| Reagent/Resource | Reference or Source | Identifier or Catalog Number |
|---|---|---|
| Experimental Models | ||
| HEK 293T cells (H. sapiens) | Forest White’s lab | ATCC CRL‐3216 |
| BV‐2 cells (M. musculus) | Li‐Huei Tsai’s lab | CVCL_0182 |
| AG09173 APOE3 induced‐pluripotent stem cell line (H. sapiens) | Li‐Huei Tsai’s lab | N/A |
| CK‐p25 (M. musculus) | Li‐Huei Tsai’s lab | Stock NO: 005706 |
| 5xFAD (M. musculus) | Jackson laboratories | Stock NO: 34840 |
| Δp35KI (M. musculus) | Li‐Huei Tsai’s lab | Stock NO: 022401 |
| Tau P301S (M. musculus) | Jackson laboratories | Stock NO: 008169 |
| C57BL/6 (M. musculus) | Jackson laboratories | Stock NO: 664 |
| Stbl3 | Thermo Fisher Scientific | C737303 |
| Human AD brain samples | Banner Sun Health Research Institute | N/A |
| Recombinant DNA | ||
| pCMV‐VSV‐G | Richard Hyne’s lab | N/A |
| pUMVC | Richard Hyne’s lab | N/A |
| psPAX2 | Addgene | 12260 |
| pMD2.G | Addgene | 12259 |
| MSCV‐IRES‐puro (MIP) | Richard Hynes’s lab | N/A |
| pINDUCER20 | Addgene | 44012 |
| MIP‐Siglec‐F‐myc | This paper | N/A |
| MIP‐Siglec‐F‐Y538F‐myc | This paper | N/A |
| MIP‐Siglec‐F‐Y561F‐myc | This paper | N/A |
| MIP‐Siglec‐F‐2xY‐>F‐myc | This paper | N/A |
| MIP‐hCD33‐myc | This paper | N/A |
| MIP‐hCD33‐myc | This paper | N/A |
| MIP‐hSiglec‐5‐myc | This paper | N/A |
| MIP‐hSiglec‐5‐2xY‐>F‐myc | This paper | N/A |
| MIP‐hSiglec‐8‐myc | This paper | N/A |
| MIP‐hSiglec‐8‐2xY‐>F‐myc | This paper | N/A |
| pINDUCER20‐Siglec‐F‐myc | This paper | N/A |
| pINDUCER20‐Siglec‐F‐dVset‐myc | This paper | N/A |
| pINDUCER20‐Siglec‐F‐2xY‐>F‐myc | This paper | N/A |
| Antibodies | ||
| Anti‐phospho‐Tyr (4G10) | Millipore | 05‐321 |
| Anti‐phospho‐Tyr (PT66) | Sigma | P3300 |
| Anti‐phospho‐Ser/Thr‐Pro (MPM‐2) | Millipore | 05‐368 |
| Anti‐MAPK/CDK Substrate (34B2) | Cell Signaling Technology | 2325 |
| Anti‐Iba1 (Polyclonal) | Synaptic Systems | 234 004 |
| Anti‐Siglec‐F (E50‐2440) | BD Biosciences | 552125 |
| Anti‐myc (9B11; Sepharose Bead Conjugate) | Cell Signaling Technology | 3400 |
| Anti‐myc (9B11) | Cell Signaling Technology | 9B11 |
| Anti‐myc (71D10) | Cell Signaling Technology | 2278 |
| Anti‐Siglec‐8 (ab38578) | Abcam | ab38578 |
| Anti‐Amyloid Beta (D54D2) | Cell Signaling Technology | 8243 |
| Anti‐MHC‐II (HLA‐DP, HLA‐DQ, HLA‐DR; CR3/43) | Agilent | M077501‐2 |
| Anti‐SHP‐1 (C14H6) | Cell Signaling Technology | C14H6 |
| Anti‐SHP‐2 (D50F2) | Cell Signaling Technology | D50F2 |
| APC‐Cy7 Anti‐Siglec‐F (E50‐2440) | BD Biosciences | 565527 |
| APC Anti‐CD33 (WM53) | BD Biosciences | 561817 |
| Alexa‐647 Anti‐Siglec‐5/14 (194128) | BD Biosciences | 564371 |
| APC Anti‐Siglec‐8 (7C9) | Biolegend | 347105 |
| Anti‐IL‐1β (Polyclonal) | R&D Systems | AF‐401‐SP |
| Anti‐β‐tubulin (Polyclonal) | Cell Signaling Technology | 2146 |
| Oligonucleotides and sequence‐based reagents | ||
| qPCR Primers | This Study | Dataset EV6 |
| Chemicals, enzymes and other reagents | ||
| PBS | Thermo Fisher Scientific | 10010023 |
| Formaldehyde | Sigma | 252549 |
| Urea | Sigma | U5128 |
| Pierce BCA Protein Assay | Thermo Fisher Scientific | 23225 |
| Dithiothreitol (DTT) | Sigma | D0632 |
| Iodoacetamide (IAA) | Sigma | I1144 |
| Sequencing Grade Modified Trypsin | Promega | V5111 |
| 99.99% Acetic Acid | Sigma | 338826 |
| Sep‐Pak Lite C18 Cartridge | Waters | WAT023501 |
| Sep‐Pak Plus C18 Cartridge | Waters | WAT020515 |
