KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Immunoblotting: Rabbit monoclonal anti-CD9 | Abcam | Cat# ab92726; RRID: AB_10561589 |
| Immunoblotting: Rabbit polyclonal anti-Calnexin | Abcam | Cat# ab10286; RRID: AB_2069009 |
| Immunoblotting: Mouse monoclonal anti-GM130 | BD Biosciences | Cat# 610823; RRID: AB_398142 |
| Immunoblotting: Rabbit monoclonal anti-Flotillin-1 | Cell Signaling Technology | Cat# 18634; RRID: AB_2773040 |
| Immunoblotting: Mouse monoclonal anti-Alix | Santa Cruz Biotechnology | Cat# sc-53540; RRID: AB_673819 |
| Immunoblotting: Rat monoclonal anti-IL-4 | Abcam | Cat# ab11524; RRID: AB_298129 |
| Immunoblotting: rabbit anti-Rat IgG (H+L) Secondary Antibody, HRP | Thermo Fisher Scientific | Cat# 61–9520; RRID: AB_2533945 |
| Immunoblotting: mouse IgG kappa binding protein (m-IgGκ BP)-HRP | Santa Cruz Biotechnology | Cat# sc-516102; RRID: AB_2687626 |
| Immunoblotting: F(ab)2-Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, HRP | Thermo Fisher Scientific | Cat# A10547; RRID: AB_2534046 |
| Flow Cytometry: Biotin anti-mouse/human CD45R/B220 antibody | BioLegend | Cat# 103204; RRID: AB_312989 |
| Flow Cytometry: Biotin anti-mouse CD4 antibody | Biolegend | Cat# 100508; RRID: AB_312711 |
| Flow Cytometry: Biotin anti-mouse CD8a antibody | Biolegend | Cat# 100704; RRID: AB_312743 |
| Flow Cytometry: Brilliant Violet 421 anti-mouse CD16/32 antibody | Biolegend | Cat# 101332; RRID: AB_2650889 |
| Flow Cytometry: Biotin anti-mouse Ly-6G/Ly-6C (Gr-1) antibody | Biolegend | Cat# 108404; RRID: AB_313369 |
| Flow Cytometry: PE/Cy7 anti-mouse CD150 (SLAM) antibody | Biolegend | Cat# 115914; RRID: AB_439797 |
| Flow Cytometry: Biotin anti-mouse TER-119/Erythroid Cells antibody | Biolegend | Cat# 116204; RRID: AB_313705 |
| Flow Cytometry: Brilliant Violet 510 anti-mouse CD41 antibody | Biolegend | Cat# 133923; RRID: AB_2564013 |
| Flow Cytometry: Biotin anti-mouse CD127 (IL-7Rα) antibody | Biolegend | Cat# 135006; RRID: AB_2126118 |
| Flow Cytometry: PE anti-mouse CD115 (CSF-1R) antibody | Biolegend | Cat# 135505; RRID: AB_1937254 |
| Flow Cytometry: FITC anti-mouse Ly-6C antibody | Biolegend | Cat# 128006; RRID: AB_1186135 |
| Flow Cytometry: PerCP/Cyanine5.5 anti-mouse/human CD11b antibody | Biolegend | Cat# 101228; RRID: AB_893232 |
| Flow Cytometry: APC anti-mouse CD45 antibody | Biolegend | Cat# 103112; RRID: AB_312977 |
| Flow Cytometry: c-Kit Monoclonal Antibody (2B8), APC-Cyanine7 | Thermo Fisher Scientific | Cat# A15423; RRID: AB_2534436 |
| Flow Cytometry: CD34 Monoclonal Antibody (RAM34), FITC | Thermo Fisher Scientific | Cat# 11-0341-85; RRID: AB_465022 |
| Flow Cytometry: Ly-6A/E (Sca-1) Monoclonal Antibody (D7), PE | Thermo Fisher Scientific | Cat# 12-5981-83; RRID: AB_466087 |
| Flow Cytometry: CD48 Monoclonal Antibody (HM48-1), APC | Thermo Fisher Scientific | Cat# 17-0481-82; RRID: AB_469408 |
| Flow Cytometry: CD135 (Flt3) Monoclonal Antibody (A2F10), PerCP-eFluor 710 | Thermo Fisher Scientific | Cat# 46-1351-82; RRID: AB_10733393 |
| Flow Cytometry: APC Rat Anti-Mouse TNF (MP6-XT22) | BD Biosciences | Cat# 554420; RRID: AB_398553 |
| Donkey anti-Rat IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 | Thermo Fisher Scientific | Cat# A-21208; RRID: AB_2535794 |
| Anti-Mouse Macrophages / Monocytes Purified (Clone MOMA-2) (rat IgG2b) | Cedarlane | Cat# CL89154; RRID: AB_10086520 |
