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 |