| Pierce Quantitative Colorimetric Peptide Assay | Thermo Fisher Scientific | 23275 |
| 6‐plex Tandem Mass Tag | Thermo Fisher Scientific | 90061 |
| 10‐plex Tandem Mass Tag | Thermo Fisher Scientific | 90110 |
| ZORBAX 300Extend‐C18 | Agilent | 770995‐902 |
| High‐Select™ Fe‐NTA Phosphopeptide Enrichment Kit | Thermo Fisher Scientific | A32992 |
| 10 μm C18 beads | YMC | ODS‐A AA12S11 |
| 5 μm C18 beads | YMC | ODS‐AQ AQ12S05 |
| Poros 20 MC Metal Chelate Affinity Packing | Poros | 1‐5429‐06 |
| Fused Silica Capillary Tubing 50 μm ID | Polymicro Technologies | 1068150017 |
| Fused Silica Capillary Tubing 100 μm ID | Polymicro Technologies | 1068150023 |
| Fused Silica Capillary Tubing 200 μm ID | Polymicro Technologies | 1068150204 |
| Neuraminidase (Sialidase) from Arthrobacter ureafaciens | Sigma | 10269611001 |
| FuGene | Promega | E2311 |
| PEI MAX | Polysciences Inc | 24765‐1 |
| .45 μm syringe filters | Sigma | 431220 |
| BD syringe | VWR | 302995 |
| RPMI 1640 Medium, GlutaMAX Supplement | Thermo Fisher Scientific | 61870036 |
| DMEM media | VWR | 10013CV |
| Fetal Bovine Serum (FBS), Certified | Thermo Fisher Scientific | 16000‐044 |
| Pen Strep | Thermo Fisher Scientific | 15140‐122 |
| 0.05% Trypsin | Thermo Fisher Scientific | 25300‐120 |
| Annexin V binding/washing buffer | Thermo Fisher Scientific | V13246 |
| Annexin V‐488 | Thermo Fisher Scientific | A13201 |
| Propidium Iodide | Thermo Fisher Scientific | P1304MP |
| PNGase F | New England BioLabs | P0704S |
| pHrodo Green Dextran | Thermo Fisher Scientific | P35368 |
| Superscript IV VILO Master Mix | Thermo Fisher Scientific | 11756050 |
| Ultrapure Water for HPLC | Sigma | 270733‐4L |
| iQ SYBR Green Supermix | Biorad | 1708882 |
| Microseal 384‐well PCR Plate | Biorad | MSP3842 |
| SHP099 | SelleckChem | S8278 |
| Bestatin | Sigma | B8385 |
| Tofacitinib citrate | Sigma | PZ0017 |
| Sodium Citrate | Sigma | S8750 |
| Hoechst 33342 | Thermo Fisher Scientific | H3570 |
| Matrigel | Corning | BD354277 |
| ReLeSR | StemCell Technologies | 5872 |
| mTESR | StemCell Technologies | 85850 |
| STEMdiff Hematopoietic Kit | StemCell Technologies | 5310 |
| ROCK inhibitor (Y‐27632 dihydrochloride) | Tocris | 1254 |
| DMEM/F12 | Thermo Fisher Scientific | 11330‐057 |
| ITS‐G | Thermo Fisher Scientific | 41400045 |
| B27 | Thermo Fisher Scientific | 17‐504‐044 |
| N2 | Thermo Fisher Scientific | 17502048 |
| Glutamax | Thermo Fisher Scientific | 35050061 |
| MEM Non‐essential Amino Acid (NEAA) Solution | Sigma | M7145‐100ML |
| Penicillin:Streptomycin Solution | Gemini Bio‐Products | 400‐109 |
| Insulin | Sigma | 91077C‐250MG |
| Monothioglycerol | Sigma | M6145‐100ML |
| M‐CSF | PeproTech | 100‐21‐1MG |
| IL‐34 | PeproTech | 300‐25‐1MG |
| TGFβ‐1 | PeproTech | 200‐34‐500UG |
| CD200 | Novoprotein | C311 |
| CX3CL1 | PeproTech | 300‐31‐1MG |
| Human IFN‐α2 | StemCell Technologies | 78076 |
| Human IFN‐β | R&D Systems | 8499‐IF |
| Human IFN‐γ | R&D Systems | 285‐IF |
| Mouse IFN‐γ | VWR | 575302‐BL |
| TRIzol | Thermo Fisher Scientific | 15596018 |
| Chloroform | Sigma | C2432 |
| Ethanol, 200 Proof | VWR | V1001 |
| RIPA Buffer (2X) | Boston BioProducts | BP‐115X |
| Halt Protease and Phosphatase Inhibitor Cocktail | Thermo Fisher Scientific | 1861281 |
| LDS Sample Buffer | Invitrogen | NP0007 |
| SDS‐PAGE gel | Invitrogen | NP0335BOX |
| Nitrocellulose Membranes, 0.2 μm | Bio‐Rad | 1620112 |
| Immun‐Blot PVDF Membrane | Bio‐Rad | 162‐0177 |
