Key Resources Table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-mouse Ly6C FITC Clone AL-21 | BD Biosciences | Cat# 553104; RRID: AB_394628 |
| Anti-mouse CD45R/B220 PE Clone RA3–6B2 | BioLegend | Cat# 103208; RRID: AB_312993 |
| Anti-mouse TER-119 PE Clone TER-119 | BD Pharmingen | Cat# 553673; RRID: AB_394986 |
| Anti-mouse CD49b (pan-NK cells) PE Clone DX5 | BioLegend | Cat# 108908; RRID: AB_313415 |
| Anti-mouse CD11b PE Clone M1/70 | BioLegend | Cat# 101208; RRID: AB_312791 |
| Anti-mouse CD90.2 (Thy1.2) PE Clone 53–2.1 | BioLegend | Cat# 140308; RRID: AB_1061145 |
| Anti-mouse Ly6G PE Clone 1A8 | BD Biosciences | Cat# 551461; RRID: AB_394208 |
| Anti-mouse NK1.1 PE Clone PK136 | BioLegend | Cat# 108708; RRID: AB_313395 |
| Anti-mouse CD45.2 PerCP/Cy5.5 Clone 104 | BioLegend | Cat# 109828; RRID: AB_893350 |
| Anti-mouse CD115 (c-fms) PerCP-eFluor 710 Clone AFS98 | eBioscience | Cat#46-1152-82; RRID: AB_10597740 |
| Anti-mouse F4/80 PE/Cy7 Clone BM8 | BioLegend | Cat# 123113; RRID: AB_893490 |
| Anti-mouse Siglec-F BV412 Clone E50–2440 | BD Biosciences | Cat# 562681; RRID: AB_2722581 |
| Anti-mouse CD64 BV421 Clone X54–5/7.1 | BioLegend | Cat# 139309; RRID: AB_2562694 |
| Anti-mouse CD8a BV421 Clone 53–6.7 | BioLegend | Cat# 100737; RRID: AB_10897101 |
| Anti-mouse CD11c BV510 Clone N418 | BioLegend | Cat# 117338; RRID: AB_2562016 |
| Anti-mouse CD4 BV510 Clone RM4–5 | BioLegend | Cat# 100553; RRID: AB_2561388 |
| Anti-mouse I-A/I-E BV605 Clone M5/144.15.2 | BioLegend | Cat# 107639; RRID: AB_2565894 |
| Anti-mouse CD24 BV605 Clone M1/69 | BioLegend | Cat# 101827; RRID: AB_2563464 |
| Anti-mouse Ki-67 BV605 Clone 16A8 | BioLegend | Cat# 652413; RRID: AB_2562664 |
| Anti-mouse IgG2a, k BV605 Clone RTK2758 | BioLegend | Cat# 400539; RRID: AB_11126979 |
| Anti-mouse CD8a BV711 Clone 53–6.7 | BioLegend | Cat#100747; RRID: AB_11219594 |
| Anti-mouse CD45 BV711 Clone 30-F11 | BioLegend | Cat# 103147; RRID: AB_2564383 |
| Anti-mouse CD45 BV711 Clone 30-F11 | BD Biosciences | Cat# 563709; RRID: AB_2687455 |
| Anti-mouse CD103 BV711 Clone M290 | BD Biosciences | Cat# 564320; RRID: AB_2738743 |
| Anti-mouse CD103 BUV395 Clone M290 | BD Biosciences | Cat# 740238; RRID: AB_2739985 |
| Anti-mouse CD64a&b Alexa Fluor 647 Clone X54–5/7.1 | BD Biosciences | Cat# 558539; RRID: AB_647120 |
| Anti-mouse CD31 Alexa Fluor 647 Clone MEC13.3 | BioLegend | Cat# 102516; RRID: AB_2161029 |
| Donkey anti-goat IgG Alexa Fluor 647 (H+L) | Invitrogen | Cat# A-21447; RRID: AB_141844 |
| Anti-mouse CD11b APC/Cy7 Clone M1/70 | BioLegend | Cat# 101226; RRID: AB_830642 |
| Anti-mouse CD45.1 Alexa 700 Clone A20 | BioLegend | Cat# 110724; RRID: AB_493733 |
| Anti-mouse I-A/I-E Alexa Fluor 700 Clone M5/114.15.2 | BioLegend | Cat# 107622; RRID: AB_493727 |
| Anti-mouse MHC II (I-A/I-E) Alexa Fluor 700 Clone M5/114.15.2 | eBioscience | Cat# 56-5321-82; RRID: AB_494009 |
| CLEC4F/CLECSF13 (goat anti-mouse) | R&D Systems | Cat# AF2784; RRID: AB_2081339 |
| Bacterial and Virus Strains | ||
| Bioluminescent Streptococcus Pneumoniae Xen10 | Caliper, LifeSciences | Strain A66.1 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Clodronate liposomes | ClodronateLiposomes.org, Haarlem | NA |
