KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Brilliant Violet 605™ anti-mouse CD45 (clone 30-F11) | Biolegend | Cat# 103140 |
| APC anti-mouse CD45 (clone 30-F11) | Biolegend | Cat# 103112 |
| PE anti-Mouse TCRβ (clone H57-597) | Biolegend | Cat# 109208 |
| BUV737 anti-Mouse TCRβ (clone H57-597) | BD | Cat# 612821 |
| Brilliant Violet 711™ anti-mouse CD4 (Clone RM4-5) | Biolegend | Cat# 100550 |
| PE-eFluor™ 610 anti-mouse CD4 (clone RM4-5) | eBioscience | Cat# 61-0042-82 |
| APC/Cyanine7 anti-mouse CD8a (clone 53-6.7) | Biolegend | Cat# 100714 |
| Brilliant Violet 605™ anti-mouse CD45 (clone 30-F11) | Biolegend | Cat# 103140 |
| PerCP/Cyanine5.5 anti-mouse CD45.1 (clone A20) | Biolegend | Cat# 110728 |
| APC/Cyanine7 anti-mouse CD45.2 (clone 104) | Biolegend | Cat# 109824 |
| PE/Cyanine7 anti-mouse CD90.1 (clone OX-7) | Biolegend | Cat# 202518 |
| PerCP/Cyanine5.5 anti-mouse CD44 (clone IM7) | Biolegend | Cat# 103032 |
| APC anti-mouse CXCR6 (clone SA051D1) | Biolegend | Cat# 151106 |
| Brilliant Violet 711™ anti-mouse CD25 (clone PC61) | Biolegend | Cat# 102049 |
| PerCP/Cyanine5.5 anti-mouse CD11b (clone M1/70) | Biolegend | Cat# 101228 |
| APC/Cyanine7 anti-mouse Ly6G (Clone 1A8) | Biolegend | Cat# 127624 |
| APC/Cyanine7 anti-mouse CD3ε (clone 145-2C11) | Biolegend | Cat# 100330 |
| PE/Cyanine7 anti-mouse TCRγδ (clome GL3) | Biolegend | Cat# 118124 |
| Pacific Blue™ anti-mouse CD31 (clone 390) | Biolegend | Cat# 102422 |
| FITC anti-mouse Ly-6A/E (Sca-1; clone E13-161.7) | Biolegend | Cat# 122505 |
| PE/Cyanine7 anti-mouse VCAM-1 (clone 429) | Biolegend | Cat# 105720 |
| PE-Cyanine7 anti-ST2 (clone RMST2-2) | eBioscience | Cat# 25-9335-82 |
| Pacific Blue™ anti-mouse Helios (clone 22F6) | Biolegend | Cat# 137220 |
| Brilliant Violet 785™ anti-T-bet (clone 4B10) | Biolegend | Cat# 644835 |
| APC anti-Foxp3 (clone FJK-16s) | eBioscience | Cat# 17-5773-82 |
| Alexa Fluor™ 488 anti-Foxp3 (clone FJK-16s) | eBioscience | Cat# 53-5773-82 |
| PE anti-RORγt (clone AFKJS-9) | eBioscience | Cat# 12-6988-82 |
| APC anti-RORγt (clone AFKJS-9) | eBioscience | Cat# 17-6988-82 |
| PE-Cyanine7 anti-c-Maf (clone sym0F1) | eBioscience | Cat# 25-9855-82 |
| Alexa Fluor™ 488 anti-Gata3 (clone TWAJ) | eBioscience | Cat# 53-9966-42 |
| Alexa Fluor® 488 anti-mouse IL-17A (clone TC11-18H10.1) | Biolegend | Cat# 506910 |
| Brilliant Violet 785™ anti-mouse IFN-γ (clone XMG1.2) | Biolegend | Cat# 505838 |
| PE anti-mouse IL-4 (clone 11B11) | Biolegend | Cat# 504104 |
| PE anti-mouse IL-5 (clone TRFK5) | Biolegend | Cat# 504304 |
| PE anti-IL-13 (clone eBio13A) | eBioscience | Cat# 12-7133-81 |
| Alexa Fluor® 700 anti-Ki-67 (clone B56) | BD | Cat# 561277 |
| Biotin anti-Areg (polyclonal) | R&D | Cat# BAF989 |
| Alexa Fluor® 647 anti-cleaved Caspase-3 (Asp175; clone D3E9) | Cell Signaling | Cat# 9602S |
| TotalSeq-A anti-mouse hashtags | Biolegend | Cat# 155811 Cat# 155813 Cat# 155815 Cat# 155817 Cat# 155819 Cat# 155821 Cat# 155823 |
| TotalSeq-C anti-mouse hashtags | Biolegend | Cat# 155861 Cat# 155863 Cat# 155865 Cat# 155867 Cat# 155869 Cat# 155871 Cat# 155873 Cat# 155875 Cat# 155877 |
