REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
7-AAD	BD Biosciences	Cat# 559925
Alexa Fluor™ 647 Phalloidin	Invitrogen	Cat# A22287
alpha Tubulin Monoclonal Antibody (DM1A)	Thermo Fisher Scientific	Cat# 62204; RRID: AB_1965960
Anti Iba1, Rabbit antibody	FUJIFILM Wako Pure Chemical Corporation	Cat# 019-19741; RRID:AB_839504
Anti-non-muscle Myosin IIB antibod antibody	abcam	Cat# ab204358; RRID: AB_2737410
APC anti-human CD11c antibody	BioLegend	Cat# 337208; RRID:AB_1279066
APC anti-mouse/human CD11b	Bio Legend	Cat# 101212; RRID: AB_312795
APC mouse anti-CD36 antibody	BD Biosciences	Cat# 550956; RRID:AB_398480
Beta Actin antibody	Proteintech	Cat# 20536-1-AP; RRID:AB_10700003
BV421 mouse anti-human CD16 antibody	BD Biosciences	Cat# 562874; RRID:AB_2716865
BV605 anti-human CD192 (CCR2) antibody	BioLegend	Cat# 357214; RRID:AB_2563876
BV605 mouse anti-human CD11b antibody	BD Biosciences	Cat# 562721; RRID:AB_2737745
Connexin 43 Antibody	Cell Signaling	Cat# 3512; RRID: AB_2294590
FITC anti-human CX3CR1 antibody	BioLegend	Cat# 341606; RRID:AB_1626272
goat anti-mouse-AlexaFluor594	Invitrogen	Cat# A11020; RRID: AB_141974
goat anti-rat-AlexaFluor488	Invitrogen	Cat# A11006; RRID: AB_141373
HLA-DR, DP, DQ antibody	BD Biosciences	Cat# 555558; RRID:AB_395940
IRDye® 680LT Donkey anti-Mouse IgG (H + L)	LI-COR Biotechnology	Cat# 926-68022; RRID: AB_10715072
IRDye® 800CW Goat anti-Rabbit IgG (H + L)	LI-COR Biotechnology	Cat# 926-32211; RRID: AB_621843
N-cadherin Polyclonal Antibody	Thermo Fisher Scientific	Cat# PA5-19486; RRID: AB_10979609
PE anti-human P2RY12 antibody	BioLegend	Cat# 392104; RRID:AB_2716007
PE anti-mouse/human CD11b antibody	Bio Legend	Cat# 101207; RRID: AB_312790
PE-Cy7 mouse anti-CD14 antibody	BD Biosciences	Cat# 557742; RRID:AB_396848
Polyclonal Rabbit anti-Human TNFAIP2 Antibody	LSBio	Cat# LS-C386457
Purified (azide-free) anti-alpha-Synuclein, 103-108 antibody	BioLegend	Cat# 807801; RRID: AB_2564730
Rabbit Anti-beta Catenin Monoclonal Antibody, Unconjugated, Clone E247	Abcam	Cat# ab32572; RRID: AB_725966
Rabbit Anti-GAPDH Antibody	Sigma-Aldrich	Cat# G9545; RRID:AB_796208
Rat anti mouse CD11b antibody	Serotec by Bio-Rad	Cat# MCA711; RRID: AB_321292
Recombinant Anti-RAB8A antibody [EPR14873]	Abcam	Cat# ab188574; RRID: AB_2814989
Rock-2 (30-J) antibody	Santa Cruz Biotechnology	Cat# sc-100425; RRID:AB_1129154
Texas Red™-X Phalloidin	Thermo Fisher Scientific	Cat#T7471
Biological Samples
Human post-mortem brain sections	Tübingen Brain Bank	N/A
Human post-mortem brain sections	DZNE Brain Bank Bonn	N/A
Chemicals, Peptides, and Recombinant Proteins
4’,6-Diamidino-2’-phenylindol-dihydrochloride (DAPI)	Thermo Fisher Scientific	Cat# 62247
ATTO-488 NHS-ester	Atto-Tec GmbH	Cat# AD 488-35
ATTO-550 NHS-ester	Atto-Tec GmbH	Cat# AD 550-35
Buprenorphine hydrochloride	Indivior Eu Ltd.	PZN# 345928
Calcium chloride	Sigma-Aldrich	Cat# 499609
Cefotaxime	MIP pharma	PZN# 3916283
CellTracer™ Violet	Thermo Fisher Scientific	Cat# C34557
Dexamethasone	Jenapharm	PZN# 8704321
Dulbecco‘s Modified Eagle‘s Medium	GIBCO by Thermo Fisher Scientific	Cat# 31966047
Dulbecco‘s Phosphate-Buffered Saline	GIBCO by Thermo Fisher Scientific	Cat# 14190169
