KEY RESOURCE TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| PE anti-mouse/human CD11b Antibody (clone M1/70) | Biolegend | Cat# 101208, RRID: AB_312791 |
| FITC anti-mouse/human CD11b Antibody (clone M1/70) | Biolegend | Cat# 101206, RRID: AB_312789 |
| Brilliant Violet 421™ anti-mouse/human CD11b (clone M1/70) | Biolegend | Cat# 101236, RRID: AB_11203704 |
| APC anti-mouse CD45.2 Antibody (clone 104) | Biolegend | Cat# 109814, RRID:AB_389211 |
| PE anti-mouse CD45.2 (clone 104) | Biolegend | Cat# 109808, RRID:AB_313445 |
| FITC anti-mouse CD45.2 (clone 104) | Biolegend | Cat# 109806, RRID:AB_313443 |
| PE/Cyanine7 anti-mouse CD45.2 (clone 104) | Biolegend | Cat# 109830, RRID:AB_1186098 |
| APC/Cyanine7 anti-mouse CD45 Antibody (Clone 30-F11) | Biolegend | Cat# 103116, RRID:AB_312981 |
| PE/Cyanine7 anti-mouse CD45 Antibody (clone 30-F11) | Biolegend | Cat# 103114, RRID:AB_312979 |
| CD282 (TLR2) Monoclonal Antibody (6C2), PE | eBioscience | Cat# 12-9021-82, RRID:AB_466230 |
| CD282 (TLR2) Monoclonal Antibody (6C2) | eBioscience | Cat# 11-9021-82, RRID:AB_465440 |
| Alexa Fluor® 647 anti-mouse CD85k (gp49 Receptor) Antibody | Biolegend | Cat# 144906, RRID:AB_2562044 |
| Alexa Fluor® 647 Mouse Anti-Akt (pS473) Clone M89-61 | BD Biosciences | Cat# 561670, RRID:AB_10896328 |
| Phospho-mTOR (Ser2448) Monoclonal Antibody (MRRBY), PE | eBioscience | Cat# 12-9718-41, RRID:AB_2572723 |
| PE Mouse Anti-Akt (pT308) Clone J1-223.371 | BD Biosciences | Cat# 558275, RRID:AB_2225329 |
| Phospho-Akt (Thr308) (244F9) Rabbit mAb | Cell Signaling Technology | Cat# 4056, RRID:AB_331163 |
| Phospho-Akt (Ser473) (D9E) | Cell Signaling | Cat# 4060, RRID:AB_2315049 |
| XP® Rabbit mAb | Technology | |
| Pho spho -NDRG1 (Thr346) (D98G11) XP® Rabbit mAb | Cell Signaling Technology | Cat# 5482, RRID:AB_10693451 |
| Histone H3 (D2B12) XP® Rabbit mAb (ChIP Formulated) | Cell Signaling Technology | Cat# 4620, RRID:AB_1904005 |
| Phospho-mTOR (Ser2448) Antibody | Cell Signaling Technology | Cat# 2971, RRID:AB_330970 |
| mTOR (7C10) Rabbit mAb antibody | Cell Signaling Technology | Cat# 2983, RRID:AB_2105622 |
| Akt (pan) (C67E7) Rabbit mAb | Cell Signaling Technology | Cat# 4691, RRID:AB_915783 |
| Anti-rabbit IgG, HRP-linked Antibody | Cell Signaling Technology | Cat# 7074, RRID:AB_2099233 |
| Rat anti Mouse CD68 antibody, (clone FA-11) | Serotec | Cat# MCA1957, RRID:AB_322219) |
| Rabbit anti-Synaptophysin (SP11) | Abcam | Cat# ab16659, RRID:AB_443419 |
| Rabbit anti-Iba1 | Wako | Cat# 019-19741, RRID:AB_839504 |
| Goat anti-Iba1 | Abcam | Cat# ab5076, RRID:AB_2224402 |
| Mouse anti-PSD95 | Chemicon | Cat# MAB1596, RRID:AB_2092365 |
| Mouse IL-33 Antibody | R&D Systems | Cat# AF3626, RRID:AB_884269 |
| Purified anti-P2RY12 Antibody | Biolegend | Cat# 848001, RRID:AB_2650633 |
| Cy™2 AffiniPure Donkey Anti-Goat IgG (H+L) | Jackson Immunoresearch | Cat# 705-225-147, RRID:AB_2307341 |
| Cy™3 AffiniPure Donkey Anti-Mouse IgG (H+L) | Jackson Immunoresearch | Cat# 715-165-150, RRID:AB_2340813 |
| Cy™3 AffiniPure Donkey Anti-Goat IgG (H+L) | Jackson Immunoresearch | Cat# 705-165-147, RRID:AB_2307351 |
| Cy™5 AffiniPure Donkey Anti-Mouse IgG (H+L) | Jackson Immunoresearch | Cat# 715-175-151, RRID:AB_2340820 |
| Cy™2 AffiniPure Donkey Anti-Rabbit IgG (H+L) | Jackson Immunoresearch | Cat# 711-225-152, RRID:AB_2340612 |
