KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
|
| ||
| Antibodies | ||
|
| ||
| anti-Ibal (rabbit monoclonal) | Cell Signaling Technology | Cat#17198; RRID: AB_2820254 |
| anti-Ibal (goat polyclonal) | Abcam | Cat#5076; RRID: AB_2224402 |
| anti-CD11c (rabbit monoclonal) | Cell Signaling Technology | Cat#97585; RRID: AB_2800282 |
| anti-CD74-AF647 (rat monoclonal) | BioLegend | Cat# 151004; RRID: AB_2632609 |
| anti-APOE (HJ6.3, biotinylated, mouse monoclonal) | Holtzman Lab (Kim et al., 20 1 299) | N/A |
| anti-SERPINA3N (goat polyclonal) | R&D Systems | Cat#AF4709; RRID: AB_2270116 |
| anti-APC (CC-1, mouse monoclonal) | MilliporeSigma | Cat#OP80; RRID: AB_2057371 |
| anti-IL33 (goat polyclonal) | R&D Systems | Cat#AF3626; RRID: AB_884269 |
| anti-GFAP (Alexa Fluor 488-labbeled, mouse monoclonal) | ThermoFisher Scientific | Cat #53–9892-82; RRID: AB_10598515 |
| anti-Vimentin (E-5, mouse monoclonal) | Santa Cruz Biotechnology | Cat#sc-373717; RRID: AB_10917747 |
| anti-MAFB (rabbit monoclonal) | BETHYL | Cat#A700–046; RRID: AB_2891845 |
| anti-STATI (rabbit monoclonal) | Cell Signaling Technology | Cat#14994; RRID: AB_2737027 |
| anti-HMGCSI (rabbit Polyclonal) | Invitrogen | Cat#PA5–29488; RRID: AB_2546964 |
| anti-Synaptophysin (Rabbit monoclonal) | Cell Signaling Technology | Cat#364065; RRID: AB_2799098 |
| anti-OLIG2 (rabbit polyclonal) | EMB Millipore | Cat#AB9610; RRID: AB_570666 |
| anti-IL33R(ST2)-PE (rat monoclonal) | Invitrogen | Cat#12–9333-80; RRID: AB_2572705 |
| CD45-APC/Cyanine7 (30-F11, rat monoclonal) | BioLegend | Cat#103116; RRID: AB_312981 |
| anti-Carbonic Anhydrase II/CA2 (rat monoclonal) | R&D Systems | Cat#MAB2184; RRID: AB_2065858 |
| anti-rabbit IgG AF555 (donkey polyclonal) | Abcam | Cat#150074; RRID: AB_2636997 |
| anti-goat IgG AF647 (donkey polyclonal) | Abcam | Cat#150131; RRID: AB_2732857 |
| anti-goat IgG AF488 (donkey polyclonal) | Abcam | Cat#150129; RRID: AB_2687506 |
| anti-rat IgG AF647 (chicken polyclonal) | Invitrogen | Cat# A-21472; RRID: AB_2535875 |
| anti-mouse IgG2b AF488 (goat polyclonal) | Invitrogen | Cat#A21141; RRID: AB_2535778 |
| anti-Streptavidin, APC | ThermoFisher Scientific | Cat#s868 |
|
| ||
| Chemicals, peptides, and recombinant proteins | ||
|
| ||
| Luxol Fast Blue Solution, 0.1% in 95% Alcohol | Electron microscopy sciences | Cat#26056–15 |
| CFDA SE (CFSE) dye | ThermoFisher Scientific | Cat# C1157 |
| Poly-L-lysine solution | MilliporeSigma | Cat#P4707 |
| 4’,6-Diamidino-2-Phenylindole, Dihydrochloride (DAPI) | MilliporeSigma | Cat# D9542 |
| DNase I | MilliporeSigma | Cat#11284932001 |
| Trypsin from bovine pancreas | MilliporeSigma | Cat#T1426 |
| Recombinant Mouse Protein S/PROS1 | R&D systems | Cat#9740-PS-050 |
