
| Mouse: TcrdCre/ERT2 | The Jackson Laboratory | 031679 |
| Mouse: Foxn1Cre | The Jackson Laboratory | 018448 |
| Mouse: RorcCre | The Jackson Laboratory | 022791 |
| Mouse: Krt5Cre/ERT2 | The Jackson Laboratory | 029155 |
| Mouse: Sox4Egfp | MMRRC | 030033-UCD |
| Mouse: Gpr183+/Egfp | Pereira et al.14 | N/A |
| Mouse: Gpr183fl/fl | Pereira et al.14 | N/A |
| Mouse: Sox4fl/fl | Malhotra et al.21 | N/A |
| Mouse: Ch25hfl/fl | Ceglia et al.39 | N/A |
| Mouse: Ch25htdTom | This paper | N/A |
| Oligonucleotides | ||
| See Table S1 for list of quantitative RT-PCR primers | N/A | N/A |
| Recombinant DNA | ||
| MSCV-IRES-Thy1.1 | Addgene | ID: 17442 |
| Software and algorithims | ||
| FlowJo v10.8 software | Tree Star | https://www.flowjo.com/solutions/flowjo/downloads |
| FACSDiva v7.0 software | BD | https://www.bdbiosciences.com/en-us/products/software/instrument-software/bdfacsdiva-software |
| ZEN 3.1 | Carl Zeiss Microscopy | https://www.zeiss.com/microscopy/en/products/software/zeiss-zen.html |
| Adobe Illustrator 2022 | Adobe Systems | N/A |
| ImageJ | NIH | https://imagej.nih.gov/ij/ |
| Prism 9 | GraphPad Software | https://www.graphpad.com/scientificsoftware/prism/ |
| Seurat R v2.3 | Butler et al.76 | https://satijalab.org/seurat/ |
| Seurat R v3.2 | Stuart et al.77 | https://satijalab.org/seurat/ |
| Other | ||
| Standard chow diet (Prolab IsoPro RMH 3000) | LabDiet | 5P76 |
| 2% high cholesterol diet | Envigo | TD.200179 |