KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Alexa Fluor 488 goat anti-chicken | Life Technologies | Cat #A11039; RRID: AB_2534096 |
| Alexa Fluor 555 goat anti-mouse | Life Technologies | Cat #A21424; RRID: AB_141780 |
| Alexa Fluor 555 goat anti-rabbit | Life Technologies | Cat #A21429; RRID: AB_2535850 |
| Alexa Fluor 633 goat anti-mouse | Life Technologies | Cat #A21052; RRID: AB_2535719 |
| Alexa Fluor 633 goat anti-rabbit | Life Technologies | Cat #A21071; RRID: AB_2535732 |
| Goat anti-CD13 | R&D Systems | Cat #AF2335; RRID: AB_2227288 |
| Anti-Iba, Rabbit | Wako | Cat #019–19741; RRID: AB_839504. |
| Anti-claudin-5 | Invitrogen | Cat #35–2500; RRID: AB_2533200 |
| Perivascular macrophages (PVMs)-CD206 | Thermo Fisher Scientific | Cat #PA5–46994; RRID: AB_2607366 |
| Anti-Human APP | R&D Biosystems | Cat #AF1168; RRID: AB_354642 |
| Mouse anti-beta-Actin | Millipore Sigma | Cat #A2228; RRID: AB_476697 |
| Rabbit anti-IBA-1 | GeneTex | Cat #GTX100042, RRID: AB_1240434 |
| LYVE1 Monoclonal Antibody | ThermoFisher | Cat #14–0443-82; RRID: Cat #14–0443-82 |
| HRP-conjugated anti-goat | Millipore Sigma | Cat #AP180P; RRID: AB_92573 |
| Goat anti-Mouse IgG (H+L) Secondary Antibody, HRP | ThermoFisher | Cat # 62–6520; RRID: AB_2533947 |
| Anti-Rabbit secondary antibodies | Millipore Sigma | Cat #AP106P; RRID: AB_92411 |
| PE-P2RY12 | BioLegend | Cat #84003; RRID: AB_11028449 |
| PE/Cy7-TMEM119 | ThermoFisher | Cat #25–6119-82; RRID: AB_2848312 |
| BV421-CD11b | BioLegend | Cat #101235; RRID: AB_10897942 |
| FITC-NK1.1 | BioLegend | Cat #156508; RRID: AB_2876526 |
| PE-B220 | BioLegend | Cat #103207; RRID: AB_312992 |
| PE/Cy7-CD45 | BioLegend | Cat #103114; RRID: AB_312978 |
| APC/Cy7-CD8 | BioLegend | Cat #100714; RRID: AB_312752 |
| Alexa 700-CD11b | BioLegend | Cat #101222; RRID: AB_493705 |
| BV421-CD3 | BioLegend | Cat #100228; RRID: AB_10900227 |
| BV510-CD11c | BioLegend | Cat #117353; RRID: AB_2562010 |
| BV785-CD4 | BioLegend | Cat #100552; RRID: AB_11218992 |
| BV605-Gr-1 | BioLegend | Cat # 108439; RRID: AB_2562333 |
| BV421-CD11b | BioLegend | Cat #101236; RRID: AB_10897942 |
| BV711-CD45 | BioLegend | Cat #304050; RRID: AB_2563465 |
| anti-CD16/32 | BD Biosciences | Cat #56–0161-82; RRID: AB_493994 |
|
Biological samples | ||
| UCI ADRC Brain Bank | https://mind.uci.edu/adrc/neuropathology-core/ | Case Numbers: 39–10, 4–14, 1–8, 29–15, 3–12, 38–14, 8–18, 22–17, 51–15, 9–18, 35–17 |
| Primary mouse microglia | ScienCell | Cat #M1900–57 |
| C57BL/6 Mouse Bone Marrow Monocytes | CellBiologics | Cat # C57–6271F |
|
Chemicals, peptides, and recombinant proteins | ||
| Triton X-100 | Fisher Scientific | Cat #BP151–500 |
| Paraformaldehyde | Sigma-Aldrich | Cat #P6148–500G |
| Sodium Azide | Sigma-Aldrich | Cat #S8032–100G |
| Goat serum | Thermo Fisher Scientific | Cat #10000C; RRID: AB_2532979 |
| Amylo-Glo RTD Amyloid Plaque Stain Reagent | Biosensis | Cat #TR-300-AG |
| DAPI Fluoromount-G | SouthernBiotech | Cat #0100–20 |
| Fluoromount-G | SouthernBiotech | Cat #0100–01 |
| Ethyl alcohol | Pure Sigma Aldrich | Cat #E7023 |
| 2-propanol | Sigma Aldrich | Cat #59304 |
