| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-CCL2 antibody (anti mouse) | BioXcell | #BE0185 |
| Isotype control antibody | BioXcell | #BE0091 |
| Anti-LGALS3 (anti mouse) | Cedarlane | #CL8942AP |
| Anti-ACTA2 (anti mouse) | Sigma | #F3777 |
| Anti-PDGFβR (anti mouse) | Abcam | #ab32570 |
| Anti-Ki-67 (anti mouse) | Abcam | #Ab15580 |
| Anti-CD68 (anti mouse) | ThermoFisher | #MCA1957 |
| Cy3-conjugated AffiniPure Goat Anti-Rat IgG (H+L) | Jackson ImmunoResearch | #112-165-071 |
| Cy5-conjugated AffiniPure Goat Anti-Rabbit IgG (H+L) | Jackson ImmunoResearch | #111-175-144 |
| Cy3-conjugated AffiniPure Goat Anti-Rabbit IgG (H+L) | Jackson ImmunoResearch | #111-165-003 |
| Anti-CD68 (anti human) | Dako | #M0876 |
| Cy3-conjugated AffiniPure Goat Anti-Mouse | Invitrogen | #A10521 |
| Fc-receptor blocking antibody | Ebioscience | # 14-0161-85 |
| Anti-CD45.2 (anti mouse) | BD Biosciences | #560694 |
| Anti-CD19 (anti mouse) | BioLegend | #152404 |
| Anti-CD3e (anti mouse) | BD Biosciences | #553062 |
| Anti-CD115 (anti mouse) | BioLegend | #15-0452-82 |
| Anti-Ly6C (anti mouse) | BioLegend | #128012 |
| Anti-Ly6G (anti mouse) | BioLegend | #127608 |
| Anti-CD45R (anti mouse) | ThermoFisher | #15-0452-82 |
| Fc-receptor blocking antibody | Ebioscience | #14-0161-86 |
| CD45+ magnetic selection beads (anti mouse) | Miltenyi Biotec | #130-052-301 |
| Anti-CD45 (anti mouse) | BD Biosciences | #557659 |
| Anti-CD11b (anti mouse) | Biolegend | #101228 |
| Anti-F4/80 (anti mouse) | Biolegend | #123110 |
| Anti-CD64 (anti mouse) | Biolegend | #139314 |
| MHCII (anti mouse) | ThermoFisher | #17-5321-82 |
| TotalSeq-B anti-mouse Hashtag antibodies no. 1-9 (anti mouse) | BioLegend | #B0301-B0309 |
| Anti-F4/80 Percp Cy5.5 (anti mouse) | BioLegend | #123128 |
| Anti-Ly6G BV711 (anti mouse) | BioLegend | #127643 |
| Anti-CD11b (anti mouse) | Biolegend | #101242 |
| Anti-Ly6C (anti mouse) | Biolegend | #128033 |
| Anti-CD14 (anti human) | Biolegend | #325619 |
| Anti-CD45 (anti human) | Miltenyi Biotec | #130-113-117 |
| Anti-CD14 Microbeads (anti human) | Miltenyi Biotec | #130-050-201 |
| Anti-CCL2 (anti mouse) | Invitrogen | #16-7096-85 |
| Isotype control | Invitrogen | #16-4888-85 |
| Anti-CCL2 (anti mouse) | Invitrogen | #16-7096-81 |
| Isotype control | Invitrogen | #16-4888-81 |
| Anti-CD16/32 antibody (anti mouse) | eBioscience | #15246827 |
| Anti-CD11b (anti mouse) | BioLegend | #101228 |
| Anti-CD64 (anti mouse) | BioLegend | #139304 |
| Anti-F4/80 (anti mouse) | BioLegend | #123132 |
| Anti-CD45 (anti mouse) | BD Biosciences | #557659 |
| Anti-CD45 (anti mouse) | BioLegend | #103132 |
| Anti-CD64 (anti mouse) | BioLegend | #139313 |
| Anti-F4/80 (anti mouse) | BioLegend | #123132 |
