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 |