KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rat Anti-Mouse CD45 (Clone 30-F11), BUV395 | BD Biosciences | Cat. 564279; RRID AB_2651134 |
| Rat Anti-Mouse CD4 (Clone GK1.5), BUV496 | BD Biosciences | Cat. 741051; RRID AB_2870666 |
| Rat Anti-Mouse CD19 (Clone 1D3), BUV563 | BD Biosciences | Cat. 749028; RRID AB_2873425 |
| Rat Anti-Mouse FR4 (Clone 12A5), BUV737 | BD Biosciences | Cat. 748995; RRID AB_2873392 |
| Rat Anti-Mouse CD274 (PDL1, Clone MIH5), BV480 | BD Biosciences | Cat. 746275; RRID AB_2743606 |
| Rat Anti-Mouse CD62L (Clone MEL-14), BUV805 | BD Biosciences | Cat. 741924; RRID AB_2871237 |
| Hamster Anti-Mouse CD80 (Clone 16-10A1), BV711 | BD Biosciences | Cat. 740698; RRID AB_2740382 |
| Armenian hamster Anti-Mouse CD11c (Clone N418), BB515 | BD Biosciences | Cat. 565586; RRID AB_2869690 |
| Rat Anti-Mouse CD16/CD32 (Fc Block, Clone 2.4G2), Purified | BD Biosciences | Cat. 553142; RRID AB_394656 |
| Rat Anti-Mouse/Human CD44 (Clone IM7), BV510 | Biolegend | Cat. 103044; RRID AB_2650923 |
| Armenian hamster Anti-Mouse CD103 (Clone 2E7), BV605 | Biolegend | Cat. 121433; RRID AB_2629724 |
| Hamster Anti-Mouse CD279 (PD-1, Clone J43), BV650 | BD Biosciences | Cat. 744546; RRID AB_2742317 |
| Armenian hamster Anti-Mouse CD69 (Clone H1.2F3), BV785 | Biolegend | Cat. 104543; RRID AB_2629640 |
| Rat Anti-Mouse/Human CD11b (Clone M1/70), PerCP-Cy5.5 | Biolegend | Cat. 101227; RRID AB_893233 |
| Rat Anti-Mouse F4/80 (Clone BM8), PE-Dazzle 594 | Biolegend | Cat. 123145; RRID AB_2564132 |
| Rat Anti-Mouse CD86 (Clone PO3), PE-Cy7 | Biolegend | Cat. 105115; RRID AB_493601 |
| Armenian hamster Anti-Mouse TCR β chain (Clone H57-597), Alexa Fluor 700 | Biolegend | Cat. 109223; RRID AB_1027654 |
| Rat Anti-Mouse CD8a (Clone 53-6.7), APC-Fire 750 | Biolegend | Cat. 100765; RRID AB_2572112 |
| Armenian hamster Anti-Mouse CD152 (CTLA-4, Clone UC10-4B9), PE | Biolegend | Cat. 106305; RRID AB_313254 |
| Rat Anti-Mouse Ki67 (Clone 16A8), Alexa Fluor 647 | Biolegend | Cat. 652407; RRID AB_2562138 |
| Armenian hamster Anti-Mouse CD11c (Clone N418), APC | Biolegend | Cat. 117309; RRID AB_313778 |
| Rat Anti-Mouse/Human CD11b (Clone M1/70), FITC | Biolegend | Cat. 101205; RRID AB_312788 |
| Rat Anti-Mouse TNFa (Clone MP6-XT22), BV421 | Biolegend | Cat. 506327; RRID AB_10900823 |
| Armenian Hamster Anti-Mouse CD3ε (Clone 145-2C11), PE | Biolegend | Cat. 100307; RRID AB_312672 |
| Rat Anti-Mouse FoxP3 (Clone FJK-16S), efluor-450 | Thermo/Fisher | Cat. 48-5773-82; RRID AB_1518812 |
| Rat Anti-Mouse/Human/Bovine Insulin (Clone 182410), APC | R&D Systems | Cat. IC1417A; RRID AB_2126535 |
| Sheep anti-Mouse/Rat Transglutaminase 2/TGM2 Antibody | R&D Systems | Cat. AF5418; RRID AB_2044738 |
| Donkey anti-Sheep IgG HRP-conjugated Antibody | R&D Systems | Cat. HAF016; RRID AB_562591 |
| Anti-β-Actin Antibody (Clone C4) | Santa Cruz Biotechnology | Cat. sc-47778; RRID AB_626632 |
| Amersham Sheep Anti-Mouse Horse Radish Peroxidase Antibody | GE Healthcare | Cat. NA93; RRID AB_772210 |
