| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rat monoclonal (clone M1/70) anti-mouse CD11b (purified, used at 1:150) | Biolegend | Cat#101201; RRID: AB_312784 |
| Hamster monoclonal (clone N418) anti-mouse CD11c (purified, used at 1:150) | Biolegend | Cat#117301; RRID:AB_313770 |
| Rat monoclonal (clone C1:A3-1) anti-mouse F4/80 (purified, used at 1:150) | Biorad/AbD Serotec | Cat#MCA497G; RRID:AB_872005 |
| Hamster monoclonal (1A8) anti-mouse Ly6G (purified, used at 1:150) | Biolegend | Cat#127607; RRID:AB_1186104 |
| Hamster monoclonal (30-F11) anti-mouse CD45 (purified, used at 1:200) | BD Bioscience | Cat#550539; RRID:AB_2174426 |
| Rat monoclonal (clone MEC 13.3) anti-mouse PECAM (purified, used at 1:200) | BD Bioscience | Cat#550274; RRID:AB_393571 |
| Rat monoclonal (clone 175410) anti-mouse RAGE (purified, used at 1:200) | R&D Systems | Cat#MAB1179; RRID:AB_2289349 |
| Rabbit polyclonal anti-mouse PECAM (used at 1:250) | MIllipore | Cat#AB3786; RRID:AB_91588 |
| Hamster monocloncal (8.1.1) anti-mouse T1α (used at 1:900) | Developmental Studies Hybridoma Bank, Univ. of Iowa | RRID: AB_531893 |
| Chicken polyclonal anti-GFP (used at 1:500) | Aves | Cat#GFP-1020; RRID:AB_10000240 |
| Rabbit polyclonal anti-RFP (used at 1:250) | Rockland | Cat#600-401-379; RRID:AB_2209751 |
| Chicken polyclonal anti-RFP (used at 1:250) | Rockland | Cat#600-901-379; RRID:AB_10704808 |
| Rat monoclonal (clone 30-F11) anti-CD45-Apc-Cy7 (used at 1:200) | Biolegend | Cat#103116; RRID:AB_312981 |
| Rat monoclonal (M1/70) anti-CD11b-PerCP-Cy5 (used at 1:200) | Tonbo | Cat#65-0112 also OWL-A11257; RRID:AB_2621885 |
| Rat monoclonal (N418) anti-CD11c-APC (used at 1:200) | Biolegend | Cat#117309; RRID:AB_313778 |
| Rat monoclonal (BM8) anti-F4/80-PE (used at 1:200) | eBioscience | Cat#12-4801-82; RRID:AB_465923 |
| Rat monoclonal (1A8) anti-Ly6G-PE-Cy7 (used at 1:400) | Biolegend | Cat#127617; RRID:AB_1877262 |
| Goat anti-Chicken IgG (H+L) Secondary Antibody, Alexa Fluor 488 (used at 1:500) | Thermo Fisher Scientific | Cat#A-11039 also A11039; RRID:AB_142924 |
| Donkey anti-Rabbit IgG (H+L) Secondary Antibody, Alexa Fluor 488 (used at 1:500) | Thermo Fisher Scientific | Cat#A-21206 also A21206; RRID:AB_2535792 |
| Donkey anti-Rat IgG (H+L) Secondary Antibody, Alexa Fluor 488 (used at 1:500) | Thermo Fisher Scientific | Cat#A-21208 also A21208; RRID:AB_141709 |
| Cy3-AffiniPure F(ab′)2 Donkey anti-Chicken IgG (H+L) Secondary Antibody (used at 1:500) | Jackson ImmunoResearch Labs | Cat#703-166-155; RRID:AB_2340364 |
| Donkey anti-Rabbit IgG (H+L) Secondary Antibody, Alexa Fluor 555 (used at 1:500) | Thermo Fisher Scientific | Cat#A-31572 also A31572; RRID:AB_162543 |
| Goat anti-Rat IgG (H+L) Secondary Antibody, Alexa Fluor 555 (used at 1:500) | Thermo Fisher Scientific | Cat#A-21434 also A21434; RRID:AB_141733 |
| Goat anti-Hamster IgG (H+L) Secondary Antibody, Alexa Fluor 647 (used at 1:500) | Thermo Fisher Scientific | Cat#A-21451; RRID:AB_2535868 |
| Goat anti-Rat IgG (H+L) Secondary Antibody, Alexa Fluor 647 (used at 1:500) | Thermo Fisher Scientific | Cat#A-21247 also A21247; RRID:AB_141778 |
| Rat monoclonal (clone 30-F11) anti-CD45-BUV395 (used at 1:100) | BD Biosciences | Cat# 564279 |
| Rat monoclonal (clone 17A1) anti-CD3-PE-Cy7 (used at 1:100) | Biolegend | Cat# 100205; RRID:AB_312662 |
| Rat monoclonal (clone RM4-5) anti-CD4-BV711 (used at 1:100) | Biolegend | Cat# 317439; RRID:AB_11219404 |
