KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-Brn-3a Antibody, POU-domain protein, clone 5A3.2 | MilliporeSigma | Cat#MAB1585; RRID:AB_94166 |
| Anti Iba1, Rabbit (for Immunocytochemistry) | FUJIFILM Wako Pure Chemical Corporation | Cat#019-19741; RRID:AB_839504 |
| Anti-P2ry12, Rabbit polyclonal | Butovsky Lab, validated in (Butovsky et al., 2015; Butovsky et al., 2014) | N/A |
| Anti-Apolipoprotein E Antibody | Sigma-Aldrich | Cat#AB947; RRID:AB_10770246 |
| Purified Mouse Anti-Human Galectin-3, Clone B2C10 (RUO) | BD Biosciences | Cat#556904; RRID:AB_396531 |
| GFP Polyclonal Antibody | Thermo Fisher Scientific | Cat#A11122; RRID:AB_221569 |
| Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 594 | Thermo Fisher Scientific | Cat#A-11005; RRID:AB_2534073 |
| Chicken anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 | Thermo Fisher Scientific | Cat# A-21441; RRID:AB_2535859 |
| Rabbit anti-Goat IgG (H+L), Superclonal™ Recombinant Secondary Antibody, Alexa Fluor 555 | Thermo Fisher Scientific | Cat#A27017; RRID:AB_2536081 |
| Rat-monoclonal anti-FCRLS (clone 4G11) | Butovsky lab, validated in (Butovsky et al., 2015; Butovsky et al., 2014) | N/A |
| PerCP/Cyanine5.5 anti-mouse Ly-6C antibody (clone HK1.4) | Biolegend | Cat#128012; RRID:AB_1659241 |
| CD11b Monoclonal Antibody (M1/70), PE-Cyanine7, eBioscience™ | Thermo Fisher Scientific | Cat#25-0112-82; RRID:AB_469588 |
| Cy™3 AffiniPure Donkey Anti-Rabbit IgG (H+L) | Jackson ImmunoResearch Labs | Cat#711-165-152; RRID:AB_2307443 |
| Cleaved Caspase-3 (Asp175) Antibody | Cell Signaling Technology | Cat#9661; RRID:AB_2341188 |
| Anti-IBA1 antibody, Guinea pig | Synaptic Systems | Cat#234 004; RRID:AB_2493179 |
| Anti-TMEM119 antibody, Rabbit | Atlas Antibodies | Cat#HPA051870; RRID:AB_2681645 |
| Galectin-3 Polyclonal antibody, Goat | R&D Systems | Cat#AF1197SP; RRID: AB_2234687 |
| Chicken-anti-rabbit AlexaFluor 647 | Thermo Fisher Scientific | Cat#A-21443; RRID:AB_2535861 |
| Donkey-guineapig AlexaFluor 488 | Jackson ImmunoResearch Labs | Cat#706-545-148; RRID:AB_2340472 |
| Donkey anti-mouse AlexaFluor 488 | Thermo Fisher Scientific | Cat#A-21202; RRID: AB_141607 |
| Biological Samples | ||
| Human eye specimens | Pathology Department, Duke University, See Table S3 | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Anhydrous DMSO | Thermo Fisher Scientific | Cat#D12345 |
| Dynabeads™ M-450 Tosylactivated | Thermo Fisher Scientific | Cat#14013 |
| Karnovsky Solution: 16% paraformaldehyde 25% Glutaraldehyde 0.2 M Sodium Cacodylate Buffer CaCl2 (calcium chloride, anhydrous) 1N NaOH |
Electron Microscopy Sciences Electron Microscopy Sciences Electron Microscopy Sciences Thermo Fisher Scientific Electron Microscopy Sciences |
Cat#15710 Cat#16220; CAS#111-30-8 Cat#11653, pH 7.4 Cat#C-76 Cat.#21170-01; CAS# 1310-73-2 |
| Tamoxifen | Sigma-Aldrich | Cat#T5648 |
| TritonX-100 | Roche | Cat#11332481001 |
| Normal Horse Serum | Thermo Fisher Scientific | Cat#NC9909742 |
| Bovine Serum Albumin | Sigma-Aldrich | Cat#A3294 |
| VectaShield with DAPI | Vector Laboratories | Cat#H-1200 |
| Alexa Fluor488 5-SDP Ester | Thermo Fisher Scientific (Molecular Probes) | Cat#A30052 |
| Alexa Flour405 5-NHS Ester | Thermo Fisher Scientific (Molecular Probes) | Cat#A30000 |
| DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) | Thermo Fisher Scientific | Cat#D1306 |
| True Black Lipofuscin Autofluorescence Quencher | Biotium | Cat#23007 |
| Galectin-3 inhibitor (TD139) | Cayman Chemicals | CAS #1450824-22-2 |
| O.C.T. Compound | Tissue-Tek® | Cat#4583 |
| SuperBlock™ (TBS) Blocking Buffer | Thermo Fisher Scientific | Cat#37535 |
| MAXblocks™ Blocking Medium | Active Motif | Cat#15252 |
| Deposited Data | ||
| RNAseq of retinal microglia from microbead-injected wildtype (C57BL/6J) mice | NCBI Gene Expression Omnibus (GEO) | GSE192509 |
| RNAseq of retinal microglia from DBA/2J mice and controls | NCBI Gene Expression Omnibus (GEO) | GSE192505 |
| RNAseq of retinal microglia from microbead-injected Apoe−/− and wildtype mice | NCBI Gene Expression Omnibus (GEO) | GSE192508 |
| RNAseq of phagocytic and nonphagocytic retinal microglia from Apoe−/− and wildtype mice following intravitreal injection of apoptotic neurons | NCBI Gene Expression Omnibus (GEO) | GSE192506 |
| RNAseq of retinal microglia from microbead-injected humanized APOE3 and APOE4 mice | NCBI Gene Expression Omnibus (GEO) | GSE192507 |
| Experimental Models: Organisms/Strains | ||
| Mouse: C57BL/6J | The Jackson Laboratory | JAX: 000664 |
| Mouse: Cx3cr1Cre/+ | The Jackson Laboratory | JAX: 025524 |
| Mouse: Cx3cr1CreERT2/+ | The Jackson Laboratory | JAX: 021160 |
| Mouse: Apoe−/− | The Jackson Laboratory | JAX: 002052 |
| Mouse: Lgals3−/− | The Jackson Laboratory | JAX: 006338 |
| Mouse: DBA/2J | The Jackson Laboratory | JAX: 000671 |
| Mouse: DBA/2J Gpnmb+:DBA/2J-Gpnmb+/SjJ | The Jackson Laboratory | JAX: 007048 |
| Mouse: Apoefl/fl | (Wagner et al., 2015) | N/A |
| Mouse: APOE2 | Taconic Biosciences | Taconic: 1547 |
| Mouse: APOE3 | Taconic Biosciences | Taconic: 1548 |
| Mouse: APOE4 | Taconic Biosciences | Taconic: 1549 |
| Mouse: APOE3fl/fl | Cure Alzheimer’s Fund | https://www.alzforum.org/research-models/apoe3-knock-floxed-curealz |
| Mouse: APOE4fl/fl | Cure Alzheimer’s Fund | https://www.alzforum.org/research-models/apoe4-knock-floxed-curealz |
| Software and Algorithms | ||
| FIJI (ImageJ) | NIH | https://imagej.net/Fiji |
| R software (v4.0.3) | N/A | https://cran.r-project.org/ |
| GraphPad Prism 7 | GraphPad Software | https://www.graphpad.com |
| BioRender | BioRender Software | https://biorender.com/ |
| Salmon (v1.4.0) | N/A | https://github.com/COMBINE-lab/salmon |
| Ensembl release 101 | EMBL-EBI | http://aug2020.archive.ensembl.org/index.html |
| DESeq2 (v1.30.1) | N/A | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| pheatmap (v1.0.12) | N/A | https://cran.r-project.org/web/packages/pheatmap/index.html |
| EnhancedVolcano (v1.8) | N/A | https://github.com/kevinblighe/EnhancedVolcano |
| ggplot2 | N/A | https://cran.r-project.org/web/packages/ggplot2/index.html |
| Ingenuity software | Ingenuity Systems | https://www.ingenuity.com |
| Zen Black | Zeiss | https://www.zeiss.com/ |
| Leica application suite software (LAS-AF-lite) | Leica | http://www.leica-microsystems.com |
| Nikon E800 software: DP Controller: 3. 3. 1.292 DP Manager version 3,3,1,222 |
Olympus Life Science Solutions | https://www.olympus-lifescience.com/en/support/downloads/ |