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. Author manuscript; available in PMC: 2022 Oct 11.
Published in final edited form as: Cancer Cell. 2021 Sep 2;39(10):1361–1374.e9. doi: 10.1016/j.ccell.2021.08.005

KEY RESOURCES TABLE

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Mouse monoclonal anti-mouse iNOS BD Biosciences Cat #610431
Goat polyclonal anti-mouse CD206 R&D Systems Cat #AF2535
Mouse monoclonal anti-β-actin Santa Cruz Biotechnology Cat #sc-47778
Rabbit monoclonal anti-NFκB p65 Cell Signaling Technology Cat #8242
Rabbit monoclonal anti-Phospho-NFκB p65 (Ser536) (93H1) Cell Signaling Technology Cat #3033
Rabbit monoclonal anti-STAT1 Cell Signaling Technology Cat #14994
Rabbit monoclonal anti-Phospho-STAT1 (Tyr701) (58D6) Cell Signaling Technology Cat #9167
Mouse monoclonal anti-GAPDH Santa Cruz Biotechnology Cat #sc-32233
IRDye 800CW Goat anti-Mouse IgG Secondary Antibody LI-COR Cat #926-32210
IRDye 800CW Donkey anti-Goat IgG Secondary Antibody LI-COR Cat #926-32214
Goat polyclonal anti-Neutrophil Elastase Santa Cruz Biotechnology Cat #sc-9521
BV785™ anti-mouse CD45 Antibody BioLegend Cat #103149
Alexa Fluor® 647 anti-mouse CD3 Antibody BioLegend Cat #100209
APC/Cy7 anti-mouse CD3 Antibody BioLegend Cat #100221
APC anti-mouse/human CD11b Antibody BioLegend Cat #101212
FITC anti-mouse CD4 Antibody BioLegend Cat #100510
PE anti-mouse CD8a Antibody BioLegend Cat #100708
APC/Cy7 anti-mouse CD8a Antibody BioLegend Cat #100714
PE/Cy5 anti-mouse CD19 Antibody BioLegend Cat #115509
PE/Cy7 anti-mouse CD11c Antibody BioLegend Cat #117318
APC/Cy7 anti-mouse CD11c Antibody BioLegend Cat #117324
APC/Cy7 anti-mouse Ly6C Antibody BioLegend Cat #128026
FITC anti-mouse Ly6G Antibody BioLegend Cat #127605
PerCP/Cy5.5 anti-mouse F4/80 Antibody BioLegend Cat #123127
Alexa Fluor® 488 anti-mouse F4/80 Antibody BioLegend Cat #123120
APC anti-mouse CD326 (EpCAM) Antibody BioLegend Cat #118214
PE/Cy7 anti-mouse CD40 Antibody BioLegend Cat #124621
FITC anti-mouse CD206 (MMR) Antibody BioLegend Cat #141704
FITC anti-mouse CD69 Antibody BioLegend Cat #104505
PE anti-mouse CD107a (LAMP-1) Antibody BioLegend Cat #121612
FITC anti-mouse CD279 (PD-1) Antibody BioLegend Cat #135213
PerCP/Cy5.5 anti-mouse/human CD44 Antibody BioLegend Cat #103032
APC anti-mouse CD62L Antibody BioLegend Cat #104412
APC anti-mouse H-2Kb bound to SIINFEKL Antibody BioLegend Cat #141605
Alexa Fluor® 647 anti-human CD326 (EpCAM) Antibody BioLegend Cat #324212
BV510™ anti-human CD45 Antibody BioLegend Cat #368525
APC anti-human CD68 Antibody BioLegend Cat #333810
PE Rat Anti-CD11b Clone M1/70 (RUO) BD Biosciences Cat #557397
CD335 (NKp46) Monoclonal Antibody (29A1.4), eFluor 450 Invitrogen Cat #48335180
iNOS Monoclonal Antibody (CXNFT), PE Invitrogen Cat #12592082