| Cy™3 AffiniPure Donkey Anti-Rabbit IgG (H+L) | Jackson Immunoresearch | at# 711-165-152, RRID:AB_2307443 |
| Proteins, Chemicals and Kits | ||
| MitoTracker™ Deep Red FM - Special Packaging | ThermoFisher Scientific | Cat# M22426 |
| Image-iT™ TMRM | ThermoFisher Scientific | Cat# I34361 |
| 2-NBDG (2-(N-(7-Nitrobenz-2-oxa-1,3-diazol-4-yl)Amino)-2-Deoxyglucose) | ThermoFisher Scientific | Cat# N13195 |
| Alexa Fluor™ 488 Phalloidin | ThermoFisher Scientific | Cat# A12379 |
| Alexa Fluor™ 594 Phalloidin | ThermoFisher Scientific | Cat# A12381 |
| MitoTracker™ Green FM - Special Packaging | ThermoFisher Scientific | Cat# M7514 |
| MitoTracker™ Red CMXRos - Special Packaging | ThermoFisher Scientific | Cat# M7512 |
| DAPI | Sigma-Aldrich | Cat# D9542 |
| Kainic acid monohydrate | Sigma-Aldrich | Cat# K0250-10MG |
| pHrodo™ iFL Green Microscale Protein Labeling Kit | ThermoFisher Scientific | Cat# P36015 |
| pHrodo™ iFL Red Microscale Protein Labeling Kit | ThermoFisher Scientific | Cat# P36014 |
| Seahorse XF Cell Mito Stress Test Kit | Agilent | Cat# 103015-100 |
| HEPES (1 M) | ThermoFisher Scientific | Cat# 15630080 |
| D-(+)-Glucose solution | Sigma-Aldrich | Cat# G8769-100ML |
| Percoll Plus | Sigma-Aldrich | Cat# GE17-5445-01 |
| PicoPure RNA Isolation Kit | Thermo Fisher Scientific | Cat# KIT0204 |
| iScript cDNA Synthesis Kit | Bio-Rad | Cat# 1708891 |
| iTaq Universal SYBR Green Supermix | Bio-Rad | Cat# 1725121 |
| TCL buffer (QIAGEN) | Qiagen | Cat# 1031576 |
| 2-Mercaptoethanol | Sigma-Aldrich | Cat# M6250 |
| Nextera XT Sample Preparation Kit | Illumina | Cat# FC-131-1096 |
| DMEM/F-12, GlutaMAX™ supplement | ThermoFisher Scientific | Cat# 10565042 |
| DMEM, high glucose | ThermoFisher Scientific | Cat# 11965126 |
| GlutaMAX™ Supplement | ThermoFisher Scientific | Cat# 35050061 |
| Trypsin-EDTA (0.05%), phenol red | ThermoFisher Scientific | Cat# 25300120 |
| Penicillin-Streptomycin Mixture | Lonza | Cat# 17-602E |
| Sodium Pyruvate Solution (100 mM) | Lonza | Cat# 13-115E |
| N-acetyl cysteine | Sigma | Cat# A9165 |
| N-2 Supplement (100X) | Gibco | Cat# 17502048 |
| Recombinant Mouse M-CSF Protein | R&D Systems | Cat# 416-ML-050 |
| Recombinant Mouse IL-33 | Biolegend | Cat# 580506 |
| UK-5099 | Sigma-Aldrich | Cat# PZ0160-5MG |
| STF-31 | Selleckchem | Cat# S7931 |
| Oligomycin | Agilent | Cat# 103015-100 |
| Antimycin | Agilent | Cat# 103015-100 |
| Rotenone | Agilent | Cat# 103015-100 |
| AZD8055 | Selleckchem | Cat# S1555 |
| Ly294002 | Selleckchem | Cat# S1105 |
| Triciribine | Selleckchem | Cat# S1117 |
| Torkinib (PP242) | Selleckchem | Cat# S2218 |
| Rapamycin (Sirolimus) | Selleckchem | Cat# S1039 |
| Oltipraz | Sigma-Aldrich | Cat# O9389-5MG |
| ProlongGold Antifade reagent | ThermoFisher Scientific |
Cat# P36930 |
| O.C.T. Compound | Electron Microscopy Sciences | Cat# 62550-01 |
| Triton X-100 | Sigma-Aldrich | Cat# T8787 |
| Normal Donkey Serum | Jackson ImmunoResearch |
Cat# 017-000-001 |
| Papain Dissociation System | Worthington | Cat# LK003150 |
| PBS, pH 7.4 | ThermoFisher Scientific |
Cat# 10010023 |
| 20X Bolt™ MOPS SDS Running Buffer | ThermoFisher Scientific |
Cat# B0001 |
| PageRuler™ Prestained Protein Ladder | ThermoFisher Scientific |
Cat# 26617 |
| Bolt™ 4 to 12%, Bis-Tris | ThermoFisher Scientific |