| Chloroform:Isoamyl alcohol | Sigma Aldrich | Cat #C0549 |
| Hydroxyapatite (HAp <200 nm) | Sigma Aldrich | Cat #677418 |
| SuperSignal West Dura Extended Duration Substrate | Thermo Fisher Scientific | Cat #34075 |
| Pierce BCA Assay Kit | Thermo Fisher Scientific | Cat #23225 |
| Laemmli Sample Buffer | BioRad | Cat #1610747 |
| Beta-mercaptoethanol | Millipore Sigma | Cat #M6250 |
| AF647-RIS | Biovinc | Cat #BV500101 |
| Iron stain kit | Abcam | Cat #ab150674 |
| Alizarin Red S | Milipore | Cat #A5533 |
| 4–15% polyacrylamide gel in Tris/Glycine/SDS buffer | BioRad | Cat #5671084 |
| 0.2µm Nitrocellulose membrane | BioRad | Cat# #1704159 |
| T-PER solution | Thermo Scientific | Cat #78510 |
| Hoeschst 33342 | ThermoFisher Scientific | Cat #R37165 |
| Monothioglycerol | Sigma Aldrich | Cat #M6145 |
| Phosphatase and protease inhibitor mixtures | Thermo Scientific | Cat #78440 |
| Caspase 3/7 reagent | Essen Biosciences | Cat #4440 |
| Insulin-Transferrin-Selenium (ITS-G) | Thermo Fisher Scientific | Cat #41400045 |
| Human Insulin | Sigma Aldrich | Cat #I2643 |
| Recombinant Human IL-34 | Peprotech | Cat #200–34 |
| Recombinant Human M-CSF | Peprotech | Cat #300–25 |
| Recombinant Human TGF-b1 (HEK293 derived) | Peprotech | Cat #100–21 |
| Recombinant Human Fractalkine (CX3CL1) | Peprotech | Cat #300–18 |
| Recombinant Human OX-2/MOX1/CD200 (C-6His) | Novoprotein | Cat #C311 |
| ReLeSR | StemCell Technologies | Cat #05872 |
| BD Matrigel Matrix Growth Factor Reduced, PhenolRed-Free | BD Biosciences | Cat #356231 |
| Thiazovivin | StemCell Technologies | Cat #72252 |
| BamBanker | Wako | Cat #NC9582225 |
| 1X DPBS, no Ca2+, no MG2+ | Thermo Fisher Scientific | Cat #14190250 |
| 10X HBSS, no Ca2+, no MG2+, no phenol red | Thermo Fisher Scientific | Cat #14185052 |
| 1X HBSS, no Ca2+, no MG2+, no phenol red | Thermo Fisher Scientific | Cat #14025126 |
| MACS BSA Stock Solution | Miltenyi Biotech | Cat #130–091-376 |
|
Critical commercial assays | ||
| Nuclei Fixation Kit | Parse Biosciences | Cat #SB1003 |
| Single Cell Whole Transcriptome - 100k cells/nuclei, up to 48 samples | Parse Biosciences | Cat #SB1003 |
| Barcoding - Whole Transcriptome | ParseBiosciences | Cat #SB1010 |
| Library Prep - Whole Transcriptome | Parse Biosciences | Cat #SB1011 |
| Nuclei EZ Lysis Buffer | Millipore Sigma | Cat # NUC101–1KT |
| RNase Inhibitor | Fisher Scientific | Cat #M0314L |
| Sucrose cushion buffer | Sigma-Aldrich | Cat #NUC-201 |
| Direct-zol RNA Miniprep Plus Kits | ZYMO Research | Cat #R2071 |
| STEMdiff Hematopoiesis kit | StemCell Technologies | Cat #05310 |
| Povidone Iodine | Phoenix | Cat #36LF58 |
| Lidocaine Hydrochloride Jelly | Akorn | Cat #NDC17478–711-30 |
| Lidocaine Hydrochloride Injectable | Phoenix | Cat #PHO5731909305 |
| Vetbond | 3M | Cat # 014006 |
| Sterile Saline | CareFusion | Cat # AL4109 |
| Isoflurane | Patterson Veterinary | Cat #14043070406 |
| Sterile Artificial Tears Ointment | Rugby | https://www.chewy.com/akorn-artificial-tears-lubricant/dp/315333 |
|
Deposited data and code | ||
| SPLiT sequencing datasets | This study | GEO series #GSE189033 |
