Key Resource Table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| APC/Cy7 anti mouse CD45 (30-F11) | BioLegend | Cat #103116; RRID: AB_312981 |
| PE/Cy7 anti mouse CD11b (M1/70) | BioLegend | Cat #101216; RRID: AB_312799 |
| PerCP/Cy5.5 anti mouse Ly6C (HK1.4) | BioLegend | Cat#128012; RRID: AB_1659241 |
| PB anti mouse Ly6G (1A8) | BioLegend | Cat#127612; RRID: AB_2251161 |
| PE anti mouse CD115 (AF598) | BioLegend | Cat#135505; RRID: AB_1937254 |
| APC anti mouse TIM4 (RMT4–54) | BioLegend | Cat#130008; RRID: AB_2271648 |
| APC anti mouse CD163 (TNKUPJ) | ThermoFisher Scientific | Cat#12–1631-80; RRID: AB_2716923 |
| PE anti mouse F4/80 (REA126) | Miltenyi | Cat#130–116-499; RRID: AB_2727574 |
| APC anti mouse VSIG4 (NLA14) | ThermoFisher Scientific | Cat#25–5752-82; RRID: AB_2637431 |
| Unconjugated anti mouse CLEC4F | R&D Systems | Cat#AF2784; RRID: AB_2081339 |
| PE/Cy7 anti mouse CD64 (X54–5/7.1) | BioLegend | Cat#139314; RRID: AB_2563904 |
| PE anti mouse CLEC2 (17D9) | BioLegend | Cat#146104; RRID: AB_2562383 |
| APC anti mouse CD45.1 (A20) | BioLegend | Cat#110713; RRID: AB_313502 |
| CFL 647 donkey anti goat IgG | Santa Cruz Biotechnology | sc-362285 |
| Alexa flour 488 anti mouse CX3CR1 (SA011F11) | BioLegend | Cat#149022; RRID: AB_2565705 |
| Alexa flour 647 anti mouse SiglecF (E50–2440 (RUO)) | BD | BD562680; RRID: AB_2687570 |
| PE anti mouse F4/80 (BM8) | BioLegend | Cat#123110; RRID: AB_893486 |
| PE/Cy7 anti mouse TIM4 (RMT4–54) | BioLegend | Cat#130009; RRID: AB_2565718 |
| Alexa flour 647 anti mouse CD102 (3C4 (MIC2/4)) | BioLegend | Cat#105611; RRID: AB_2122183 |
| Alexa flour 488 donkey anti rat IgG (H+L) | ThermoFisher Scientific | A21208; RRID: AB_2535794 |
| Ki-67 eFluor 660 (SolA15) | Invitrogen | Cat#50–5698-82; RRID: AB_2574235 |
| Anti-Desmin | Abcam | ab15200; RRID: AB_301744 |
| Alex flour 555 goat anti rabbit IgG (H+L) | Abcam | ab150078; RRID: AB_2722519 |
| Anti CD31 (MEC 13.3) | BD | BD550274; RRID: AB_393571 |
| PB anti mouse CD11c (N418) | BioLegend | Cat#117321; RRID: AB_755987 |
| MC-21 anti mouse CCR2 | Jung Lab (Weizmann Institute of Science) (Mack et al., 2001) | Clone: MC-21 |
| Chemicals, Peptides and Recombinant Proteins | ||
| APC BRDU FLIW KIT | BD | BD552598 |
| APAP | Merck | A7085 |
| BODIPY 493/503 | ThermoFisher Scientific | D3922 |
| CFSE | Merck | Cat#65–0850 |
| Collagenase VIII from Clostridium histolyticum | Merck | C5138–500MG |
| Dexamethasone | Merck | D4902–25MG |
| Dnase I (Deoxyribonuclease I from bovine pancreas) | Merck | 10104159001 DN25–100MG |
| DPBS | Biological Industries | 02–023-1A |
| DTT (Dithiothreitol) | Formidum | 3483–12-3 |
| EDTA (Ethylenediaminetetraacetic acid disodium salt dihydrate) | Merck | E5134 |
| Fetal Bovine Serum | Biological industries | 04–001-1A |
| Fixation/Permeablization Kit | BD | BD554714; RRID: AB_2869008 |
| HBSS −/− | gibco | 2183113 |
| Clodronate | Liposoma | C-005 |
| Paraformaldehyde 32% | Electron microscopy sciences | 15714 |
| Protease inhibitor | Merck | P8340 |
| RIPA buffer | Cell Signaling | C-9806S |
| Tissue-Tek O.C.T | Scigen | 23–730-625 |
| TRIzol® reagent | Merck | T9424–100ML |
| Critical Commercial Assays | ||
| cDNA reverse transcription kit | Applied Biosystems | 4368814 |