CD103 (Integrin alpha E) Monoclonal Antibody (2E7), FITC Invitrogen Cat #11103182
PE anti-mouse CD40 Antibody BioLegend Cat #124610
FITC anti-mouse CD8a Antibody BioLegend Cat #100706
Rat monoclonal anti-PyMT antigen Abcam Cat #ab15085
Alexa Fluor 488 goat anti-Rat IgG secondary antibody Invitrogen Cat #A11006
Alexa Fluor® 647 anti-mouse CD4 Antibody BioLegend Cat #100424
Rat monoclonal anti-Mouse F4/80 Bio-Rad Cat #MCA497R
Rabbit anti-Phospho-NFkB p65 (Ser276) Antibody Invitrogen Cat #PA5-37718
Rabbit polyclonal anti-CFP Bio-Rad Cat #AHP2986
Alexa Fluor 488 goat anti-rabbit IgG secondary antibody Invitrogen Cat #A11070
Goat polyclonal anti-Mouse IL-12 R&D Systems Cat #AF-419-NA
Rat monoclonal anti-Mouse TNF-alpha R&D Systems Cat #MAB4101
Goat polyclonal anti-Mouse CXCL9/MIG R&D Systems Cat #AF-492-NA
InVivoMAb anti-mouse CD8α BioXCell Cat #BE0004-1
InVivoMAb anti-mouse CD4 BioXCell Cat #BE0003-1
InVivoMAb anti-mouse CSF1R (CD115) BioXCell Cat #BE0213
InVivoMAb anti-mouse CSF1 BioXCell Cat #BE0204
InVivoPlus anti-mouse PD1 BioXCell Cat #BP0273
Biological Samples
Metastatic pleural effusions from breast cancer patients New York University IRB #i17-01382
Chemicals, Peptides, and Recombinant Proteins
Matrigel Corning Cat #356231
Human M-CSF ProSpec Cat #CYT-308
L-glutamine Gibco Cat #25030081
Sodium pyruvate Gibco Cat #11360070
2-mercaptoethanol Gibco Cat #31350010
B27 supplement Gibco Cat #17504044
Human EGF ProSpec Cat #CYT-217
Insulin Gibco Cat #12585014
Collagenase/hyaluronidase STEMCELL Technologies Cat #07912
DNase I Roche Cat #4716728001
Dispase STEMCELL Technologies Cat #07913
Collagenase D Sigma Cat #11088866001
DNase I Sigma Cat #045362820
Liberase DL Sigma Cat #05466202001
TrypLE Express Enzyme Gibco Cat #12605010
Mouse M-CSF ProSpec Cat #CYT-439
Fibronectin Sigma Aldrich Cat #F1141
CellTracker™ Deep Red Dye Invitrogen Cat #C34565
CellTracker™ Green CMFDA Dye Invitrogen Cat #C7025
LPS Sigma Aldrich Cat #L4391
MPLA for in vitro experiments InvivoGen Cat #tlrl-mpls
MPLA for in vivo experiments InvivoGen Cat #vac-mpls
PolyI:C InvivoGen Cat #tlrl-picw
Mouse IFNγ R&D Systems Cat #485-MI/CF
Human IFNγ R&D Systems Cat #285-IF/CF
TMP195 MedChemExpress Cat #HY-18361
IPI-549 MedChemExpress Cat #HY-100716
PLX3397 (Pexidartinib) MedChemExpress Cat #HY-16749
L-NIL (N6-(1-Iminoethyl)-L-lysine hydrochloride) TOCRIS Cat #1139
Creatine Selleckchem Cat #S5588
JSH-23 Selleckchem Cat #S7351
SR11302 TOCRIS Cat #2476
CellTiter 96® AQueous One Solution reagent Promega Cat #G3582
PowerUp™ SYBR™ Green Master Mix Applied Biosystems Cat #A25780
Taqman™ Universal Master Mix II, no UNG Applied Biosystems Cat #4440040
RIPA lysis buffer Thermo Fisher Scientific Cat #89990
Protease and phosphatase inhibitor Thermo Fisher Scientific Cat #78440