| Armenian Hamster Anti-Mouse CD3e (Clone 145-2C11), PE | Thermo/Fisher | Cat. 12-0031-82; RRID AB_465496 |
| Rat Anti-Mouse CD4 (Clone GK1.5), APC | Biolegend | Cat. 100412; RRID AB_312697 |
| Armenian Hamster Anti-Mouse TCR β chain (Clone H57-597), FITC | Biolegend | Cat. 109205; RRID AB_313428 |
| Rat Anti-Mouse CD8a (Clone 53-6.7) efluor450 | Thermo/Fisher | Cat. 48-0081-82; RRID AB_1272198 |
| Rat Anti-Mouse TotalSeq™-C0302 (Clone M1/42; 30-F11) | Biolegend | Cat. 155863; RRID AB_2800694 |
| Rat Anti-Mouse TotalSeq™-C0303 (Clone M1/42; 30-F11) | Biolegend | Cat. 155865; RRID AB_2800695 |
| Rat Anti-Mouse TotalSeq™-C0305 (Clone M1/42; 30-F11) | Biolegend | Cat. 155869; RRID AB_2800697 |
| Rat Anti-Mouse TotalSeq™-C0306 (Clone M1/42; 30-F11) | Biolegend | Cat. 155871; RRID AB_2819910 |
| Rat Anti-Mouse TotalSeq™-C0308 (Clone M1/42; 30-F11) | Biolegend | Cat. 155875; RRID AB_2819912 |
| Rat Anti-Mouse TotalSeq™-C0309 (Clone M1/42; 30-F11) | Biolegend | Cat. 155877; RRID AB_2819913 |
| Bacterial and Virus Strains | ||
| Enterococcus faecalis Str. OG1RF | Murray et al. 1993. | NCBI:txid474186 |
| Enterococcus faecalis Str. TX5266 | Qin et al. 2001. | N/A |
| Enterococcus faecalis Str. TX5243 | Sifri et al. 2002. | N/A |
| Enterococcus faecalis Str. TX5264 | Singh et al. 1998. | N/A |
| Enterococcus faecalis Str. JRC105 | Kristich et al. 2007. | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Dextrose (D-Glucose) Anhydrous | Fisher Scientific | Cat. D16-500 |
| Insulin Solution Human | Sigma-Aldrich | SKU: I9278-5ML, |
| Erythromycin | Sigma-Aldrich | SKU: E5389-1G |
| Nicin from Lactococcus lactis 2.5% (balance sodium chloride) | Sigma-Aldrich | SKU: N5764-1G |
| BBL Brain Heart Infusion Agar | BD Difco | Item no. 211065 |
| Bacto Brain Heart Infusion | BD Difco | Item no. 237500 |
| 5(6)-CFDA, SE; CFSE (5-(and-6)-Carboxyfluorescein Diacetate, Succinimidyl Ester), mixed isomers | Invitrogen | Cat. C1157 |
| Polymyxin B-Agarose | Sigma-Aldrich | SKU: P1411-5ML |
| DMEM, high glucose, GlutaMAX supplement | Gibco | Cat. 10566-016 |
| Cell Dissociation Buffer Enzyme-Free PBS-Based | Gibco | Cat. 13151-014 |
| 0.5% Trypsin-EDTA 10X | Gibco | Cat. 15400-054 |
| Click's Medium | Irvine Scientific | Cat. 9582 |
| Histopaque-1119 | Sigma-Aldrich | Cat. 11191 |
| SuperSignal™ West Femto Maximum Sensitivity Substrate | Thermo Scientific | Cat. 34095 |
| Pierce Protease Inhibitor Tablets | Thermo Scientific | Cat. A32963 |
| Thioglycollate Medium without Dextrose | BD Difco | Cat. DF0363-17-2 |
| Collagenase P from Clostridium histolyticum | Roche | SKU: 11213857001 |
| Collagenase D from Clostridium histolyticum | Roche | SKU: 11088858001 |
| Deoxyribonuclease I from bovine pancreas | Sigma-Aldrich | SKU: DN25-10MG |
| Whetpro 80 Gluten | ADM | https://www.adm.com/products-services/food/adm-milling/products/wheat-glutens/wheat-gluten |
| Protein Transport Inhibitor (Containing Brefeldin A) | BD Biosciences | Cat. 555029; RRID AB_2869014 |
| Gliadin from Wheat | Sigma Aldrich | SKU: G3375 |