| Rat anti-mouse CD206 | Bio-Rad Laboratories | Cat# MCA2235; RRID: AB_324622 |
| TruStain FcX Antibody | Biolegend | Cat# 101320; RRID: AB_1574975 |
| BV786 Streptavidin | BD Biosciences | Cat# 563858 |
| CD14 MicroBeads, human | Miltenyi Biotec | Cat#130-118-906; RRID: AB_2665482 |
| Anti-F4/80 MicroBeads, mouse | Miltenyi Biotec | Cat#130-110444 |
| Anti-APC MicroBeads, mouse | Miltenyi Biotec | Cat# 130-090-855; RRID: AB_244367 |
| Chemicals, Peptides and Recombinant Proteins | ||
| DiR (DiIC18(7) (1,1’-Dioctadecyl-3,3,3′,3′- Tetramethylindotricarbocyanine Iodide)) |
Invitrogen | Cat# D12731 |
| Fast SYBR Green Master Mix | Applied Biosystems | Cat# 4385614 |
| RBC Lysis Buffer (10X) | BioLegend | Cat# 420301 |
| iScript Reverse Transcription Supermix | Bio-Rad Laboratories | Cat# 1708841 |
| 10% Mini-PROTEAN TGX Gels | Bio-Rad Laboratories | Cat# 4561034 |
| 4x Laemmli Sample Buffer | Bio-Rad Laboratories | Cat# 1610747 |
| RIPA buffer (10x) | Cell Signaling Technology | Cat# 9806 |
| Amersham ECL Prime Western Blotting Detection Reagent | GE Healthcare | Cat# RPN2232 |
| Penicillin-Streptomycin | GIBCO | Cat# 15140122 |
| L-Glutamine | GIBCO | Cat# 25030-081 |
| Recombinant Murine IL-4 | Peprotech | Cat# 214-14 |
| Recombinant Murine IL-4 | Abcam | Cat# ab9729 |
| Recombinant Murine M-CSF | Peprotech | Cat# 315-02 |
| Recombinant Human M-CSF | Peprotech | Cat# 300–25 |
| Animal-Free Recombinant Murine TPO | Peprotech | Cat# AF-315-14 |
| Animal-Free Recombinant Murine SCF | Peprotech | Cat# AF-250-03 |
| Poly (vinyl alcohol) | Sigma-Aldrich | Cat# P8136 |
| miRCURY LNA RT Kit | QIAGEN | Cat# 339340 |
| miRCURY LNA SYBR Green PCR Kit | QIAGEN | Cat# 339347 |
| RD Western Diet | Research Diets | Cat# D12079B |
| OptiPrep density gradient medium | Sigma-Aldrich | Cat# D1556-250ML |
| Oil Red O | Sigma-Aldrich | Cat# O1391 |
| Mayer’s Hematoxylin | Thermo Fisher Scientific | Cat# 72804 |
| BLOXALL Blocking Solution | Vector Laboratories | Cat# SP-6000 |
| ImmPACT NovaRED Peroxidase (HRP) Substrate | Vector Laboratories | Cat# SK-4805 |
| D-Glucose solution | Sigma-Aldrich | Cat# G8769-100ML |
| Lipopolysaccharides from Escherichia coli O55:B5 | Sigma-Aldrich | Cat# L2880 |
| Tissue-Tek O.C.T Compound | Sakura FineTek | Cat# 4583 |
| Sucrose, 20% Sterile Solution | VWR | Cat# E543-100ML |
| 10X Tris-EDTA, pH 7.4 | Fisher Scientific | Cat# BP24771 |
| CountBright Absolute Counting Beads | Thermo Fisher Scientific | Cat# C36950 |
| RNase A/T1 Mix | Thermo Fisher Scientific | Cat# EN0551 |
| jetPRIME transfection reagent | Polyplus | Cat# 114-07 |
| VECTASHIELD Antifade Mounting Medium with DAPI | Vector Laboratories | Cat# H-1200 |
| Seahorse XF base medium | Agilent | Cat# 103335-100 |
| Seahorse XF 100 mM pyruvate solution | Agilent | Cat# 103578–100 |
| Novex 6% TBE Gels | Thermo Fisher | Cat# EC6265BOX |
| TruSeq SR Cluster Kit v3 - cBot - HS | Illumina | Cat# GD-401-3001 |
| TruSeq SBS Kit v3 - HS | Illumina | Cat# FC-401-3002 |
| T4 DNA Ligase | NEB | Cat# M0202 |
| Trypsin-EDTA (0.05%) | GIBCO | Cat# 25300054 |
| Opti-MEM | GIBCO | Cat# 31985–062 |
| Glutamax | GIBCO | Cat# 35050061 |
| Ficoll-Plaque Plus | GE Healthcare | Cat#17-1440-02 |
| Critical Commercial Assays | ||
| miRNeasy Mini Kit | QIAGEN | Cat# 217004 |
| Pierce BCA Protein Assay Kit | Thermo Fisher Scientific | Cat# 23225 |
| Quant-iT RiboGreen RNA Assay Kit | Thermo Fisher Scientific | Cat# R11490 |