Cisplatin MBL Cat #JM-1550-1000
Sodium citrate solution Sigma Cat #C3821
ABTS Substrate Solution Thermo Fisher Scientific Cat #37615
Fc receptor blocker Innovex Cat #NB309
Goat serum Dako Cat #X0907
Mounting media Electron Microscopy Sciences Cat #17985-16
OVA-Q4H7 peptide AnaSpec Cat #AS-64405
Critical Commercial Assays
RNeasy Mini kit Qiagen Cat #74104
TaqMan™ Reverse Transcription Reagents Invitrogen Cat #N8080234
Cell Death Detection ELISA Kit Roche Cat #11774425001
Proteome Profiler Mouse XL Cytokine Array Kit R&D Systems Cat #ARY028
Mouse CXCL9/MIG DuoSet ELISA R&D Systems Cat #DY492
Mouse CCL5/RANTES DuoSet ELISA R&D Systems Cat #DY478
DuoSet ELISA Ancillary Reagent Kit 2 R&D Systems Cat #DY008
TruSeq Stranded mRNA Library Prep Kit Illumina Cat #20020594
Fixation/Permeabilization Solution Kit BD Biosciences Cat #554714
Comprehensive Chemistry test of serum IDEXX BioAnalytics Cat #6006
CD8a+ T Cell Isolation Kit, mouse Miltenyi Biotec Cat #130-104-075
Deposited Data
RNA-seq data This paper GEO: GSE146211
Experimental Models: Cell Lines
Mouse: 4T1 cells ATCC Cat #CRL-2539
Mouse: ID8-p53−/− cells Walton et al., 2016 N/A
Experimental Models: Organisms/strains
MMTV-PyMT mice (on C57BL/6 background) Jackson Laboratory Cat #022974
MMTV-PyMT mice (on FVB/N background) Jackson Laboratory Cat #002374
MMTV-PyMT-chOVA mice (on C57BL/6 background) Engelhardt et al., 2012 N/A
ACTB-ECFP mice Jackson Laboratory Cat #004218
OT1 mice Jackson Laboratory Cat #003831
Tlr4 KO mice (on C57BL/6 background) Jackson Laboratory Cat #029015
MMTV-PyMT; ACTB-ECFP mice (on C57BL/6 background) This paper N/A
Oligonucleotides
Primers for human CD40, ACTB, NOS2, TNF, MRC1, IL12B, IL10, mouse Stat1, Stat2, Ifit1, Irgm2, Gbp2, Cxcl9, Igfbp3, Col4a1, Actb, Tnf, Il12b, Il10, Nos2, Mrc1, Arg1, see Table S2 This paper N/A
Taqman Probe for mouse Tbp Thermo Fisher Scientific Mm00446973-m1
Taqman Probe for mouse Cd86 Thermo Fisher Scientific Mm00444543-m1
Taqman Probe for mouse H2-Q2 Thermo Fisher Scientific Mm04213368-g1
Software and Algorithms
STAR Dobin et al., 2012 N/A
FeatureCounts Liao et al., 2013 N/A
DESeq2 Love et al., 2014 N/A
Other
CD326 (EpCAM) microbeads, human Miltenyi Biotec Cat #130-061-101
CD11b MicroBeads, human and mouse Miltenyi Biotec Cat #130-049-601
24-well glass bottom plate MatTek Cat #P24G-1.5-13-F
PVDF membrane Bio-Rad Cat #1620177
Relfex 7 mm wound clips CellPoint Scientific Cat #203-1000
96-well Enzyme ImmunoAssay/Radio Immuno-Assay (EIA/RIA) plates Costar Cat #3590
Not TC-treated culture dishes Corning Cat #430597
Cell culture insert for 24-well Plate with 1.0 μm Transparent PET Membrane Corning Cat #353104
Rodent Chow 5053 With PLX3397 Diet Research Diets, Inc. N/A
Rodent Chow 5053 With IPI-549 Diet Research Diets, Inc. N/A