| Casein, Bovine Milk | Sigma Aldrich | SKU: 281680 |
| Bovine Serum Albumin (BSA) (Fraction V) Heat-Shock Treated | Fisher Scientific | Cat. BP1600-100 |
| NRPA7 Peptide (KYNKANAFL) | Sigma Aldrich | N/A |
| AI4 Mimotope Peptide (YFIENYLEL) | Sigma Aldrich | N/A |
| InsB15-23 Peptide (LYLVCGERG) | Sigma Aldrich | N/A |
| DQ8-glia-alpha1 Peptide (SGEGSFQPSQENPQ) | Sigma Aldrich | N/A |
| DQ2.5-glia-omega2 Peptide (FPQPEQPFPWQP) | Sigma Aldrich | N/A |
| Critical Commercial Assays | ||
| Diastix Reagent Strips for Urinalysis, Glucose | Ascensia Diabetes Care, Purchased from Walmart | Model: 00193-2802-50 |
| OneTouch UltraMini Blood Glucose Meter | OneTouch Solutions | N/A |
| GenUltimate! Test Strips | GenUltimate! | UPC: 868906000100 |
| CD4+ T Cell Isolation Kit | Miltenyi Biotec | Cat. 130-104-454 |
| Mouse TNF ELISA Set II | BD Biosciences | Cat. 558534; RRID AB_2869215 |
| ELISA MAX™ Standard Set Mouse IL-6 | Biolegend | Cat. 431301 |
| ELISA MAX™ Standard Set Mouse IL-2 | Biolegend | Cat. 431001 |
| eBioscience™ Foxp3 / Transcription Factor Staining Buffer Set | Invitrogen | Cat. 00-5523-00 |
| Zombie NIR™ Fixable Viability Kit | Biolegend | Cat. 423105 |
| Chromium Single Cell 3’ Library & Gel Bead Kit | 10X Genomics | PN-120237 |
| Chromium Single Cell Mouse TCR Amplification Kit | 10X Genomics | PN-1000254 |
| Chromium Single Cell 5’ Library Construction Kit | 10X Genomics | PN-1000020 |
| Chromium Single Cell 5’ Library & Gel Bead Kit | 10X Genomics | PN-1000014 |
| UltraComp eBeads™ Compensation Beads | Invitrogen | Cat. 01-2222-41 |
| DNeasy PowerSoil HTP 96 Kit | Qiagen | Cat. 12955-4 |
| UltraClean 96 PCR Cleanup Kit | Qiagen | Cat. 12596-4 |
| Quant-iT™ PicoGreen™ dsDNA Assay Kits and dsDNA Reagents | Invitrogen | Cat. P7589 |
| Limulus Amoebocyte Lysate (LAL) kinetic chromogenic test kit Endochrome-K | Charles River | Code R1708K |
| Endotoxin Specific Buffer for LAL Assay | Charles River | Code BG120 |
| Endotoxin free 96 well plates for LAL assay | Greiner Bio-One GmbH | Cat. 655101 |
| Mouse IFN-γ ELISPOT Pair | BD Biosciences | Cat. 551881 |
| HRP Streptavidin for ELISPOT | BD Biosciences | Cat. 557630 |
| MultiScreen-IP Filter Plate, 0.45 μm, white, sterile | Millipore-Sigma | Cat. S2EM004M99 |
| Mouse Insulin ELISA Kit | Alpco | Ref. 80-INSMS-E01 |
| Deposited Data | ||
| Raw and analyzed scRNA-Seq on NOD.SCID islets | This paper. | GEO: GSE217495 |
| Raw and analyzed scRNA-Seq on NOD/ShiLtJ islets | This paper. | GEO: GSE217493 |
| Raw and analyzed scTCR-Seq on NOD/ShiLtJ islets | This paper. | GEO: GSE218336 |
| 16S rRNA Sequencing | This paper. | https://github.com/akds/microbiome-T1D |
| Experimental Models: Cell Lines | ||
| 578_BV7_AV12: BW58α-β cells expressing human CD4 and TCR from a DQ2.5-glia-ω2–reactive CD4 T cell clone (TCC 578) | Dahal-Koirala et al. 2016. | N/A |
| Human Lymphoblastoid Cell Line Expressing HLA-DQ2.5 | Generous Gift from Dr. Carole Ober, The University of Chicago | N/A |
| TCC489.2.1.4 hybridoma recognizing DQ8-glia-alpha1 | Qiao et al. 2011. | N/A |