| Paraformaldehyde 32% | Electron Microscopy Sciences | Cat#15714-S |
| Formaldehyde Aqueous Solution, EM Grade | Electron Microscopy Sciences | Cat#15710 |
| Dexamethasone | MilliporeSigma | Cat#D1756 |
| Cuprizone (bis-cyclohexanone oxaldihydrazone) | MilliporeSigma | Cat#c9012 |
| EDTA | Corning | Cat#46–034-Cl |
| Triton X-100 | MilliporeSigma | Cat#T8787 |
|
| ||
| Critical commercial assays | ||
|
| ||
| Chromium Single Cell 5’ Library & Gel Bead Kit, 16 rxns | 10x Genomics | Cat#PN-1000006 |
| Chromium Next GEM Single Cell 5’ Kit v2, 16 rxns | 10x Genomics | Cat#PN-1000263 |
| Mouse Vitamin K-dependent protein S (PROS1) ELISA Kit | Abebio | Cat#AE25758MO |
| PE Annexin V Apoptosis Detection Kit I | BD Biosciences | Cat#559763 RRID: AB_2869265 |
| DC protein assay | BIO-RAD | Cat#5000112 |
|
| ||
| Deposited data | ||
|
| ||
| 10x Single Nucleus RNA-seq | This paper | GEO: GSE204770 |
|
| ||
| Experimental models: Cell lines | ||
|
| ||
| Primary murine microglia | This paper | N/A |
| Primary murine astrocytes | This paper | N/A |
|
| ||
| Experimental models: Organisms/strains | ||
|
| ||
| Mouse: C57BL/6J | Jackson Laboratory | Cat #000664 |
| Mouse: wildtype | In house | N/A |
| Mouse: Trem2−/− | In house | N/A |
|
| ||
| Software and algorithms | ||
|
| ||
| MATLAB | MathWorks |
http://www.mathworks.com/products/ matlab/;RRID:SCR_001622 |
| ImageJ | National Institutes of Health | https://imagej.net/;RRID:SCR_003070 |
| FlowJo (v10.8.1) | FlowJo | https://www.flowjo.com/solutions/flowjo/;RRID:SCR_008520 |
| Imaris (v9.8.0) | Bitplane | http://www.bitplane.com/imaris/imaris/;RRID:SCR_007370 |
| R(v4.1.0) | R Core Team (2017). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. | http://www.r-project.org/; RRID:SCR_001905 |
| RStudio (v1.4.1717) | https://posit.co | RRID: SCR_000432 |
| Seurat (v4.0) | http://seurat.r-forge.r-project.org/ | RRID: SCR_007322 |
| Slingshot (v2.1.0) | Street etal.,2018100 | N/A |
| scCODA (v0.1.8) | Büttner et al., 2021101 | N/A |
| scVelo (v0.2.4) | La Manno et al., 201838 | N/A |
| NicheNet (v1.0.0) | Browaeys et al., 201976 | N/A |
|
| ||
| Python (v3.9.13) | Python Software Foundation |
https://www.python.org/; RRID:SCR_008394 |
| BBrowser (v2.7.5) | BioTuring Inc. | www.bioturing.com/bbrowser |
| Cell Ranger (v3.0.2) | 10x Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome |
| JupyterLab (v3.4.7) | https://jupyter.org/ | RRID:SCR_022695 |
| GraphPad Prism (v8.0.2) | http://www.graphpad.com/ | RRID:SCR_002798 |
| BioRender | https://biorender.com/ | RRID: SCR_018361 |
| Metascape | http://metascape.org/gp/index.html#/main/step1 | RRID:SCR_016620 |
| Code | This paper | https://github.com/marcocolonnalab/CPZ |
|
| ||
| Other | ||
|
| ||
| Cuprizone Diet (2018, 0.2%) | Envigo | TD.06172 |