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. Author manuscript; available in PMC: 2019 Nov 25.
Published in final edited form as: Cell Rep. 2018 Nov 20;25(8):2177–2191.e7. doi: 10.1016/j.celrep.2018.10.082

KEY RESOURCES TABLE

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
APC/Cy7 anti-human CD14 Antibody Biolegend Cat#325620; RRID:AB_830693
APC/Cy7 Mouse IgG1 κ Isotype Ctrl Biolegend Cat#400128
Alexa Fluor® 647 anti-human CD163 Antibody Biolegend Cat#333619;
RRID:AB_2563474
Alexa Fluor® 647 Mouse IgG1, κ Isotype Ctrl Biolegend Cat#400130
FITC anti-human CD163 Antibody Biolegend Cat#333618;
RRID:AB 2563094
FITC Mouse IgG1, κ Isotype Ctrl Biolegend Cat#400110
Brilliant Violet 605™ anti-human CD86 Antibody Biolegend Cat#305429;
RRID:AB_11203889
Brilliant Violet 605™ Mouse IgG2b, κ Isotype Ctrl Biolegend Cat#400349
PE anti-human CD80 Antibody Biolegend Cat#305208;
RRID:AB_314504
PE Mouse IgG1, κ Isotype Ctrl Biolegend Cat#400112
Human TruStain FcX Biolegend Cat#422302
Anti-Actin antibody produced in rabbit Sigma Aldrich Cat#A2066;
RRID:AB_476693
Monoclonal Anti-β-Tubulin antibody produced in mouse Sigma-Aldrich Cat#T4026;
RRID:AB_477577
Human Serpin E1/PAI-1 Antibody goat anti-human R&D Systems Cat#AF1786;
RRID:AB_2187024
Human gp130 PE-conjugated Antibody R&D Systems Cat#FAB228P-025
Human IL-6 R alpha Fluorescein-conjugated Antibody R&D Systems Cat#FAB227F-025
Phospho-Stat3 (Tyr705) Antibody Cell Signaling Cat#9131;
RRID:AB_331586
Stat3 (79D7) Rabbit mAb Cell Signaling Cat#4904
Phospho-p38 MAPK (Thr180/Tyr182) (D3F9) XP® Rabbit mAb Cell Signaling Cat#4511;
RRID:AB_2139682
p38 MAPK Antibody Cell Signaling Cat#9212;
RRID:AB_330713
Phospho-NF-KB p65 (Ser536) (93H1) Rabbit mAb Cell Signaling Cat#3033;
RRID:AB_331284
NF-κB p65 (D14E12)XP (R) Rabbit mAb Cell Signaling Cat#8242;
RRID:AB_10859369
Unconjugated rabbit anti-rat IgG Antibody Vector Laboratories Cat#AI-4000
Goat Biotinylated anti-rabbit IgG (H+L) Vector Laboratories Cat#BA-1000;
RRID:AB_2313606
Goat Biotinylated anti-rat IgG (H+L) Vector Laboratories Cat#BA-9400;
RRID:AB_2336202
DyLight 488 anti-rabbit IgG Vector Laboratories Cat#DI-1488;
RRID:AB_2336402
Anti-F4/80 Antibody Abcam Cat#ab6640;
RRID:AB_1140040
Anti-iNOS antibody Abcam Cat#ab15323;
RRID:AB_301857
Anti-pSTAT3 antibody Cell Signaling Cat#9145L
Anti-CD206 antibody Abcam Cat#64693
goat anti-rabbit 800CW LI-COR Cat#926–32211;
RRID:AB_621843
donkey anti-mouse 680LT LI-COR Cat#926–68022;
RRID:AB_10715072
donkey anti-goat 800CW LI-COR Cat#926–32214;
RRID:AB_621846
donkey anti-goat 680LT LI-COR Cat#926–68024;
RRID:AB_10706168
Anti-arginase I Antibody (H-52) Santa Cruz Cat#sc20150;
RRID:AB_2058955