| Anti-Myogenin (clone F5D) | Santa Cruz | Cat# sc-12732 |
| Anti-Myosin Heavy Chain (clone MF20) | R&D | Cat# MAB4470 |
| Cy™3 Donkey Anti-Mouse IgG | Jackson ImmunoResearch | Cat# 715-165-150 |
| InVivoMAb anti-mouse/human/rat CCL2 (clone 2H5) | BioXCell | Cat# BE0185 |
| InVivoMAb polyclonal Armenian hamster IgG | BioXCell | Cat# BE0091 |
| InVivoMAb anti-mouse MHC Class II (I-A/I-E) (clone M5/114) | BioXCell | Cat# BE0108 |
| InVivoMAb rat IgG2b control (clone LTF-2) | BioXCell | Cat# BE0090 |
| Bacterial and Virus Strains | ||
| Clostridium ramosum | Geva-Zatorsky et al.,201796 | NA |
| Peptostreptococcus magnus | Geva-Zatorsky et al.,201796 | NA |
| Chemicals, peptides, and recombinant proteins | ||
| Cardiotoxin from Naja mossambica | Sigma-Aldrich | Cat# C9759 |
| Cardiotoxin from Naja pallida | Sigma-Aldrich | Cat# 217503 |
| FTY720 | Cayman Chemical | Cat# 10006292 |
| CP-105696 | Sigma-Aldrich | Cat# PZ0363 |
| Diphtheria Toxin | Sigma-Aldrich | Cat# D0564 |
| Recombinant murine IL-17A | Peprotech | Cat# 210-17 |
| Metronidazole | Sigma-Aldrich | Cat# M1547 |
| Ampicillin | Sigma-Aldrich | Cat# A0166 |
| Neomycin | Fisher Scientific | Cat# BP2669-25 |
| Vancomycin | RPI | Cat# 1404-93-9 |
| FITC-Dextran, 4 kDa | Chondrex | Cat# 4013 |
| Collagenase type II (Gibco) | Thermo Fisher Scientific | Cat# 17101015 |
| Collagenase type IV (Gibco) | Thermo Fisher Scientific | Cat# 17104-019 |
| Dispase | Thermo Fisher scientific | Cat# 17105041 |
| DNase I from bovine pancreas | Sigma-Aldrich | Cat# DN25 |
| Phorbol 12-Myristate 13-acetate (PMA) | Sigma-Aldrich | Cat# P8139 |
| Ionomycin | Sigma-Aldrich | Cat# I0634 |
| Protein Transport Inhibitor Cocktail | eBioscience | Cat# 00-4980-03 |
| Percoll | GE Healthcare | Cat# 17089109 |
| 2-Mercaptoethanol | Sigma-Aldrich | Cat# M7522 |
| TCL RNA lysis buffer | Qiagen | Cat# 1031576 |
| TRIzol | Invitrogen | Cat# 15596026 |
| Critical commercial assays | ||
| Foxp3 / Transcription Factor Staining Buffer Set | eBioscience | Cat# 00-5523-00 |
| Click-iT™ EdU Cell Proliferation Kit for Imaging, Alexa Fluor™ 488 dye | Thermo Fisher Scientific | Cat# C10337 |
| Zombie UV™ Fixable Viability Kit | Biolegend | Cat# 423108 |
| RNeasy Lipid Tissue Mini Kit | Qiagen | Cat# 74804 |
| RNAClean XP beads | Beckman Coulter | Cat# A63987 |
| Nextera DNA Sample Prep Kit | Illumina | Cat# FC-121-1030 |
| Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3 | 10x | Cat# PN-1000092 |
| Chromium Single Cell B Chip Kit | 10x | Cat# PN-1000074 |
| Chromium i7 Multiplex Kit | 10x | Cat# PN-120262 |
| Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1 | 10x | Cat# PN-1000167 |
| Chromium Single Cell 5’ Library Construction Kit | 10x | Cat# PN-1000020 |
| Chromium Single Cell 5’ Feature Barcode Library Kit | 10x | Cat# PN-1000080 |
| Chromium Single Cell V(D)J Enrichment Kit, Mouse T Cell | 10x | Cat# PN-1000071 |
| Chromium Next GEM Chip G Single Cell Kit | 10x | Cat# PN-1000127 |
| Single Index Kit T Set A | 10x | Cat# PN-1000213 |
