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. Author manuscript; available in PMC: 2018 Jul 6.
Published in final edited form as: Cell Stem Cell. 2017 May 11;21(1):120–134.e7. doi: 10.1016/j.stem.2017.03.024
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
HHS Vulnerability Disclosure