| Anti-CD11b (anti mouse) | Biolegend | #101241 |
| Anti-CD11c (anti mouse) | BioLegend | #117323 |
| Anti-Lyve-1 (anti mouse) | ThermoFisher | #50-0443-82 |
| Anti-CD11b (anti mouse) | BioLegend | #101236 |
| Anti-MHCII (anti mouse) | BioLegend | #107636 |
| Anti-CD206 (anti mouse) | BioLegend | #141721 |
| Anti-DC80 (anti mouse) | BioLegend | #104732 |
| Anti-CD204 (anti mouse) | BD Biosciences | #748088 |
| Anti-Tim4 (anti mouse) | BioLegend | #141721 |
| Anti-Mertk (anti mouse) | BioLegend | #151506 |
| Anti-CD64 (anti mouse) | BioLegend | #139320 |
| Anti-CCL2 (anti mouse) | Invitrogen | #16-7096-81 |
| Isotype control | Invitrogen | #16-4888-81 |
| Anti-CD11c (anti mouse) | BioLegend | #117318 |
| Anti-F4/80 (anti mouse) | BioLegend | #123128 |
| Anti-CD36 (anti mouse) | BD Biosciences | #56-0362-82 |
| Anti-CD68 (anti human) | Thermo | #4-0688-82 |
| Anti-aSMA (anti human) | Zytomed | #MOB001 |
| Anti-F4/80 (anti mouse) | eBioscience | #15287387 |
| Anti-CD11c (anti mouse) | ThermoFisher Scientific | #14-0114-82 |
| Goat anti rat Alexa Fluor 555 | Invitrogen | #A-21434 |
| Goat anti Armenian hamster Alexa Fluor 647 | Invitrogen | #A78967 |
| Anti-GAPDH antibody | Abcam | #9484 |
| Anti-ACTA2 biotin-conjugated antibody | Abcam | #ab125057 |
| Streptavidin AlexaFluor 647 | Biolegend | #405237 |
| Anti-MCP1 | Abcam | #ab25124 |
| Anti-MIF | Abcam | #ab7207 |
| Anti-CD31 | Abcam | # ab222783 |
| Anti-CD36 | Abcam | # ab124515 |
| Anti-FOLR2 | Abcam | # ab228643 |
| Chemicals, peptides, and recombinant proteins | ||
| Tamoxifen | Sigma-Aldrich | #10540-29-1 |
| Corn Oil | Sigma-Aldrich | # C8267 |
| Western Diet | Sniff EF | #D12079 |
| SMC medium | PELO Biotech | #PB-MH-200-2190 |
| RPMI1640 | Sigma Aldrich | R8758 |
| FBS | Biosell | #S 0613 |
| Penicillin-Streptomycin | Sigma Aldrich | #P4333 |
| b-Mercaptoethanol | Sigma Aldrich | #M3148 |
| b-Estradiol | Sigma Aldrich | #50-28-2 |
| M-CSF | Immunotools | #11343115 |
| Accutase | Sigma Aldrich | # A6964 |
| CellTrackerTM Red CMTPX | Invitrogen | # C34552 |
| CCL2 | Biolegend | # 571406 |
| MIF | Biolegend | # 599406 |
| Saponin | Roth | #4185.1 |
| PBS (10X) | Gibco | #70011-036 |
| PBS (1X) | Gibco | #14190-094 |
| Hoechst 33342 | Invitrogen | # H3570 |
| ApopTag® Red In Situ Apoptosis Detection Kit | Sigma-Aldrich | #S7165 |
| Oil-red-O solution | Sigma | #O1391 |
| Mayer’s hemalaum solution | Roth | #T865.2 |
| Masson Trichrome staining | ScyTek Laboratories | #TRM-1 |
| Sucrose | Sigma-Aldrich | #S1888 |
| Formaldehyde 4% | Microcos GmbH | #50-00-0 |
| Methylene-free formaldehyde solution | Thermos scientific | #28908 |
| Sudan III | Merck | #C.I. 26100 |
| BSA Albumin Fraction V ≥98 %, powdered | Carl Roth | #8076.1 |