| Slide-A-Lyzer MINI Dialysis Device, 10K MWCO | Thermo Fisher Scientific | Cat# 88404 |
| LS Columns | Miltenyi Biotec | Cat# 130-042-401 |
| Subcloning Efficiency DH5a Competent Cells | Thermo Fisher Scientific | Cat# 18265017 |
| Zyppy Plasmid Miniprep | Zymo Research | Cat# D4036 |
| Seahorse XFe24 FluxPaks | Agilent | Cat# 102340-100 |
| Seahorse XF Cell Mito Stress Test Kit | Agilent | Cat# 103015-100 |
| BioAnalyzer High Sensitivity DNA Analysis | Agilent | Cat# 5067-4626 |
| NEXTFLEX Small RNA Sequencing kit for Illumina Platforms | Perkin Elmer | Cat# NOVA-5132-06 |
| Fixation/Permeabilization Solution Kit | BD Biosciences | Cat# 554714 |
| Qubit Protein Assay Kit | Thermo Fisher Scientific | Cat# Q33211 |
| PKH26 Red Fluorescent cell Linker kit | Sigma | Cat# PKH26GL-1KT |
| Exosome Spin Columns | Invitrogen | Cat# 448449 |
| Seahorse XFe24 Cell Culture Microplates | Agilent | Cat# 100777-004 |
| Vectastain Elite ABC Kit, Peroxidase (Rat IgG) | Vector Laboratories | Cat# PK-6104 |
| nCounter® Low RNA Input Kit | Nanostring Technologies | Cat# LOW-RNA-48 |
| Autoimmune Profiling Panel | Nanostring Technologies | Cat# XT-CSO-MAIPI1-12 |
| V-Plex Mouse Custom Cytokine Kit MCP-1 | Meso Scale Discovery | Cat# K152A0H-1 |
| MethoCult GF | StemCell Technologies | Cat#GF M3434 |
| Deposited Data | ||
| miRNA-Seq | This paper | exRNA atlas: EXRNA-KJENS1DIAB, https://exrna-atlas.org/exat/datasets/EXR-KJENS1Lz9cll-AN |
| Experimental Models: Cell Lines | ||
| iBMDM-NFKB-Cas9 Cells | Covarrubias et al., 2017 | N/A |
| Experimental Models: Organisms/Strains | ||
| Mouse: B6.129P2-Apoetm1Unc/J | Jackson Laboratories | JAX:002052 |
| Mouse: C57BL6/J | Jackson Laboratories | JAX:000664 |
| Oligonucleotides | ||
| hsa-miR-146b-5p miRCURY LNA miRNA PCR Assay | QIAGEN | Cat# YP00204553 |
| hsa-miR-16-5p miRCURY LNA miRNA PCR Assay | QIAGEN | Cat# YP00205702 |
| hsa-miR-21-5p miRCURY LNA miRNA PCR Assay | QIAGEN | Cat# YP00204230 |
| hsa-miR-99a-5p miRCURY LNA miRNA PCR Assay | QIAGEN | Cat# YP00204521 |
| mmu-miR-378a-3p miRCURY LNA miRNA PCR Assay | QIAGEN | Cat# YP00204179 |
| U6 snRNA (hsa, mmu) miRCURY LNA miRNA PCR Assay | QIAGEN | Cat# YP00203907 |
| UniSp6 miRCURY LNA miRNA PCR Assay | QIAGEN | Cat# YP00203954 |
| 5′-IRD 800-labeled miR-146b | IDT | N/A |
| Primers for qRT-PCR and plasmid construction: see Table S1 | This paper | N/A |
| Recombinant DNA | ||
| psPAX2 | Addgene | RRID: Addgene_12260 |
| pMD2.G | Addgene | RRID: Addgene_12259 |
| Software and Algorithms | ||
| FlowJo | FlowJo | https://www.flowjo.com/ |
| ImageJ | NIH | https://imagej.nih.gov/ij/ |
| Photoshop CC | Adobe | https://www.adobe.com/products/photoshop.html |
| Prism 7 | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| 2100 Expert Bioanalyzer | Agilent | https://www.agilent.com/en/product/automated-electrophoresis/bioanalyzer-systems/bioanalyzer-software/2100-expert-software-228259 |
| XFe Wave software | Agilent | https://www.agilent.com/en/products/cell-analysis/cell-analysis-software/data-analysis/wave-desktop-2–6 |
| NTA 3.2 | Malvern Panalytical | https://www.malvernpanalytical.com/en/support/product-support/software/NanoSight-NTA-software-update-v3–2 |
| NIS Elements BR 4.3 | Nikon | https://www.nikon.com/products/microscope-solutions/support/download/software/imgsfw/nis-br_v4300164.htm |
| nSolver Analysis Software | Nanostring Technologies | https://www.nanostring.com/products/analysis-software/nsolver |