| Rat monoclonal (clone 6D5) anti-CD19-BV650 (used at 1:100) | Biolegend | Cat#115541; RRID:AB_11204087 |
| Rat monoclonal (clone PK136) anti-NK-1.1-BV650 (used at 1:100) | Biolegend | Cat#108735; RRID:AB_11147949 |
| Rat monoclonal (clone RB6-8C5) anti-Ly6-G/Ly6-C-BV650 (used at 1:100) | Biolegend | Cat#108441; RRID:AB_2562401 |
| Rat monoclonal (clone M1/70) anti-CD11b-BV650 (used at 1:100) | Biolegend | Cat#101239; RRID:AB_11125575 |
| Rat monoclonal (clone N418) anti-CD11c-BV785 (used at 1:100) | Biolegend | Cat# 117335 RRID:AB_11219204 |
| Rat monoclonal (clone E50-2440) anti-SiglecF-APC (used at 1:100) | BD Biosciences | Cat#562680 |
| Rat monoclonal (PC61) anti-CD25-APC-Cy7 (used at 1:100) | Biolegend | Cat#102025; RRID:AB_830744 |
| Rat monoclonal (53-2.1) anti-CD90.2-BV605 (used at 1:100) | Biolegend | Cat#140317; RRID:AB_11203724 |
| Rat monoclonal (DJ8) anti-T1/ST2-PE (used at 1:100) | MD Biosciences | Cat#101001PE |
| Rat monoclonal (2F1) anti-KLRG1/MAFA-PerCP-eFluor710 (used at 1:100) | eBioscience | Cat#46-5893-80 also 46-5893; RRID:AB_10671072 |
| Rat monoclonal (MAR-1) anti-FcεRIα Pacific Blue (used at 1:100) | Biolegend | Cat#134313; RRID:AB_10612933 |
| Rat monoclonal (TAWJ) anti-Gata-3-eFluor660 (used at 1:20) | eBioscience | Cat#50-9966-41 also 50-9966; RRID:AB_10597909 |
| Rat monoclonal (SolA15) anti-Ki67-FITC (used at 1:100) | eBioscience | Cat#11-5698-80; RRID:AB_11151689 |
| Rat monoclonal (RPA-T4) anti-hCD4-APC (used at 1:100) | eBioscience | Cat#17-0049-41; RRID:AB_1272118 |
| Rat monoclonal (A20) anti-hCD45.1-PE (used at 1:200) | Biolegend | Cat#110707; RRID:AB_313496 |
| Rat monoclonal (104) anti-hCD45.2-APC (used at 1:200) | Biolegend | Cat#109813; RRID:AB_389210 |
| CD16/CD32 Fc Receptor Block | BD Biosciences | Cat# 553142 RRID:AB_394657 |
| Rat monoclonal (clone 30-F11) anti-CD45-Apc (used 2 ug/mouse for in vivo labeling) | Biolegend | Cat#103112 |
| Bacterial and Virus Strains | ||
| Biological Samples | ||
| Chemicals, Peptides, and Recombinant Proteins | ||
| Buprenex (0.3 mg/mL) | Reckitt Benckiser | Cat# NDC 12496-0757-5 |
| Lidocaine (5 mg/mL) | Phoenix | Cat# NDC 57319-533-05 |
| Bupivacaine (2.5 mg/mL) | Hospira | Cat# NDC 0409-1159-01 |
| Donkey Serum | Sigma-Aldrich | Cat#D9663-10ML |
| Goat Serum | Sigma-Aldrich | Cat#G9023-10ML |
| Bovine Serum Albumin | Fisher | Cat#BP1600-100 |
| Tamoxifen | Sigma-Aldrich | Cat#T5648 |
| EdU (5-ethynyl-2′-deoxyuridine) | Thermo Fisher Scientific | Cat#E10415 |
| Collagenase Type I (used at 450 U/mL) | Gibco Life Tech | Cat##17100–017 |
| Elastase (used at 4 U/mL) | Worthington Biochemical Corporation | Cat##LS002279 |
| Dispase (used at 5 U/mL) | BD Biosciences | Cat#354235 |
| DNaseI (used at 0.33 U/mL) | Roche | Cat#10104159001 |
| Red Blood Cell Lysis Buffer | Biolegend | Cat#420301-BL |
| Liberase TM | Roche | Cat#05401119001 |
| Sytox Blue | Life Tech | Cat#S34857 |
| AbC Anti-Mouse Bead kit | Molecular Probes | Cat#A10344 |
| Fix and Perm Cell Permeabilization Kit | Thermo Fisher Scientific | Cat#GAS003 |
| DMEM/F12 + GlutaMAX | Gibco Life Tech | Cat#10565-018 |
| Matrigel (Growth Factor Reduced) | BD Biosciences | Cat#356230 |
| Characterized Fetal Bovine Serum (used at 10%) | HyClone | Cat#SH30071 |
| Insulin-Transferrin-Selenium (used at 1x) | Gibco Life Tech | Cat#41400-045 |
| Epidermal Growth Factor (used at 20 ng/mL) | R&D Systems | Cat#2028-EG-200 |
| Fibroblast Growth Factor 2 or Basic (used at 25 ng/mL) | Gibco Life Tech | Cat#PMG0033 |
