KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| FITC rat anti-CD45 | Biolegend | 103107; RRID: AB_312972 |
| Alexa Fluor 700 rat anti-Ly6G | BD Biosciences | 561236; RRID: AB_10611860 |
| APC-Cy7 rat anti-CD11b | BD Biosciences | 561039; RRID: AB_2033993 |
| APC hamster anti-CD11c | BD Biosciences | 561119; RRID: AB_10562405 |
| PE rat anti-IA/IE | BD Biosciences | 562010; RRID: AB_10893194 |
| PE-Cy7 mouse anti-CD64 | Biolegend | 139313; RRID: AB_2563903 |
| BV421 rat anti-CD24 | BD Biosciences | 562563; RRID: AB_2737002 |
| PerCP-Cy5.5 rat anti-Ly6C | ThermoFisher Scientific | 45-5932-80; RRID: AB_2723342 |
| BV786 hamster anti-CD69 | BD Biosciences | 564683; RRID: AB_2738890 |
| BV510 rat anti-CD8a | Biolegend | 100751; RRID: AB_2561389 |
| BV605 rat anti-CD4 | Biolegend | 100451; RRID: AB_2564591 |
| PE-CF594 hamster anti-gdTCR | BD Biosciences | 563532; RRID: AB_2661844 |
| BUV395 hamster anti-CD3ε | BD Biosciences | 563565; RRID: AB_2738278 |
| Rabbit anti-pH2A.X (Ser139) | Cell Signaling Technology | 9718S; RRID: AB_2118009 |
| Rabbit anti-pH-H3 (Ser10) | Cell Signaling Technology | 9701S; RRID: AB_331535 |
| Rabbit anti-pSTAT3 (Tyr705) | Cell Signaling Technology | 9145; RRID: AB_2491009 |
| Rabbit anti-cleaved CSP3 | Cell Signaling Technology | 9661S; RRID: AB_2341188 |
| truStain fcX (rat anti-CD16/32) | Biolegend | 101320; RRID: AB_1574975 |
| Rat anti-mouse IL-10R (CD210), 1B1.3A | Bio X Cell | BE0050; RRID: AB_1107611 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Neomycin sulfate – 500 mg tablets | Hi-Tech Pharmacal | 50383-565-10 |
| Metronidazole – 500 mg/100 mL | Claris Lifesciences | 36000-001-24 |
| 4 kDa FITC-dextran | ThermoFisher Scientific | D3305 |
| Liberase TM | Sigma-Aldrich | 5401119001 |
| DNase I | Sigma-Aldrich | D5025 |
| Ultracomp eBeads | ThermoFisher Scientific | 01-2222-41 |
| Critical Commercial Assays | ||
| 16S library preparation | MR DNA (Molecular Research) | bTEFAP |
| mRNA-Seq library preparation (Illumina) | SeqMatic | 20020594 |
| nCounter Mouse Immunology Panel | Nanostring | XT-CSO-MIM1-12 |
| Mouse Lipocalin-2/NGAL DuoSet ELISA | R&D Systems | DY1857 |
| Deposited Data | ||
| RNA-Seq (Tnfr1−/− versus WT, 8 wks of age) | Gene Expression Omnibus (GEO) | GSE107933 |
| RNA-Seq (Tnfr1−/− versus WT, 2 wks of age) | Gene Expression Omnibus (GEO) | GSE155654 |
| RNA-Seq (Il10−/− Tnfr1−/− versus Il10−/−, 2 wks of age) | Gene Expression Omnibus (GEO) | GSE155626 |
| Experimental Models: Organisms/Strains | ||
| Mice: C57Bl6/J | Jackson Labs | 000664 |
| Mice: Il10−/− | Jackson Labs | 002251 |
| Mice: Tnfr1−/− | Jackson Labs | 002818 |
| Software and Algorithms | ||
| Kallisto/sleuth v0.44.0 | Pachter Lab | https://pachterlab.github.io/kallisto/ |
| nSolver v3.0 | Nanostring | https://www.nanostring.com/products/analysis-software/nsolver |
| mothur v1.40.1 | Schloss Lab | https://mothur.org/ |
| FlowJo v10.4 | FlowJo | https://www.flowjo.com/ |