| Single Index Kit N Set A | 10x | Cat# PN-1000212 |
| 123count eBeads | Invitrogen | Cat# 01-1234-42 |
| Deposited data | ||
| scRNA-seq/scTcr-seq of muscle and colon Treg cells | This paper | GSE196337 |
| Bulk RNA-seq | This paper | GSE195966 |
| scRNA-seq of colon CD4+ T cells | Kiner et al., 202188 | GSE160053 |
| scRNA-seq of muscle Treg cells at day 4 after injury | DiSpirito et al., 201828 | GSE109742 |
| scRNA-seq of whole muscle | Oprescu et al., 202050 | GSE138826 |
| scRNA-seq of injured heart CD4+ T cells | Xia et al., 202057 | GSE155619 |
| Experimental models: Organisms/strains | ||
| Mouse: C57BL/6J | Jackson Laboratory | 000664 |
| Mouse: B6.CD45.1 | Jackson Laboratory | 002014 |
| Mouse: B6.129P2-Tcrbtm1Mom/J | Jackson Laboratory | 002118 |
| Mouse: B6.129P2(Cg)-Rorctm2Litt/J | Jackson Laboratory | 007572 |
| Mouse: B6.Foxp3GFP | Bettelli et al., 200679 | N/A |
| Mouse: B6.Foxp3Thy1.1 | Liston et al., 200881 | N/A |
| Mouse: B6.Foxp3DTR | Kim, et al., 200782 | N/A |
| Mouse: B6.Kaede | Tomura et al., 200830 | N/A |
| Mouse: B6.Foxp3Cre | Rubtsov et al., 200883 | N/A |
| Mouse: B6.Maffl/fl | Wende et al, 201284 | N/A |
| Germ Free C57BL/6J mice | GF C57BL/6 colony housed in the animal facility at Harvard Medical School. | N/A |
| Software and algorithms | ||
| Cell Ranger (v2.1.0, v4.0.0 and v6.0.0) | 10X Genomics | |
| CITE-seq-count v1.4.3 | doi:10.5281/zenodo.2590196 | https://hoohm.github.io/CITE-seq-Count/ |
| R v4.1.1 | The R Foundation | https://www.r-project.org |
| Seurat v4.0.3 | Hao et al., 202197 | https://satijalab.org/seurat/ |
| Harmony v0.1.0 | Korsunsky et al., 201992 | |
| Nebulosa v1.3.0 | Alquicira-Hernandez et al., 2021 91 | https://www.bioconductor.org/packages/release/bioc/html/Nebulosa.html |
| scRepertoire v1.4.0 | Borcherding et al., 2020 32 | https://github.com/ncborcherding/scRepertoire |
| Cuffquant version 2.2.1 | Trapnell et al., 201298 | http://cole-trapnell-lab.github.io/cufflinks/install/ |
| DESeq2 v1.28.1 | Love et al, 201499 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Limma | Ritchie et al, 2015 100 | https://bioconductor.org/packages/release/bioc/html/limma.html |
| GenePattern software package | Broad Institute | http://software.broadinstitute.org/cancer/software/genepattern/ |
| maSigPro | Nueda et al., 201493 | https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html |
| Scanpy | Wolf et al., 2018101 | https://github.com/scverse/scanpy |
| Metascape | Zhou et al., 2019 102 | https://metascape.org/ |
| Enrichr | Kuleshov et al., 2016103 | https://maayanlab.cloud/Enrichr/ |
| PRISM v9.2.0 | GraphPad | https://www.graphpad.com |
| FlowJo 10.6.2 | FlowJo, LLC | https://www.flowjo.com |
| ImageJ v2.1.0/1.53c | Schindelin et al., 201295 | https://imagej.net/software/fiji/ |
| Other | ||
| Control diet: L-Amino Acid Rodent Diet With 10 kcal% Fat (Amino Acid Complete) | Research Diets | Cat# A08051501i |
| CDAHFD: L-Amino Acid Diet With 45 kcal% Fat With 0.1% Methionine and No Added Choline | Research Diets | Cat#: A06071309i |