Cy™3 AffiniPure Donkey Anti-Rat IgG (H+L) Jackson ImmunoResearch Cat#712-165-153;
RRID:AB_2340667
Anti-human PAI (inhibitory) antibody Molecular Innovations Cat#MA-8H9D4
LEAFtm Purified Mouse IgG1 K isotype cntr Biolegend Cat#400124
Bacterial and Virus Strains
Biological Samples
Chemicals, Peptides, and Recombinant Proteins
puromycin Sigma-Aldrich Cat#P9620
Histopaque Sigma-Aldrich Cat#10771–500ML
0.1% Poly-L-Lysine solution Sigma-Aldrich Cat#P8920
Sodium butyrate Sigma-Aldrich Cat#B5887
BMS-345541 Sigma-Aldrich Cat#B9935–5MG
Doxycycline hyclate Sigma-Aldrich Cat#D9891–25g
4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) Sigma-Aldrich Cat#H3375
Penicillin-Streptomycin (10,000 U/mL) Gibco Cat#15140–122
Cell Dissociation buffer, Enzyme free, PBS Gibco Cat#13151–014
Geneticin Gibco Cat#10131-035
Falcon® Permeable Support for 24 Well Plate with 8.0μm Transparent PET Membrane Corning Cat#353097
Dulbecco’s Modified Eagle’s Medium (DMEM) Corning Cat#10-013-CV
phosphate-buffered saline (PBS) Corning Cat#21–031-CV
Roswell Park Memorial Institute (RPMI) Corning Cat#10-040-CV
DAPI Thermo Fisher Scientific Cat#D21490
HaltTM Protease and Phosphatase inhibitor single use cocktail Thermo Fisher Scientific Cat#78442
AmpFLSTR Identifiler PCR Kit Thermo Fisher Scientific Cat#4322288
Human PAI-1 (stable mutant form) Molecular Innovations Cat#CPAI
Human PAI-1 (stable mutant, no LRP binding) Molecular Innovations Cat#HPAI-R76E-I91L
Human PAI-1 (substrate form - P12 Arginine P14 Arginine double mutant) Molecular Innovations Cat#HPAI-RR
Low Endotoxin Human RAP Molecular Innovations Cat#RAP-LE
Vectashield antifade mounting medium with DAPI Vector Laboratories Cat#H-1200
Vectastain ELITE ABC-HRP peroxidase kit Vector Laboratories Cat#PK-6100
Antigen unmasking solution Vector Laboratories Cat#H-3300
Bloxall Vector Laboratories Cat#SP-6000
ImmPACTTM DAB Vector Laboratories Cat#SK-4105
Methyl Greene Vector Laboratories Cat#H-3402
Tris(hydroxymethyl)aminomethane (Tris) Invitrogen Cat#15504-020
Lipofectamine 2000 Invitrogen Cat#11668019
ER retrieval solution pH 6.0 BOND Novocastra Leica Cat#RE7113-CE
Bond Polymer Refine Red detection kit Leica Biosystems Cat#DS9390
Actemra (Tocilizumab) Genentech Cat#NDC 50242135-01
Tiplaxtinin Axon Medchem Cat#Axon1383
4–15% Mini-Protean® TGXTM Precast Protein gels BIO-RAD Cat#456-1084
siLentFectTMLipid Reagent for RNAi,0.5 ml BIO-RAD Cat#1703360
Ruxolitinib Selleckchem Cat#S1378
0.45 μM syringe filters VWR International Cat#28145-479
SB203580 Cell Signaling Cat#5633
Cytoseal XYL Richard-Allan Scientific Cat#8312-4
EasySepTM Human Monocyte Enrichment Kit StemCell Cat#19059
Odyssey Blocking Buffer (PBS) LI-COR Cat#927-40000
Proteinase K, recombinant PCR grade Roche Cat#03115828001
