KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-TLR4 | Abcam | Cat# ab22048 |
| Anti-CD36 | Abcam | Cat# ab23680 |
| Anti-NeuN | Abcam | Cat# ab104224 |
| Anti-LAMP1 | Abcam | Cat# ab25630 |
| Anti-CD11b | Abcam | Cat# ab8878 |
| Anti-TMEM119 | Abcam | Cat# ab209064 |
| Anti-cleaved-caspase 3 | Cell Signaling | Cat# 9664 |
| Anti-FIP200 | Cell Signaling | Cat# 12436 |
| Anti-ATG5 | Cell Signaling | Cat# 12994 |
| Anti-Rubicon (D9F7) | Cell Signaling | Cat# 8465 |
| Anti-Aβ 82E1 | IBL | Cat# 10326 |
| Anti-Iba1 | Novus | Cat# NB100-1028 |
| Anti-TREM2 | R&D Systems | Cat# MAB17291 |
| Anti-FLAG M2 | Sigma-Aldrich | Cat# F3165 |
| Anti-β-actin | Thermo | Cat# MA1-91399 |
| Anti-phospho-tau (S202/T205) | Thermo | Cat# 44-768G |
| Bacterial and Virus Strains | ||
| pLenti-V2 lentivirus (for CRISPR) | This Paper | N/A |
| lentiBrite-GFP-LC3 Sensor | Millipore | Cat# 17-10193 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| β-amyloid (1-42) peptide - unlabeled | Anaspec | Cat# AS-20276 |
| β-amyloid (1-42) peptide - TAMRA | Anaspec | Cat# AS-60476 |
| β-amyloid (1-42) peptide – Hilyte 488 | Anaspec | Cat# AS-60479-01 |
| β-amyloid (1-42) peptide - TAMRA | SJCRH Core | Custom Synthesis |
| β-amyloid (1-42) scrambled peptide – TAMRA | SJCRH Core | Custom Synthesis |
| Dextran – Texas Red | Invitrogen | Cat# D1863 |
| Zymosan A – AF594 | Invitrogen | Cat# Z23374 |
| ProLong Diamond DAPI mounting media | Invitrogen | Cat# P36971 |
| pHRodo Zymosan Bioparticles | Invitrogen | Cat# P35364 |
| Rapamycin | Sigma-Aldrich | Cat# R8781 |
| Latrunculin A | Sigma-Aldrich | Cat# L5163 |
| Critical Commercial Assays | ||
| Neural Tissue Dissociation Kit | Miltenyi | Cat# 130-092-628 |
| Microglia Isolation Kit | Miltenyi | Cat# 130-093-634 |
| Universal SYBR Green | Bio-Rad | Cat# 1725271 |
| M-MLV Kit | Invitrogen | Cat# 28025013 |
| pHRodo iFL Labeling Kit | Invitrogen | Cat# P36014 |
| Mouse Multianalyte Inflammatory Cytokine ELISA Kit | Qiagen | Cat# MEM-004A |
| RNeasy Mini Kit | Qiagen | Cat# 74104 |
| Experimental Models: Cell Lines | ||
| BV2 murine microglia | Washington University | Herbert Virgin |
| RAW264.7 murine macrophage | ATCC | Cat# SC-6003 |
| Primary murine BMDM | This Paper | N/A |
| Primary murine microglia | This Paper | N/A |
| Experimental Models: Organisms/Strains | ||
| 5xFAD transgenic mice | Jackson Laboratory | Cat# 34840-JAX |
| CX3CR1-creERT2 | Jackson Laboratory | Cat# 021160 |
| FIP200fl/fl LysM-Cre+, 5xFAD | This Paper | N/A |
| ATG5fl/fl LysM-Cre+, 5xFAD | This Paper | N/A |
| Rubicon−/−, 5xFAD | This Paper | N/A |
| Rubiconfl/fl CX3CR1-creERT2, 5xFAD | This Paper | N/A |
| FIP200fl/fl CX3CR1-creERT2, 5xFAD | This Paper | N/A |
| Beclin1fl/fl LysM-Cre+ | University of Kentucky | Edmund Rucker |
| ATG7fl/fl LysM-Cre+ | TMIMS | Masaaki Komatsu |
| ATG14fl/fl LysM-Cre+ | Washington University | Herbert Virgin |
| VPS34fl/fl LysM-Cre+ | Yale University | Richard Flavell |
| ULK1−/− LysM-Cre+ | SJCRH | Mondira Kundu |
| Oligonucleotides | ||
| Rubicon-sgRNA1 5’ – CACCGAGGAGACTCGTCCATACACG – 3’ 3’ – AAACCGTGTATGGACGAGTCTCCTC – 5’ |
This paper | N/A |
| Rubicon-sgRNA2 5’ – CACCGTGATGAGGAACGGGCGAAGA – 3’ 3’ – AAACTCTTCGCCCGTTCCTCATCAC – 5’ |
This paper | N/A |
| ATG5-sgRNA1 5’ – GTGAGCCTCAACCGCATCCT – 3’ 3’ – CACTCGGAGTTGGCGTAGGA – 5’ |
This paper | N/A |
| ATG5-sgRNA2 5’ – CGGAACAGCTTCTGGATGAA – 3’ 3’ – GCCTTGTCGAAGACCTACTT – 5’ |
This paper | N/A |
| FIP200-sgRNA1 5’ – AGAGTGTGTACTTACAGCGC – 3’ 3’ – TCTCACACATGAATGTCGCG – 5’ |
This paper | N/A |
| FIP200-sgRNA2 5’ – GAGGATCATGCTCCTAGAAC – 3’ 3’ – CTCCTAGTACGAGGATCTTG – 5’ |
This paper | N/A |
| Actin qPCR F: ATGGAGGGGAATACAGCCC R: TTCTTTGCAGCTCCTTCGTT |
This paper | N/A |
| TNFα qPCR F: CCTGTAGCCCACGTCGTAGC R: AGCAATGACTCCAAAGTAGACC |
This paper | N/A |
| IL1β qPCR F: CACAGCAGCACATCAACAAG R: GTGCTCATGTCCTCATCCTG |
This paper | N/A |
| IL6 qPCR F: GAGGATACCACTCCCAACAGACC R: AAGTGCATCATCGTTGTTCATACA |
This paper | N/A |
| CCL5 qPCR F: CCAATCTTGCAGTCGTGTTTGT R: CATCTCCAAATAGTTGATGTATTCTTGAAC |
This paper | N/A |
| Iba1 qPCR F: CAGACTGCCAGCCTAAGACA R: AGGAATTGCTTGTTGATCCC |
This paper | N/A |
| Recombinant DNA | ||
| pLenti-V2 plasmid | Addgene | Cat# 52961 |
| psPAX plasmid | Addgene | Cat# 12260 |
| pVSVg plasmid | Addgene | Cat# 8454 |
| pMXs-FLAG plasmid | Cell Biolabs | Cat# RTV-016 |
| pMXs-FLAG-mATG4B-C74A | This Paper | N/A |
| pMXs-FLAG-RavZ | This Paper | N/A |
| Software and Algorithms | ||
| Slidebook 6 | 3i | https://www.intelligent-imaging.com/slidebook |
| Nikon NIS-elements Advanced Research | Nikon | https://www.microscope.healthcare.nikon.com/products/software/nis-elements |
| FlowJo v10.4 | Tree Star | https://www.flowjo.com/solutions/flowjo |
| LiCOR Image Studio | LiCOR | https://www.licor.com/bio/image-studio/ |
| GraphPad Prism 7.0 | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| G*Power | University of Dusseldorf | http://www.gpower.hhu.de/ |