Key resources table.
Total seq reagents
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| BUV496 - B220 (clone RA3–6B2) | BD Biosciences | 564662 |
| APC - c-Kit (clone 2B8) | BD Biosciences | 553356 |
| Brilliant Violet 605 - CD11b (clone M1/70) | BioLegend | 101257 |
| FITC - CD11c (clone HL3) | BD Biosciences | 553801 |
| BUV395 - CD19 (clone 1D3) | BD Biosciences | 563557 |
| BUV395 - CD25 (clone PC61) | BD Biosciences | 564022 |
| PerCP-Cy5.5 - CD4 (clone RM4–5) | Tonbo Bioscience | 65–0042-U100 |
| BUV496 - CD4 (clone GK1.5) | BD Biosciences | 564667 |
| APC - CD44 (clone IM7) | Tonbo Bioscience | 20–0441-U100 |
| Brilliant Violet 570 – CD45 (clone 30-F11) | Biolegend | 103136 |
| Brilliant Violet 711 - CD5 (clone 53–7.3) | Biolegend | 100639 |
| Brilliant Violet 605 - CD62L (clone MEL-14) | Biolegend | 104438 |
| PerCP-Cy5.5 - CD64 (clone X54–5/7.1) | Biolegend | 139308 |
| BUV737 - CD8α (clone 53–6.7) | BD Biosciences | 564297 |
| APC - CD90.1 (clone HIS51) | ThermoFisher | 17–0900-82 |
| APC-eFluor780 - CD90.1 (clone HIS51) | ThermoFisher | 47–0900-82 |
| Brilliant Violet 785 - CD90.2 (clone 30-H12) | Biolegend | 105331 |
| PE eFluor610 - F4|80 (clone BM8) | ThermoFisher | 61–4801-82 |
| PE - FcεRIα (clone MAR-1) | ThermoFisher | 12–5898-82 |
| APC - Foxp3 (clone FJK-16s) | ThermoFisher | 17–5773-82 |
| PerCP-Cy5.5 - GM-CSF (clone MP1–22E9) | Biolegend | 505410 |
| PE-Cy7 - Gr-1 (clone RB6–8C5) | ThermoFisher | 25–5931-82 |
| Pacific Blue - Helios (clone 22F6) | Biolegend | 137210 |
| APC - IFNγ (clone XMG1.2) | ThermoFisher | 17–7311-82 |
| Brilliant Violet 421 - IL-10 (clone JES5–16E3) | Biolegend | 505021 |
| PE-eFluor610 - IL-17A (clone 17B7) | ThermoFisher | 61–7177-82 |
| PE - IL-4 (clone 11B11) | ThermoFisher | 12–7041-82 |
| PerCP-Cy5.5 - Ki67 (clone SolA15) | ThermoFisher | 46–5698 |
| Brilliant Violet 710 - Ly-6C (clone HK1.4) | Biolegend | 128037 |
| redFluor710 - MHC-II (clone M5/114.15.2) | Tonbo Bioscience | 80–5321-U100 |
| eFluor 450 - NK1.1 (clone PK136) | ThermoFisher | 48–5941-82 |
| PE-eFluor610 - Nrp-1 (clone 3DS304M) | ThermoFisher | 61–3041-82 |
| Brilliant Violet 421 - RORγt (clone Q31–378) | BD Biosciences | 562894 |
| Brilliant Violet 421 - Siglec-F (clone E50–2440) | BD Biosciences | 562681 |
| APC-Cy7 - TCR-β (clone H57–597) | BioLegend | 109220 |
| PE-eFluor610 - TCR-β (clone H57–597) | ThermoFisher | 61–5961-82 |
| Brilliant Violet 605 - TCRγδ (clone GL3) | Biolegend | 118129 |
| Brilliant Violet 605 - TNFα (clone MP6-XT22) | Biolegend | 506329 |
| Brilliant Violet 650 - XCR1 (clone ZET) | Biolegend | 148220 |
| Mcpt1 | R&D systems | MAB5146 |
| Alexa Fluor 647 - EpCAM | BioLegend | 118212 |
| Polyclonal rabbit anti-mouse GFP Alexa Fluor 488 | ThermoFisher | A-21311 |
| Chemicals, peptides, and recombinant proteins | ||
| Ampicillin | Sigma-Aldrich | A0166–5G |
| Brefeldin A | Millipore Sigma | B7651 |
| Collagenase A from Clostridium histolyticum | Sigma-Aldrich | 11088793001 |
| Diphtheria Toxin | List Biological Laboratories | 150 |
| DNase I grade II, from bovine pancreas | Sigma-Aldrich | 10104159001 |
| Ghost Dye Violet 510 | Tonbo Biosciences | 13–0870 |
| Ionomycin calcium salt | Millipore Sigma | I0634 |