| Tables providing cell-type specific gene expression differences and WGCNA analyses | This study | Mendeley https://doi.org/10.5281/zenodo.6565145 |
| Code used to process and analyze SPLiT-seq dataset | This study | https://doi.org/10.5281/zenodo.6565145 |
|
Experimental models: Cell lines | ||
| mono-allelic mEGFP-tagged WTC11 Ipsc line | Coriell | Cat# AICS-0036–006 |
| TREM2 CRISPR knockout on mEGFP-tagged WTC11 iPSC | Blurton-Jones lab | see McQuade et al., 2020 |
|
Experimental models: Organisms/strains | ||
| Mouse: 5X-FAD; B6.Cg-Tg(APPSwFlLon,PSEN1*M146L*L286V) 6799Vas/Mmjax | The Jackson Laboratory | Jax stock no. 34848-JAX |
| Csf1rDFIRE/DFIRE *C57BL/6 | David A. Hume & Clare Pridans | See Rojo et al., 2019 |
| Mouse: 5x-FIRE cross: | This paper | 5x-FIRE mice |
|
Software and algorithms | ||
| GraphPad Prism 9 | GraphPad | RRID:SCR_002798 |
| ImageJ | NIH | RRID:SCR_003070 |
| FlowJo software V10.8 | FlowJo; Ashland, OR | RRID:SCR_008520 |
| Imaris (9.2.0) | Imaris | RRID:SCR_007370 |
| BioRender | BioRender | RRID:SCR_018361 |
| Split-pipe software (v0.7.7p, Parse Biosciences) | Parse Biosciences | Split-pipe software (v0.7.7p) |
| R (v3.6.3) | https://cran.r-project.org/web/packages/Matrix/index.html | RRID:SCR_001905 |
| Seurat (v3.2.2) | https://www.r-project.org/ | RRID:SCR_016341 |
| DoubletFinder (v2.0.3) | Stuart et al., 2019 | RRID:SCR_018771 |
| Harmony (v1.0) | McGinnis et al., 2019 | RRID:SCR_022206 |
| Python (v3.7.9) | https://www.python.org | RRID:SCR_008394 |
| SCANPY (v1.6.0) | Wolf et al., 2018 | RRID:SCR_018139 |
| scWGCNA R package (v 0.0.0.9000) | Morabito et al., 2021 | https://github.com/smorabit/scWGCNA |
| WGCNA (v1.69) | Langfelder and Horvath, 2008 | RRID:SCR_003302 |
| ComplexHeatmap (v2.7.6.1010) | Gu et al., 2016 | RRID:SCR_017270 |
| Enrichr | Chen et al., 2013, Kuleshov et al., 2016 | RRID:SCR_001575 |
| CellChat (v1.0.0) | Jin et al., 2021 | RRID:SCR_021946 |
|
Other | ||
| Olympus FV3000RS confocal microscope | Olympus | https://www.olympus-global.com/news/2016/nr160405fv3000e.html |
| Keyence BZ-X810 | Keyance | https://www.keyence.com/products/microscope/fluorescence-microscope/bz-x700/models/bz-x810/ |
| Fortessa flow cytometer | BD Biosciences | https://www.bdbiosciences.com/en-eu/products/instruments/flow-cytometers/research-cell-analyzers/bd-lsrfortessa |
| 6-well plates | Corning | Cat #3516 |
| Microscope slides | VWR | Cat #16004–392 |
| Coverslips | Fisher Scientific | Cat #12–548-5M |
| Masterflex L/S Perfusion Pump | Masterflex L/S Perfusion Pump | https://www.masterflex.com/collections/masterflex-ls-complete-pump-systems |
| 10uL Gastight syringe, Model 1701 RN | Hamilton | Cat #7653–01 |
| 30-gauge, Small hub RN needle, 12mm, Pt:4, 45 tip | Hamilton | Cat #7803–07 |
| Germinator 500 Dry Sterilizer | Cell Point Scientific | Cat #GER5287120V |
| Sliding microtome | Leica SM 2010R | Leica SM 2010R |
| Agilent 4200 Tapestation | Agilent | Part Number:G2991BA |
| Illumina NovaSeq 6000 S4 | Illumina | https://www.illumina.com/systems/sequencing-platforms/novaseq.html |
| BioRad Molecular Imager ChemiDoc XRS | BioRad | ChemiDoc™ XRS+ System with Image Lab™ Software #1708265 |