Cat# NW04120BOX |
| Bolt™ Transfer Buffer (20X) | ThermoFisher Scientific |
Cat# BT00061 |
| Power Blotter Pre-cut Membranes and Filters, PVDF, regular size | ThermoFisher Scientific | Cat# PB9320 |
| 4X Bolt™ LDS Sample Buffer | ThermoFisher Scientific |
Cat#B0008 |
| Western Blotting Filter Paper, 0.83 mm thick, 7 × 8.4 cm | ThermoFisher Scientific | Cat# 84783 |
| Pierce™ ECL Western Blotting Substrate | ThermoFisher Scientific | Cat# 32209 |
| RIPA Lysis and Extraction Buffer | ThermoFisher Scientific |
Cat# 89900 |
| Paraformaldehyde solution 4% in PBS | Santa Cruz | Cat# sc-281692 |
| Sucrose | Sigma-Aldrich | Cat# S0389 |
| cOmplete™, Mini, EDTA-free Protease Inhibitor Cocktail | Roche | Cat# 4693159001 |
| Buffer TCL (125 mL) | QIAGEN | Cat# 1031576 |
| B-Mercaptoethanol | Sigma-Aldrich | Cat# M3148-100ML |
| Recombinant RNase Inhibitor | Takara | Cat# 2313B |
| Deoxynucleotide (dNTP) Solution Mix | New England Biolabs | Cat# N0447L |
| Maxima H Minus Reverse Transcriptase (200 U/uL) | Thermo Fisher Scientific | Cat# EP0753 |
| KAPA HiFi HotStart ReadyMix PCR Kit | Roche | Cat# KK2602 |
| Agencourt RNAClean (RNA SPRI beads) | Beckman Coulter | Cat# A63987 |
| Nuclei EZ Prep | Sigma-Aldrich | Cat# NUC101-1KT |
| AMPureXP SPRI (DNA SPRI beads) | Beckman Coulter | Cat# A63881 |
| Nextera XT DNA Library Preparation Kit | Illumina | Cat# FC-131-1096 |
| NextSeq 500 high output kit V2, 75 cycles | Illumina | Cat# FC-404-2005 |
| 10X Chromium Single Cell 30 Kit | 10X Genomics | Cat# 120237 |
| Oligonucleotides | ||
| sgRNA sequences | See Table S5 | NA |
| qPCR primer sequences | See Table S5 | NA |
| Experimental Model: Strains | ||
| Mouse: C57BL/6J | Jackson Laboratory | JAX:000664, RRID:IMSR_JAX:000664 |
| Mouse: B6J.B6N(Cg)-Cx3cr1tm1.1(cre)Jung/J | Jackson Laboratory | JAX:025524, RRID:IMSR_JAX:025524 |
| Mouse: B6;FVB-Tg(Aldh1l1-EGFP/Rpl10a)JD133Htz/J | Jackson Laboratory | JAX:030248, RRID:IMSR_JAX:030248 |
| Mouse: B6.129S4(Cg)-Mapttm1(EGFP)Klt/J | Jackson Laboratory | JAX:029219, RRID:IMSR_JAX:029219 |
| Mouse: B6.Cg-Tg(Gfap-cre)73.12Mvs/J | Jackson Laboratory | JAX:012886, RRID:IMSR_JAX:012886 |
| Mouse: ilirl1tmIAnnm | (Townsend et al., 2000) | N/A |
| Mouse: Il33−/− | (Oboki et al., 2010) | N/A |
| Mouse: Il1rl1 flox | (Chen et al., 2015) | N/A |
| Mouse: Il33 flox | (Chen et al., 2015) | N/A |
| Mouse: C;129S4-Ptentm1Hwu/J | (Groszer et al., 2001) | JAX:004597, RRID:IMSR_JAX:004597 |
| Deposited Data | ||
| Raw and analyzed data | This paper | GSE127449 |
| Software and Algorithms | ||
| ImageJ | (Schneider et al., 2012) | https://imagej.nih.gov/ij/ |
| Imaris | Bitplane | https://imaris.oxinst.com/ |
| GraphPad Prism 8 | GraphPad Software | https://www.graphpad.com/scientificsoftware/prism/ |
| FlowJo | TreeStar | https://www.flowjo.com/solutions/flowjo |
| RSEM version 1.2.8 | (Li and Dewey, 2011) | http ://deweylab. github. io/RSEM/ |
| edgeR version 3.5.2 | (Robinson et al., 2010) | https://gist.github.com/jdblischak/11384914 |
| Seurat version 2.3.3 | (Satija et al., 2015) | https://github.com/satijalab/seurat |
| 10x Cell Ranger version 1.2 | 10X Genomics |
https://support.10xgenomics.com/singlecell/software/overview/welcome
|
| Monocle version 2.8.0 | (Qiu et al., 2017) | http://cole-trapnell-lab.github.io/monocle-release/ |