| Sytox red dead cell staining | Invitrogen | # S34859 |
| collagenase I | Sigma-Aldrich | #C0130 |
| collagenase XI | Sigma-Aldrich | #C7657 |
| DNase I | Sigma-Aldrich | #D4527 |
| Hyaluronidase | Sigma-Aldrich | #H3506 |
| Sytox green | ThermoFisher | #S34860 |
| Collagenase type 2 | Worthington Biochemical | #LS004174 |
| Elastase | Worthington Biochemical | #LS002292 |
| Collagenase type XI | Sigma-Aldrich | #C7657 |
| DNase type 1 | Sigma-Aldrich | #H3506 |
| Collagenase type 1 | Sigma-Aldrich | #C0130 |
| Hyaluronidase | Sigma-Aldrich | #H3506 |
| Sytox orange | ThermoFisher | #S34861 |
| Sytox blue | ThermoFisher | #S34857 |
| Sytox red | ThermoFisher | #S34859 |
| Liberase | Roche | #5401127006 |
| DNase | Sigma-Aldrich | #D4527 |
| Hyaluronidase | Sigma-Aldrich | #H3506 |
| NEBNext Single Cell / Low Input RNA Kit for Illumina | New England Biolabs | #E6420S |
| Fluorescent dye-based Qubit® ds DNA HS Assay kit | Thermo Fisher Scientific | #Q33230 |
| RLT-Buffer | Qiagen | #79216 |
| b-Mercapto-Ethanol | Thermo | #Sigma M6250 |
| Proteinase K | Life Technologies | #AM2548 |
| DNase I | ThermoFisher | #EN0521 |
| Maxima H-enzyme | ThermoFisher | #EP0753 |
| Maxima H-Buffer | ThermoFisher | #EP0753 |
| dNTPs | ThermoFisher | #R0186 |
| Exonuclease I | New England Biolabs | #M0293L |
| 1X Kapa HS Ready Mix | Roche | #07958935001 |
| DNase/RNase-Free Distilled Water | ThermoFisher | #10977-049 |
| Quant-iT PicoGreen dsDNA Assay Kit | ThermoFisher | #P7581 |
| High-Sensitivity DNA Kit | Agilent | #5067-4627 |
| NEBNext Ultra II FS Library Preparation Kit | New England Biolabs | #E6177S |
| SPRI-select Beads | #B23317 | Beckman Coulter |
| Q5 Master Mix | New England Biolabs | M0544L |
| Ficoll® Paque Plus | Cytiva | #GE17-1440-02 |
| Chromium Next GEM Single Cell 3′reagent kit v3.1 | 10X Genomics | #CG000206 Rev D protocol with reagens |
| RNeasy Mini Kit | Qiagen | #74104 |
| TruSeq Stranded mRNA LP technology kit | Illumina | #20020594 |
| ISO-1 | Merck Millipore (Calbiochem) | #CAS 478336-92-4 |
| dsDNA | InvivoGen | #tlrl-ecdna |
| Non-oxidizable 3S-HMGB1 | HMGBiotech | #HM-132 |
| HSP60 | Enzo | #ADI-SPA-806-F |
| ODN2216 | InVivogen | #tlrl-2216-5 |
| RNeasy Micro Kit | Qiagen | #74004 |
| High Capacity cDNA synthesis kit | Applied Biosystems | #4368814 |
| DMEM VLE | Bio&Sell | #BS.FG1445 |
| Antibiotics-antimycotics | Thermo | #15240062 |
| LDL from human plasma | Invitrogen | #L3482 |
| eFluor proliferation dye | Invitrogen | #65-0840-85 |
| ISO-1 | MedChemExpress | #HY-16692 |
| DMSO | SigmaAldrich | #D2650-5X5ML |
| Fixable viability Dye eFluor780 | eBioscience | #64-0865 |
| Quantitect Primer assay | Qiagen | #249900 |
| Ssoadvanced SYBR green supermix | BioRad | #1725270 |