| Novex Tris‐Glycine Transfer Buffer | Thermo Fisher Scientific | LC3675 |
| Tris‐Buffered Saline | Corning | 46‐012‐CM |
| Tween 20 | Fisher BioReagents | BP337 |
| Intercept Blocking Buffer | Li‐Cor | 927‐70001 |
| TrueBlack Lipofuscin Autofluorescence Quencher | Biotium | 23007 |
| Direct‐zol RNA MicroPrep Kit | Zymo Research | R2061 |
| Dynabeads mRNA Direct Kit | Thermo Fisher Scientific | 61012 |
| Kapa mRNA Hyperprep Kit | Roche | 8098115702 |
| pENTR/D‐TOPO Cloning Kit | Thermo Fisher Scientific | K240020 |
| Gateway LR Clonase | Thermo Fisher Scientific | 11791020 |
| Software | ||
| Proteome Discoverer (v2.2.1) | Thermo Fisher Scientific | https://www.thermofisher.com/us/en/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-software/multi-omics-data-analysis/proteome-discoverer-software.html |
| MASCOT (v2.4.1) | Matrix Science | https://www.matrixscience.com/ |
| XCalibur (v2.2) | Thermo Fisher Scientific | https://www.thermofisher.com/order/catalog/product/OPTON-30965 |
| IncuCyte ZOOM (v2016A) | Sartorius | https://www.essenbioscience.com/en/products/incucyte-zoom-resources-support/software-modules-incucyte-zoom/ |
| STAR (v2.5.3a) | (Dobin et al, 2013) | https://github.com/alexdobin/STAR/releases |
| RSEM (v1.3.0) | (Li & Dewey 2011) | http://deweylab.github.io/RSEM/ |
| DESeq2 (v1.18.1) | Bioconductor | https://www.bioconductor.org/packages/devel/bioc/html/DESeq2.html |
| GSEA (v3.0 beta‐2) | Mootha et al (2003), Tamayo et al (2005) | https://www.gsea-msigdb.org/gsea/ |
| R (v3.4.4) | N/A | https://www.r-project.org/ |
| Salmon (v0.9.1) | Patro, Duggal, Love, Irizarry, and Kingsford (2017) | https://combine-lab.github.io/salmon/ |
| Python (v3.7.1) | N/A | https://www.python.org |
| MAGIC (v1.5.5) | van Dijk et al(2018) | https://www.krishnaswamylab.org/projects/magic |
| pyproteome (v0.11.0) | This publication | https://github.com/white-lab/pyproteome |
| scikit‐learn (v0.21.1) | Pedregosa et al (2012) | https://scikit-learn.org/stable/ |
| scipy (v1.3.1) | Virtanen et al(2020) | https://www.scipy.org/ |
| numpy (v1.17.0) | Van Der Walt, Colbert, and Varoquaux (2011) | https://numpy.org/ |
| pandas (v0.25.0) | McKinney (2010) | https://pandas.pydata.org/ |
| seaborn (v0.10.0) | Waskom (2018) | http://seaborn.pydata.org/ |
| matplotlib (v3.1.1) | Hunter (2007) | http://matplotlib.org/ |
| goenrich (v1.12) | Rudolph et al (2016) | https://github.com/jdrudolph/goenrich |
| goatools (v1.0.3) | Klopfenstein et al(2018) | https://github.com/tanghaibao/goatools |
| Cytoflow (v1.0) | N/A | https://bpteague.github.io/cytoflow/ |
| MSigDB (v6.1) | Liberzon et al (2015), Subramanian et al (2005) | http://software.broadinstitute.org/gsea/msigdb/ |
| Fiji‐ImageJ (v1.52u) | National Inst. Of Health | https://imagej.net/Fiji |
| ZEN (v2.1 SP3) | Zeiss | https://www.zeiss.com/microscopy/us/products/microscope-software/zen.html |
| Other | ||
| Q Exactive Plus | Thermo | IQLAAEGAAPFALGMBDK |
| Q Exactive HF‐X | Thermo | IQLAAEGAAPFALGMBFZ |
| LTQ Orbitrap | Thermo | N/A |
| VT100S vibratome | Leica | N/A |
| LSM 710 | Zeiss | N/A |
| LSM 880 | Zeiss | N/A |
| BD FACS Canto Cell Sorter | BD Biosciences | N/A |
| Li‐Cor Odessey CLx | LI‐COR Biosciences | N/A |
| Incucyte Plate Imager | Essen Bioscience | N/A |
| Illumina HiSeq 2000 | Illumina | N/A |
| CFX384 Touch Real‐Time PCR | Biorad | N/A |
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