| DAPI | Thermo Fisher Scientific | Cat# F10347 |
| MMPSense FAST | Perkin Elmer | Cat# NEV10168 |
| pHrodo Green E.coli BioParticles | ThermoFisher Scientific | Cat# P35366 |
| Recombinant EGF | PeProtech | Cat# 315–09 |
| Recombinant IFNɣ | PeProtech | Cat# 315–05 |
| Tamoxifen | Sigma-Aldrich | Cat# T5648 |
| WGA Alexa Fluor 647 | Thermo Fisher Scientific | Cat# W32466 |
| Critical Commercial Assays | ||
| Amphiregulin ELISA Kit | Abcam | Cat# ab100668 |
| Anti-PE microbeads | Miltenyi Biotec | Cat# 130-048-801 |
| BrdU Kit | BD Biosciences | Cat# 552598 |
| CD11b microbeads | Miltenyi Biotec | Cat# 130-049-601 |
| CTNI Serum/Plasma ELISA Kit | CTNI-1-US | Cat# Life Diagnostics |
| Foxp3/Transcription Factor Staining Buffer Set | eBioscience | Cat# 00-5523-00 |
| High-Capacity RNA-to-cDNA kit | Thermo Fisher Scientific | Cat# 4387406 |
| In Situ Cell Death Detection Kit, TMR red | Sigma Aldrich | Cat# 12156792910 |
| Mouse EGF ELISA Kit | R&D Systems | Cat# MEG00 |
| Mouse IFN-gamma Quantikine ELISA kit | R&D Systems | Cat# MIF00 |
| RNeasy Micro kit | Qiagen | Cat# 74004 |
| TaqMan Fast Universal PCR Master Mix | Thermo Fisher Scientific | Cat# 4352042 |
| TNFα Quantikine ELISA Kit | Lifespan Biosciences Inc. | Cat# LS-F5435–1 |
| PicoPure RNA Isolation Kit | Thermo Fisher Scientific | Cat# KIT0204 |
| Deposited Data | ||
| Tissue macrophages after remote injury | GEO datasets http://www.ncbi.nlm.nih.gov/geo/ | GEO: GSE104342 |
| Experimental Models: Organisms/Strains | ||
| B6.129P-Cx3cr1tm1Litt/J | The Jackson Laboratory | JAX: 005582 |
| B6.129P2(Cg)-Cx3cr1tm2.1(cre/ERT)Litt/WganJ | The Jackson Laboratory | JAX: 021160 |
| B6;C3Fe a/a-Csf1op/J | The Jackson Laboratory | JAX: 000231 |
| B6.129S6-Egfrtm1Dwt/Mmnc | MMRRC | 031765-UNC |
| B6.Cg-Gt(ROSA)26Sortm9(CAG-tdTomato)Hze/J | The Jackson Laboratory | JAX: 007909 |
| B6.129S7-Rag1tm1Mom/J | The Jackson Laboratory | JAX: 002216 |
| B6.129S4-Ifngtm3.1Lky/J | The Jackson Laboratory | JAX: 017581 |
| C57BL/6 | The Jackson Laboratory | JAX: 000664 |
| C57BL/6J-Tg(Itgax-cre,-EGFP)4097Ach/J | The Jackson Laboratory | JAX: 007567 |
| C57BL/6N-Ifngr1tm1.1Rds/J | The Jackson Laboratory | JAX: 025394 |
| Ccr2−/− B6.129S4-Ccr2tm1Ifc/J | The Jackson Laboratory | JAX: 004999 |
| CD45.1 B6.SJL-Ptprca Pepcb/BoyJ | The Jackson Laboratory | JAX: 002014 |
| IL10-flox | Axel Roers et al. | NA |
| LysMCre B6.129P2-Lyz2tm1(cre)Ifo/J | The Jackson Laboratory | JAX: 004781 |
| Software and Algorithms | ||
| Amira 3D | FEI Software | http://www.fei.com/software/amira-3d-for-life-sciences/ |
| Bioconductor’s Oligo package | Bioconductor | https://www.bioconductor.org/ |
| Bioconductor’s topGO package | Bioconductor | https://www.bioconductor.org/ |
| Bioconductor’s clusterProfiler package | Bioconductor | https://www.bioconductor.org/ |
| javaGSEA Desktop Application | Broad Institute | http://software.broadinstitute.org/gsea) |
| StringDB | STRING | https://string-db.org/ |
| Cytoscape | Cytoscape | http://www.cytoscape.org/ |
| FlowJo v10 | FlowJo | https://www.flowjo.com/ |
| GraphPad Prism v7.0a | GraphPad Software | http://www.graphpad.com/ |
| ImageJ v1.48 | NIH | http://imagej.net/ |
| iVision v4.5.2 | BioVision Technologies | http://www.biovis.com/ivision.html |