| Experimental Models: Organisms/Strains | ||
| Mouse: NOD.TLR4 KO | Burrows et al. 2015. Bred in house. | N/A |
| Mouse: NOD.TGM2 KO | This paper | N/A |
| Mouse: NOD.Cg-Tg(TcraBDC2.5,TcrbBDC2.5)1Doi/DoiJ; (NOD.BDC2.5) | The Jackson Laboratory | Stock No: 004460; RRID:IMSR_JAX:004460 |
| Mouse: NOD.Cg-Prkdcscid/J; (NOD.SCID) | The Jackson Laboratory | Stock No: 001303; RRID:IMSR_JAX:001303 |
| Mouse: NOD.129P2(C)-Tcratm1Mjo/DoiJ; (NOD.TCRa KO) | The Jackson Laboratory | Stock No: 004444; RRID:IMSR_JAX:004444 |
| Mouse: NOD/ShiLtJ | The Jackson Laboratory | Stock No: 001976; RRID:IMSR_JAX:001976 |
| Mouse: NOD.MyD88 KO | Wen et al. 2008. Bred in house | N/A |
| Oligonucleotides | ||
| Genotyping and 16S Amplicon Primers (Table S1) | This paper | N/A |
| Tgm2 Guide RNA: >sgRNA 1745 - EXON 1 GTCGCCGCTAGCGTGG/CCA | This paper | N/A |
| Tgm2 Guide RNA: >sgRNA 1747 - EXON 2 GATTTGGAGATTCAGGC/CAA | This paper | N/A |
| Recombinant DNA | ||
| pMSP3535: Shuttle vector with Nisin Inducible Promoter | Bryan et al. 2000. | NCBI:txid244879; RRID:Addgene_46886 |
| pMSP3614: pMSP3535 containing gelE following the Nisin inducible promoter. | Waters et al. 2003. | N/A |
| Software and Algorithms | ||
| BD FACSDiva v. 8.0.2 | BD Biosciences | https://www.bdbiosciences.com/en-us/products/software/instrument-software/bd-facsdiva-software |
| SpectroFlo v. 2.2.04 | Cytek Biosciences | https://cytekbio.com/pages/spectro-flo |
| FlowJo v. 10.7.1 | FlowJo | https://www.flowjo.com/solutions/flowjo/downloads |
| UMAP Plugin v. 3.1 | McInnes et al. 2020. | https://www.flowjo.com/exchange/#/plugin/profile?id=6 |
| R v. 3.6.3 | The R Project for Statistical Computing | https://cran.r-project.org/bin/macosx/ |
| Python v. 3.7.4 | Python Software Foundation | https://www.python.org/downloads/macos/ |
| MATLAB v. R2020a | MathWorks | https://www.mathworks.com/products/matlab/whatsnew.html |
| CellRanger v.4.0.0 | 10X Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest? |
| Seurat v. 3.1.5 | Hao et al. 2021. | https://satijalab.org/seurat/articles/install.html |
| Scanpy v. 1.4.5.1 | Wolf et al. 2018. | https://pypi.org/project/scanpy/ |
| Scirpy v. 0.10.1 | Sturm et al. 2020. | https://github.com/scverse/scirpy |
| Seaborn v. 0.11.2 | Waksom. 2021. | https://seaborn.pydata.org/ |
| GSEA v. 4.1.0 | Mootha et al. 2003 and Subramanian et al. 2005. | http://www.gsea-msigdb.org/gsea/downloads.jsp |
| STRING v. 11.0 | Szklarczyk et al. 2011. | https://string-db.org/cgi/input?sessionId=bfTlTaC7SUO2&input_page_show_search=off |
| QIIME v. 1.9 | Caporaso et al. 2010. | http://qiime.org/index.html |
| Prism v. 9.1.2 | GraphPad | https://www.graphpad.com/ |
| Other | ||
| 16% Hydrolyzed Casein + 4% WhetPro 80 Gluten Custom Diet | Envigo | TD.150366 |
| 16% Hydrolyzed Casein + 4% Gem of the West Gluten Custom | Envigo | TD.130340 |
| NIH-31 Modified Open Formula Mouse/Rat sterilizable diet | Envigo | 7013 |
| 20% Hydrolyzed Casein Custom Diet | Envigo | TD.120338 |
| 20% Intact Casein Custom Diet | Envigo | TD.120337 |