Key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Chemical compound, drug | BLZ945; CSF1R inhibitor |
PMID:24056773 | CAS No. 953769-46-5 | |
| Chemical compound, drug | Tamoxifen | Millipore-Sigma | Cat# T5648 | |
| Biological sample (C. macaque) | NHP brain samples | Charles River Labs | freshly isolated same day | |
| Other | DAPI | ThermoFisher | Cat# 62248 | Cell impermeant blue-fluorescent DNA stain for viability used at a concentration of 0.1 µg/mL |
| Antibody | anti-mouse CD11b BV510 (rat monoclonal) | Biolegend | RRID:AB_2561390 | FlowCyt (1:200) |
| Antibody | anti-mouse CD45 BV785 (rat monoclonal) | Biolegend | RRID:AB_2564590 | FlowCyt (1:200) |
| Antibody | anti-mouse CX3CR1 BV421 (rat monoclonal) | Biolegend | RRID:AB_2565706 | FlowCyt (1:200) |
| Antibody | anti-mouse P2RY12 PE (rat monoclonal) | Biolegend | RRID:AB_2721644 | FlowCyt (1:200) |
| Antibody | anti-mouse TMEM119 (rabbit monoclonal) | AbCam | RRID:AB_2744673 | FlowCyt (1:100) |
| Antibody | anti-rabbit AlexaFluor488 (rat monoclonal) | Biolegend | RRID:AB_2563203 | FlowCyt (1:400) |
| Other | AnnexinV AlexaFluor647 | ThermoFisher | Cat# A23204 | Apoptotic cell labeling reagent |
| Antibody | anti-mouse CD68 FITC (rat monoclonal) | Biolegend | RRID:AB_10575475 | FlowCyt (1:300) |
| Antibody | anti-mouse LAMP1 AlexaFluor647 (rat monoclonal) | Biolegend | RRID:AB_571990 | FlowCyt (1:200) |
| Antibody | anti-mouse KI-67 BV421 (rat monoclonal) | Biolegend | RRID:AB_2629748 | FlowCyt (1:100) |
| Antibody | anti-mouse Ly6G PE (rat monoclonal) | BD Biosciences | RRID:AB_394208 | FlowCyt (1:100) |
| Antibody | anti-mouse Ly6C PE (rat monoclonal) | Biolegend | RRID:AB_1186133 | FlowCyt (1:100) |
| Antibody | anti-mouse CD3 PE (rat monoclonal) | BD Biosciences | RRID:AB_395699 | FlowCyt (1:100) |
| Antibody | anti-mouse CD19 PE (rat monoclonal) | BD Biosciences | RRID:AB_395050 | FlowCyt (1:100) |
| Antibody | anti-mouse NK1.1 PE (rat monoclonal) | BD Biosciences | RRID:AB_396674 | FlowCyt (1:100) |
| Antibody | anti-mouse CD45 AF488 (rat monoclonal) | Biolegend | RRID:AB_493531 | FlowCyt (1:100) |
| Antibody | anti-mouse CX3CR1 BV785 (rat monoclonal) | Biolegend | RRID:AB_2565938 | FlowCyt (1:200) |
| Antibody | anti-mouse CD11b APC (rat monoclonal) | Biolegend | RRID:AB_312794 | FlowCyt (1:200) |
| Antibody | anti-NHP CD45 BV786 (mouse monoclonal) | BD Biosciences | RRID:AB_2738454 | FlowCyt (5 µL/test) |
| Antibody | anti-NHP CD11b BV510 (mouse monoclonal) | BD Biosciences | RRID:AB_2737996 | FlowCyt (5 µL/test) |
| Genetic reagent (M. musculus) | Cx3cr1tm2.1(cre/ERT2)Jung (Cx3cr1–CreERT2) | PMID:23273845 | RRID:IMSR_JAX:020940 | Dr. Steffen Jung (Weizmann Institute of Science, Israel) |
| Genetic reagent (M. musculus) | Atg5flox | PMID:16625204 | Dr. Noboru Mizushima, (University of Tokyo) | |
| Genetic reagent (M. musculus) | Fcer1g-/- | Taconic Biosciences | Model 583 | PMID:8313472 |
| Genetic reagent (M. musculus) | Trem2-/- | KOMP repository | RRID:MMRRC_050209-UCD | |
| Genetic reagent (M. musculus) | Mbpshi | Jackson Laboratory | RRID:IMSR_JAX:001428 | PMID:6168677 |
| Genetic reagent (M. musculus) | Cln3e × 7/ex8 (Cln3 KI) | PMID:12374761 | Dr. Susan Cotman (Harvard Medical School) | |
| Software, algorithm | FlowJo V10 | TreeStar | RRID:SCR_008520 | |
| Software, algorithm |
Prism 8.0 | Graphpad | RRID:SCR_002798 | |
| Software, algorithm | FIJI | FIJI | RRID:SCR_002285 | |
| Software, algorithm | MaxQuant Version 1.6.0.16 | Max Planck | RRID:SCR_014485 | |
| Software, algorithm | Perseus | Max Planck | RRID:SCR_015753 | |
| Software, algorithm | Ingenuity Pathway Analysis | Qiagen | RRID:SCR_008653 | |
| Other | Percoll | GE Healthcare | Cat# 17-0891-01 | Medium for density gradient centrifugation |
| Other | Mitotracker DeepRedFM | ThermoFisher | Cat# M22426 | Mitochondrial fluorescent dye, used at 50 nM |
| Other | CellROX DeepRed | ThermoFisher | Cat# C10491 | ROS fluorescent detection agent, used at 500 nM |
| Sequence based reagent | Atg5 Taqman primers | ThermoFisher | AssayID: Mm01187301_m1, Cat# 4351372 | Spanning exons 3–4 |
| Commercial assay or kit | RNEasy Plus Micro | Qiagen | Cat# 74034 | |
| Commercial assay or kit | SuperScript IV VILO kit | ThermoFisher | Cat# 11754050 | |
| Sequence based reagent | Gapdh endogenous control primers, M. musculus | ThermoFisher | Cat# 4352339E | |
| Commercial assay or kit | QuantiTect Multiplex PCR | Qiagen | Cat# 204541 | |
| Software, algorithm | PANTHER | PANTHER | RRID:SCR_004869 | |
| Peptide, recombinant protein | Lysyl Endopeptidase, Mass Spectrometry Grade (Lys-C) | Wako | Cat# 121–05063 | |
| Peptide, recombinant protein | Sequencing Grade Modified Trypsin | Promega | Cat# V5113 |