KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| BV421 Flt3 A2F10.1 | BD Bioscience | 562898 RRID:AB_2737876 |
| BV421 Tim4 RMT4-54 | BD Bioscience | 744874 RRID:AB_2742551 |
| BV421 CD64 X54-5/7.1 | Biolegend | 139309 RRID:AB_2562694 |
| BV650 CX3CR1 SA011F11 | Biolegend | 149033 RRID:AB_2565999 |
| BV650 CD105 MJ7/18 | BD Bioscience | 740609 RRID:AB_2740309 |
| BV786 CD64 X54-5/7.1 | BD Bioscience | 741024 RRID:AB_2740644 |
| BV711 Ly6G 1A8 | BD Bioscience | 563979 RRID:AB_2565971 |
| PE Tim4 RMT4-54 | BD Bioscience | 564147 RRID:AB_2738621 |
| PE-CF594 CD105 MJ7/18 | BD Bioscience | 562762 RRID:AB_2737776 |
| PE-CF594 CD4 RM4-5 | BD Bioscience | 56228 RRID:AB_11154410 |
| PE-CF594 CD8 53-6.7 | BD Bioscience | 562315 |
| PE Cy7 MHCII M5/114.15.2 | Biolegend | 107630 |
| PE Cy7 CD62L MEL-14 | Biolegend | 104418 |
| PerCPCy5.5 CD11b M1/70 | BD Bioscience | 550993 RRID:AB_394002 |
| FITC CD43 S7 | BD Bioscience | 553270 RRID:AB_394747 |
| APC MerTK 2B10C42 | Biolegend | 151508 |
| AF647 CX3CR1 SA011F11 | Biolegend | 149004 |
| APC CD43 S7 | BD Bioscience | 560663 RRID:AB_1727479 |
| AF647 CD177 Y127 | BD Bioscience | 566599 RRID:AB_2869790 |
| APC CD19 1D3 | BD Bioscience | 550992 RRID:AB_398483 |
| AF700 CD45 30-F11 | BD Bioscience | 560510 |
| AF700 NK1.1 PK136 | BD Bioscience | 560515 |
| APCCy7 Ly6c AL-21 | BD Bioscience | 560596 |
| BUV395 CD43 S7 | BD Bioscience | 740224 RRID:AB_2739972 |
| BUV661 CD45 30-F11 | BD Bioscience | 612975 |
| BUV737 CD11c HL3 | BD Bioscience | 612796 RRID:AB_2870124 |
| V500 CD45 30-F11 | BD Bioscience | 561487 RRID:AB_10697046 |
| CD68 | BioLegend | 916104 |
| CD11b | Abcam | ab133357 |
| TIMD4 | Atlas | HPA015625 |
| TREM2 | CST | 91068 |
| CCR2 | Proteintech | 16154-1-AP |
| VE-Cad | CST | 93467 |
| MHC II | CST | 68258T |
| MERTK | Abcam | ab176887 |
| CD15 | CST | 4744T |
| CD206 | CST | 91992T |
| Thy1/CD90 | CST | 13801S |
| CD11c | CST | 45581T |
| CD163 | CST | 93498T |
| CD14 | CST | 75181T |
| Goat anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor™ Plus 555 | Invitrogen | A32727 |
| Goat anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor™ Plus 647 | Invitrogen | A32728 |
| Goat anti-Mouse IgM (Heavy Chain) Secondary Antibody, Alexa Fluor™ 647 | Invitrogen | A21238 |
| Biological Samples | ||
| K/BxN serum was obtained at 8 weeks from the progeny of the KRN X NOD | Mice bred in house | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| HBSS | Thermo Fisher | 14190250 |
| Dispase II (neutral protease, grade II) | Millipore Sigma | 4942078001 |
| Collagenase D | Millipore Sigma | 11088858001 |
| DNAse I | Roche | 10104159001 |
| BD PharmLyse | BD Bioscience | 555899 |
| eBioscience™ Fixable Viability Dye eFluor™ 506 | Thermo Fisher | 65-0866-18 |
| Purified Rat Anti-Mouse CD16/CD32 | BD Bioscience | 553141 |
| Paraformaldehyde, 20% solution | VWR | 100496-494 |
| BD FACS lysing solution | BD Bioscience | 349202 |
| PBS | Gibco | 14190250 |
| Clodronate-laden liposomes | Liposoma | C-010 |
| 123count eBeads™ Counting Beads | Thermo Fisher | 01-1234-42 |
| Busulfan | (Sigma #) | B2635-10G |
| ketamine (Vetalar, Ketaset, Ketalar) | Veterinarian supplied | N/A |
| Xylazine (Rompun) | Veterinarian supplied | N/A |
| Trimethoprim/Sulfamethoxazole | Hi-Tech Pharmacal | 50383-823-16 |
| Tamoxifen | Millipore Sigma | T5648-5G |
| Progesterone | Millipore Sigma | P0130 |
| Critical Commercial Assays | ||
| PicoPure RNA Isolation kit | ThermoFisher | KIT0204 |
| QuantSeq 3’ mRNA sequencing kit | Lexagon | N/A |
| SMART-seq v4 Ultra Low Input Kit for Sequencing | Takara | N/A |
| Deposited Data | ||
| Sequencing Data | Gene Expression Omnibus (GEO) | GSE225803 |
| Experimental Models: Organisms/Strains | ||
| C57Bl/6J | Jackson labs | IMSR_JAX:000664 |
| NR4A1−/− (C57BL/6-Rr39em1Ched /J) | Jackson labs | IMSR_JAX:030204 |
| CCR2−/− (B6.129S4-Ccr2tm1lfc /J) | Jackson labs | IMSR_JAX:004999 |
| LFA1−/− (B6.129S7-Itgal tm1.1Bll /J) | Jackson labs | IMSR_JAX:005257 |
| B6.CD45.1 (B6.SJL-PtprcaPepcb/BoyJ) | Jackson labs | IMSR_JAX:002014 |
| CX3CR1f/wtCreER.zsGFP (B6.129P2(C)-Cx3cr1tm2.1(cre/ERT2)Jung /J | Jackson labs | IMSR_JAX:020940 |
| Zbt46.zsGFP (B6.129S6(C)-Zbtb46tm1.1Kmm /J) | Jackson labs | IMSR_JAX:027618 |
| MafBCremCherry (B6N(129S4)-Mafb tm1.1(cre)Kmm /J) | Jackson labs | IMSR_JAX:029664 |
| Software and Algorithms | ||
| FlowJo V10 | N/A | N/A |
| BBDuk version 37.22 | N/A | N/A |
| STAR47 | N/A | N/A |
| HTSeq48 | N/A | N/A |
| Trimmomatic (version 0.36),49 | N/A | N/A |
| Tophat aligner (tophat 2.1.0) | N/A | N/A |
| Gorilla50,51 | N/A | N/A |
| cellranger 3.1.0 pipeline | N/A | N/A |
| Seurat v3.1 | N/A | N/A |
| BioMart R package | N/A | N/A |
| singleR R package | N/A | N/A |
| Gene-E | N/A | N/A |
| R version 3.3.1 | N/A | N/A |
| GraphPad Prism V8 | N/A | N/A |
| Other | ||
| BD LSR II | N/A | N/A |
| BD FACSAria | N/A | N/A |
| BD Symphony | N/A | N/A |
| Nordion Cs-137 based Gammacell-40 irradiator | N/A | N/A |