| Metronidazole | Sigma-Aldrich | M1547–25G |
| Monensin sodium salt | Millipore Sigma | M5273 |
| Neomycin | Sigma-Aldrich | N6386–100G |
| Phorbol 12-myristate 13-acetate (PMA) | Millipore Sigma | P8139 |
| Tamoxifen | Sigma-Aldrich | T5648–5G |
| Trizol Reagent | ThermoFisher | 15596018 |
| Vancomycin | Fresenius-Kabi | C314061 |
| Critical commercial assays | ||
| 123count eBeads | ThermoFisher | 01–1234-42 |
| CD4 (L3T4) MicroBeads, mouse | Miltenyi | 130–117-043 |
| Chromium Next GEM Single Cell 5’ Kit v2 | 10x Genomics | 1000263 |
| Chromium Single Cell 3ʹ GEM, Library & Gel Bead Kit v3 | 10x Genomics | 1000075 |
| Chromium Single Cell Mouse TCR Amplification Kit | 10x Genomics | 1000254 |
| Dynabeads Flowcomp Mouse CD4 Kit | Thermo Fisher | 11461D |
| Dynabeads MyOne SILANE | ThermoFisher | 37002D |
| eBioscience Foxp3 / Transcription Factor Staining Buffer Set | ThermoFisher | 00–5523-00 |
| Fixation/Permeabilization Solution Kit (Cytofix/Cytoperm) | BD Biosciences | 554714 |
| KAPA Hyper Prep Kit | Kapa Biosystems | KK8504 |
| SMART-Seq v4 Ultra Low Input RNA Kit | Clonetech | 63488 |
| SPRIselect beads | Beckman Coulter | B23318 |
| Deposited data | ||
| Bulk-cell RNA-seq data | This paper | GSE176237 |
| Single-cell RNA-seq data mesenteric lymph node | This paper | GSE176293 |
| Single-cell RNA-seq data colon lamina propria | This paper | GSE193780 |
| Microarray data from Spleen and Colon Treg cells | PMID: 26272906 | GSE71316 |
| RNA-seq data from WT and Maf-deficient Treg cells | PMID: 29414937 | GSE108184 |
| Experimental models: Cell lines | ||
| LLC cells | Provided by J. Massague (Memorial Sloan Kettering Cancer Center, New York, NY) | N/A |
| Experimental models: Organisms/strains | ||
| Foxp3DTR-GFP: B6.129(Cg)-Foxp3tm3(DTR/GFP)Ayr/J | PMID: 17136045 | JAX:016958 |
| CD4CreER: Cd4tm1(cre/ERT2)Thbu | PMID: 24115907 | MGI:5549971 |
| Rosa26lsl-tdTomato: B6.Cg-Gt(ROSA)26Sortm14(CAG-tdTomato)Hze/J | PMID: 20023653 | JAX: 007914 |
| Foxp3Thy1.1: Foxp3tm10.1(Casp9,-Thy1)Ayr | PMID: 18695219 | MGI:5451201 |
| Foxp3GFP: B6.129-Foxp3tm2Ayr/J | PMID: 15780990 | MGI:3574964 |
| Foxp3GFP∆CNS: Foxp3tm5.2Ayr | PMID: 20072126 | MGI:4430232 |
| Foxp3 ΔEGFPiCre | PMID: 31384057 | N/A |
| Rosa26lsl-DTR: Gt(ROSA)26Sortm1(HBEGF)Awai | PMID: 15908920 | JAX:007900 |
| Foxp3GFPKO: Foxp3tm8Ayr | PMID: 17220874 | MGI: 4436759 |
| Foxp3 loxP-Thy1.1-STOP-loxP-GFP | PMID: 34426690 | N/A |
| SPRET/EiJ | N/A | JAX:001146 |
| Software and algorithms | ||
| FlowJo (v10) | FlowJo, LLC | https://www.flowjo.com/solutions/flowjo |
| R | The Comprehensive R Archive Network | https://cran.r-project.org/ |
| Prism (v9) | GraphPad | https://www.graphpad.com/scientific-software/prism |
| STAR | PMID: 23104886 | https://github.com/alexdobin/STAR |
| DESeq2 (R Package) | PMID: 25516281 | https://bioconductor.org/packages/DESeq2 |
| Genome Analysis Toolkit (GATK) | PMID: 20644199 | https://gatk.broadinstitute.org/hc/en-us |
| Cellranger | 10X Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest |
| Scanpy | PMID: 29409532 | https://github.com/theislab/scanpy |
| MAGIC | PMID: 29961576 | https://github.com/KrishnaswamyLab/MAGIC |
| Phenograph | PMID: 26095251 | https://github.com/jacoblevine/PhenoGraph |