Fetal Bovine Serum (Tetracycline-free) Omega Scientific Cat#FB-15
Hema 3 stain set for Wright-Giemsa stain Protocol Cat#123–869
MycoAlert Mycoplasma detection kit Lonza LT07-118
Critical Commercial Assays
Human IL-12/IL-23 p40 DuoSet, 5 Plate R&D Systems Cat#DY1240-05
Human IL-10 DuoSet,5 Plate R&D Systems Cat#DY217B-05
Human IL-6 DuoSet, 15 Plate R&D Systems Cat#DY206
Mouse IL-10 DuoSet ELISA R&D Systems Cat#DY417-05
Proteome Profiler Human Phospho-Kinase Array Kit R&D Systems Cat#ARY003B
EndoLISA® ELISA-based Endotoxin Detection Assay Hyglos Cat#609033
SuperScript® III First-Strand Synthesis System Invitrogen Cat#18080-051
Taqman IL-6 assay 4331182 Applied Biosystems Cat#Hs00985639_m1
Taqman GAPDH assay 4331182 Applied Biosystems Cat#Hs03929097_g1
TaqMan® Universal Master Mix II, no UNG Applied Biosystems Cat#4440040
Taqman ACTB assay 4331182 Applied Biosystems Cat#Hs99999903_m1
Taqman 18S assay 4453320 Applied Biosystems Cat#Hs99999901_s1
Deposited Data
Experimental Models: Cell Lines
Human Embryonic Kidney 293 cells ATCC Cat#CRL-1573
HT-1080 [HT1080] ATCC CCL-121TM ATCC Cat#CCL-121
A549 Lieber et al., 1976 N/A
Experimental Models: Organisms/Strains
Rag1−/− PAI-1−/− and Rag1−/− PAI-1+/+ immunodeficient female and male mice were obtained by mating PAI-1- deficient mice (PAI-1−/−) and their corresponding wild- type mice (PAI-1+/+) on a mixed genetic background of 87% C57BL/6 and 13% 129 strain [25] with Rag-1- deficient mice (Rag-1−/−: B6; 129 s-Rag-1tm/Mom/J) [26]. Carmeliet et al., 1993
Bajou et al., 2008 		N/A
Oligonucleotides
ON-TARGET plus Set of 4 siRNA MAPK14 Dharmacon J-003512-20
ON-TARGET plus Set of 4 siRNA MAPK14 Dharmacon J-003512-20
ON-TARGET plus Set of 4 siRNA MAPK14 Dharmacon J-003512-20
ON-TARGET plus Set of 4 siRNA MAPK14 Dharmacon J-003512-20
ON-TARGET plus Set of 4 siRNA NF-κB p65 Dharmacon J-003533-06
ON-TARGET plus Set of 4 siRNA NF-κB p65 Dharmacon J-003533-06
ON-TARGET plus Set of 4 siRNA NF-κB p65 Dharmacon J-003533-06
ON-TARGET plus Set of 4 siRNA NF-κB p65 Dharmacon J-003533-06
ON-TARGET plus Non-targeting control Dharmacon D-001810-10-05
shPAI-1 5′-
CCGGCAGACAGTTTCAGGCTGACTTCTCGAGAAGTCAGCC
TGAAACTGTCTGTTTTT-3′		 TRCN0000052271
shPAI-2 5′-
AATTAAAAACAGACAGTTTCAGGCTGACTTCTCGAGAAGT
CAGCCTGAAACTGTCTG-3′		 TRCN0000052271
Scramble 1 5′-
CCGGAATTCTCCGAACGTGTCACGTCTCGAGACGT		 N/A
GACACGTTCGGAGAATTTTTTT-3′
Scramble 2 5′-
AATTAAAAAAATTCTCCGAACGTGTCACGTCTCGAGACGTG
ACACGTTCGGAGAATT-3′		 N/A
Recombinant DNA
Tet-pLKO-puro lentiviral vector Wee et al., 2008; Wiederschain et al., 2009 Addgene
Cat#21915
psPAX2 Gift from Didier Trono lab Addgene Cat#12260
pMD2.G Gift from Didier Trono lab Addgene Cat#12259
Software and Algorithms
Other