| miRNeasy Mini Kit | QIAGEN | 217084 |
| SYBR Green PCR Master Mix kit | Applied Biosystems | 4309155 |
| TUNEL staining | Promega | G3250 |
| Deposited Data | ||
| KCs steady state: Bulk MARS-Seq | This paper | GEO: GSE183493 |
| Ly6Chi monocytes AILI 24 h: Bulk RNAseq | This paper | GEO: GSE183494 |
| BM Ly6Chi monocytes: Bulk RNAseq | This paper | GEO: GSE183495 |
| Ly6Chi monocytes AILI 24 h: Single cell RNAseq | This paper | GEO: GSE183367 |
| RNAseq SuperSeries bundle of all four datasets | This paper | GEO: GSE183756 |
| RAW Western blot images (refer to Figures 4G, 5F) | This paper | Mendeley, DOI: 10.17632/kfst2hy224.1 |
| Experimental Models: Organisms/Strains | ||
| Mouse: Commd10fl/fl | Generated by our lab, (Mouhadeb et al., 2018) | N/A |
| Mouse: Cx3cr1cre/+ (Cx3cr1tm1.1(cre)Jung) | Jung Lab (Weizmann Institute of Science) (Yona et al., 2013) | Stock No: 025524 |
| Mouse: Lyz2cre/+ (B6.129P2-Lyz2tm1(cre)Ifo) | The Jackson Laboratories | Stock No: 004781 |
| Mouse: Clec4fcre/+ | Guilliams Lab (Ghent University) (Scott et al., 2018) | N/A |
| Mouse: CD45.1 (B6.SJL-Ptprca Pepcb/Boy) | The Jackson Laboratories | Stock No: 002014 |
| Mouse: CD45.2 C57BL/6JOlaHsd male mice | Envigo (Israel) | Stock No: 000664 |
| Mouse: Ccr2−/−Cx3cr1gfp/+ | Jung Lab (Weizmann Institute of Science) (Zigmond et al., 2012) | N/A |
| Oligonucleotides | ||
| Commd10 FWD: GAGAGCCCCAGCATGAAGAA | Merck | N/A |
| Commd10 REV: AATCCGGCTGAGAAGTCGTG | Merck | N/A |
| Rplp0 FWD: TCCAGCAGGTGTTTGACAAC | Merck | N/A |
| Rplp0 REV: CCATCTGCAGACACACACT | Merck | N/A |
| Arg1 FWD:CAGAAGAATGGAAGAGTCAG | Merck | N/A |
| Arg1 REV:CAGATATGCAGGGAGTCACC | Merck | N/A |
| Trem2 FWD: GGCCCATGCCAGCGTGTGGT | Merck | N/A |
| Trem2 REV: CCAGAGATCTCCAGCATC | Merck | N/A |
| Spp1 FWD: AGCAAGAAACTCTTCCAAGCAA | Merck | N/A |
| Spp1 REV: TGAGATTCGTCAGATTCATCCG | Merck | N/A |
| More Oligonucleotides appear in Figure S7 | ||
| Sofwere and Algorithms | ||
| FlowJo 10.7.1 | Flow jo | https://www.flowjo.com/solutions/flowjo/downloads |
| GraphPad Prism 5 | GraphPad Software | https://www.graphpad.com/ |
| ImageJ v1.51j | NIH | https://imagej.nih.gov/ij/ |
| StepOne v2.3 | StepOne software | https://www.thermofisher.com/il/en/home/technicalresources/software-downloads/StepOne-and-StepOnePlus-Real-Time-PCR-System.html |
| ZEN 2011 | Zeiss | https://www.zeiss.com/microscopy/int/products/microscopesoftware/zen-lite.html |
| Partek Genomics Suite | Partek | https://www.partek.com/partek-genomics-suite/ |
| Cutadapt | DOI:10.14806/ej.17.1.200 | https://cutadapt.readthedocs.io/en/stable/ |
| Ensembl | DOI:10.1093/nar/gkaa942 | https://www.ensembl.org/index.html |
| DESeq2 | Bioconductor, (Love et al., 2014) | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| snakemake | (Koster and Rahmann, 2012) | https://snakemake.readthedocs.io/en/stable/ |
| STAR | (Dobin et al., 2013) | http://code.google.com/p/rna-star/. |
| MouseMine | (Motenko et al., 2015) | http://www.mousemine.org/mousemine/begin.do |
| CellMarker | (Zhang et al., 2019) | http://biocc.hrbmu.edu.cn/CellMarker/ |
| Ingenuity Pathway Analysis | QIAGEN Bioinformatics | https://www.qiagenbioinformatics.com/products/ingenuitypathway-analysis/ |