| Keratinocyte Growth Factor or Fibroblast Growth Factor 7 (used at 10 ng/mL) | Gibco Life Tech | Cat#PHG0094 |
| Hepatocyte Growth Factor (used at 10 ng/mL) | Gibco Life Tech | Cat#PHG0254 |
| RIPA Lysis and Extraction Buffer | Thermo Fisher Scientific | Cat#89900 |
| Complete, Mini Protease Inhibitor Cocktail | Roche | Cat#11-836-153-001 |
| Protein Assay Dye Reagent Concentrate | Bio-Rad | Cat#500-0006 |
| Protector RNase Inhibitor | Roche | Cat#03-335-402-001 |
| Critical Commercial Assays | ||
| Click-iT EdU Alexa Fluor 647 Imaging Kit (for flow cytometry) | Invitrogen | Cat#C10340 |
| Click-iT Plus EdU Alexa Fluor 647 Imaging Kit (for tissue histology) | Invitrogen | Cat#C10640 |
| Proteome Profiler Mouse Cytokine Array Kit, Panel A | R&D Systems | Cat#ARYOO6 |
| RNAeasy Plus Micro Kit | Qiagen | Cat#74O34 |
| SuperScript IV VILO Master Mix | Invitrogen Life Tech | Cat#11756050 |
| SYBR GreenER qPCR Supermix Universal | Invitrogen Life Tech | Cat#1176202K |
| Agilent RNA 600 Pico Kit | Agilent Technologies | Cat#5067-1513 |
| C1 Single-Cell Reagent Kit for mRNA Seq | Fluidigm | Cat#100-6201 |
| Nextera XT DNA Library Preparation Kit | Illumina | Cat#FC-131-1096 |
| Quant-iT™ PicoGreen® dsDNA Assay Kit | Thermo Fisher Scientific | Cat#P7589 |
| Deposited Data | ||
| Raw data files for RNA sequencing (PNX) | NCBI GEO | GEO: GSE96104 |
| Raw data files for RNA sequencing (sham) | NCBI GEO | GEO: GSE96105 |
| Experimental Models: Cell Lines | ||
| Experimental Models: Organisms/Strains | ||
| Mouse: Csf1r-GFP : B6N.Cg-Tg(Csf1r-EGFP)1Hume/J | Jackson Laboratories | Stock No. 018549 |
| Mouse: Ccr2−/− : cCR2tm1Mae | Kuziel et al., 1997 | |
| Mouse: Ccr2RFP/+ : B6.129(Cg)-Ccr2ím2.1,fc/J | Jackson Laboratories | Stock No. 017586 |
| Mouse: Cx3cr1GFP/+: B6.129P-C×3cr1tm1Ltt/J | Jackson Laboratories | Stock No. 005582 |
| Mouse: Sftpc-CreER: Sftpctm1(cre/ERT2)Blh | Jackson Laboratories | Stock No. 028054 |
| Mouse: Rosa-dtomato : Gt(ROSA)26Sortm2(CAG-tdTomato)Fawa | Rock et al., 2011 | |
| Mouse: Rosa-fGFP : Gt(ROSA)26Sortm1(CAG-EGFP)Blh | Rawlins et al., 2009 | |
| Mouse: YARG : B6.129S4-Arg1tm1Lky/J | Jackson Laboratories | Stock No. 015857 |
| Mouse: Il4ra−/− : BALB/c-Il4ratm1Sz/J | Jackson Laboratories | Stock No. 003514 |
| Mouse: ll5tm11(Cre)Lky | Nussbaum et al., 2013 | |
| Mouse: lL13tm2.1Lky: C.129S4(Cg)-Il13ím2.1Lky/J | Jackson Laboratories | Stock No. 018869 |
| Mouse: CD45.1 : B6-Ly5.1/Cr | Charles River | Stock No. 564 |
| Oligonucleotides | ||
| Genotyping primers-See Supplemental Table 1 | This paper | |
| qRT-PCR primers-See Supplemental Table 2 | This paper | |
| Recombinant DNA | ||
| Software and Algorithms | ||
| ImageJ | NIH | https://imagej.nih.gov/ij/ |
| FlowJo (v10.1r5) | TreeStar Inc. | https://www.flowjo.com/ |
| GraphPad Prism 6.0 | GraphPad Software Inc. | http://www.graphpad.com/scientificsoftware/prism/ |
| Tophat (v2.1.0) | Kim et al., 2013; Trapnell et al., 2012 | |
| Bowtie2 (v2.2.8) | Kim et al., 2013; Trapnell et al., 2012 | |
| Cufflinks (v2.2.1) | Kim et al., 2013; Trapnell et al., 2012 | |
| Picard tools | http://broadinstitute.github.io/picard/ | |
| HTSeq-count | Anders et al., 2015 | http://www-huber.embl.de/users/anders/HTSeq/doc/count.html |
| Trimmatic | Bolger et al., 2014 | http://www.usadellab.org/cms/?page=trimmomatic |
| RSEM | Li and Dewey, 2011 | |
| Other | ||
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