| EdU | Invitrogen | #A10044 |
| Protease 1 | Roche | #05266688001 |
| Smooth muscle cell growth medium | PromoCell | #C-22062 |
| TNFa | BioLegend | #570102 |
| NuPAGE 4-12% Bis-Tris Gel | Invitrogen | #NP0002 |
| Spectra Multicolor Broad Range Protein Ladder | ThermoFisher | #226634 |
| Recombinant mouse CCL2 | BioLegend | #578404 |
| Trypsin-EDTA (0,25%) | Gibco | #11560626 |
| Ripa Lysis and Exraction Buffer | ThermoFisher | #89900 |
| CellTracker Green | Invitrogen | #C2925 |
| Critical commercial assays | ||
| MIF ELISA | BioLegend | #444107 |
| CCL2 ELISA | IBL international | #BE45241 |
| Cholesterol Kit | Abcam | #Ab65390 |
| CCL19 ELISA | Sigma-Aldrich | RAB0052 |
| CXCL12/SDF-1 alpha | Bio-techne | #DSA00 |
| Peritoneal Macrophage isolation kit | Miltenyi Biotec | #130-110-434 |
| Experimental models: Cell lines | ||
| HCASMCs | PromoCell | #C-12511 |
| Primary murine smooth muscle cell | Cell Biologics | #C57-6080 |
| Jurkat cells | Merck | #88042803 |
| Murine SMCs | Cell Biologics | #PB-A57-6080 |
| Experimental models: Organisms/strains | ||
| ApoE-/- | The Jackson Laboratory | #002052 |
| Myh11cre-ERT2 | The Jackson Laboratory | #019079 |
| Rosa26tdTomato | The Jackson Laboratory | #007914 |
| Ng2DsRed | The Jackson Laboratory | #008241 |
| Ng2Cre | The Jackson Laboratory | #029926 |
| Ccl2RFP-fl/fl | The Jackson Laboratory | #016849 |
| PC-G5-tdT | The Jackson Laboratory | #024477 |
| Cx3cr1-CreER | The Jackson Laboratory | #021160 |
| Cx3cr1GFP/+ | The Jackson Laboratory | #005582 |
| LysM-eGFP | MGI | MGI ID: 2654931 |
| MIFfl/fl | Fingerle-Rowson et al.102 | PMID ID: 12878730 |
| Software and algorithms | ||
| Imaris Software | Bitplane | Version 8.4.1 |
| ZEN Software Black | Zeiss | Version 2.3 |
| ImageJ | FIJI | Version 2.9.0 |
| AxioVision | Zeiss | Version 4.8 |
| FlowJo | BD Biosciences | Version 10 |
| Fastqc | Andrews103 | Version 0.11.8 |
| Cutadapt | Martin104 | Version 1.12 |
| zUMI pipeline | Parekh et al.105 | Version 2.9.4.d |
| STAR | Dobin et al.106 | Version 2.7.3a |
| RSubread | Liao et al.107 | Version 1.32.4 |
| Hisat2 | Kim et al.108 | Version 2.1.0 |
| Feature Counts | Liao et al.109 | Version 1.6.3 |
| DESeq2 | Love et al.110 | Version 1.30.0 |
| DAVID | Huang et al.111,112 | Version 6.8 |
| ClustVis | Metsalu and Vilo113 | Online version |
| Seurat | Stuart et al.114 | Version 3.1.1 |
| SCTransform | Hafemeister and Satija115 | Version 0.2.0 |
| CellRanger | 10X Genomics | Version 6.0.2 |
| Seurat | Stuart et al.114 | Version 4.0.4 |
| SCTransform | Hafemeister and Satija115 | Version 0.3.2 |
| MAST | Finak et al.116 | Version 1.14.0 |
| QuPath | Bankhead et al.117 | Version 0.3.2 |
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