Fetal Bovine Serum	LIFE Technologies	Cat# 10270106
Glucose	Sigma-Aldrich	Cat# G7528
GlutaMAX	GIBCO	Cat# 35050061
Halt Protease Phosphatase Inhibitor Cocktail	Thermo Fisher Scientific	Cat# 78441
Ketamine	Ratiopharm	PZN# 7538837
Lipopolysaccharide from Escherichia coli K12	InvivoGen	Cat# tlrl-eklps
N2-Supplement	GIBCO by Thermo Fisher Scientific	Cat# 17502048
Normal goat serum	Abcam	Cat# ab7481
Normal Horse Serum	Abcam	Cat# ab139501
NuPAGE® 4–12% Bis-Tris gel	Invitrogen	Cat# NP0323BOX
Paraformaldehyde	Sigma-Aldrich	Cat# P6148
Penicillin/Streptomycin	GIBCO by Thermo Fisher Scientific	Cat# 15070063
Phosphate-Buffered Saline	Biochrom GmbH	Cat# L 182-10
Poly-D-lysine hydrobromide	Sigma-Aldrich	Cat# P6407
Poly-L-lysine hydrobromide	Sigma-Aldrich	Cat# P1524
Proteinase K	Thermo Fisher Scientific	Cat# 10181030
Sodium bicarbonate	Sigma-Aldrich	Cat# S5761
Sodium dodecyl sulfate (SDS)	Carl Roth	Cat# CN30.2
Superfrost ultra plus slides	Thermo Fisher Scientific	Cat# J3800AMNZ
Thioflavin T	Sigma-Aldrich	Cat# T3516-25G
Tissue-Tek® Optimal Cutting Temperature (OCT) compound	Sakura by Thermo Fisher Scientific	Cat# 4583
Trypsin-EDTA (0.5%), no phenol red	LIFE Technologies	Cat# 15400054
Xylazine	Serumwerk Bernburg	PZN# 10124950
Critical Commercial Assays
Mouse IL-1 beta/IL-1F2 DuoSet ELISA	R&D Systems	Cat# DY401
Mouse IL-10 DuoSet ELISA	R&D Systems	Cat# DY417
Mouse IL-6 DuoSet ELISA	R&D Systems	Cat# DY406
Mouse TNF-alpha DuoSet ELISA	R&D Systems	Cat# DY410
Pierce™ BCA Protein Assay kit	Thermo Fischer Scientific	Cat# 23225
Proteome Profiler Mouse Cytokine Array Kit, Panel A	R&D Systems	Cat# ARY006
RNeasy Micro Kit	QIAGEN	Cat# 74004
Pierce LAL Chromogenic Endotoxin Quantification Kit	Fisher Scientific	Cat# 88282
XF Cell Mito Stress Test	Agilent	Cat# 103015-100
Deposited Data
GEO Dataset	https://www.ncbi.nlm.nih.gov/geo/	GEO accession number: GSE152100
GEO Dataset	https://www.ncbi.nlm.nih.gov/geo/	GEO accession number: GSE166127
Experimental Models
E.coli BL21 DE3 CodonPlus cells	Aligent Technologies	Cat# 230245
Human: peripheral blood mononuclear cells (PBMCs)	University of Bonn - Medical Center	N/A
Mouse: C57BL/6	Charles River Laboratories	RRID: IMSR_JAX:000664
Mouse: C57BL/6 Cx3cr1GFP	The Jackson Laboratory	RRID: IMSR_JAX:005582
Mouse: C57BL/6 LRRK2 G2019S	Taconic Biosciences	RRID: IMSR_TAC:13940
Mouse: C57BL/6 ROCK1flox	kind gift of Prof. Henneberger	N/A
Mouse: C57BL/6 ROCK2flox	kind gift of Prof. Henneberger	N/A
Software and Algorithms
CellProfiler	Broad Institute of Harvard and MIT	v3.1.8
FACSDIVA™ software	Becton Dickinson	N/A
Fiji ImageJ	Wayne Rusband	v2.0.0-rc-69/1.52n
FlowJo	FlowJo, LLC	v3.05470
ggplot2	CRAN	v3.2.1
Graph Pad Prism	GraphPad Software Inc.	v7.0e and v8.0
Image Studio, v5.2	LI-COR Biosciences	N/A
Imaris	Bitplane by Oxford Instruments plc	v9.2.1
NIS-elements	Nikon	AR 4.20.03
Partek Genomics Suite and R	Parket Inc.	v3.5.0
tidyr	CRAN	v1.0.2
Other
BD FACSCANTOII	BD Biosciences	equipment
HiSeq2500	Illumina	equipment
Infinite M200 Pro	TECAN	equipment
Leica TCS SP8 STED	Leica	equipment
Nikon Eclipse Ti fluorescence microscope	Nikon	equipment
ODYSSEY CLx Imaging System	LI-COR Biotechnology	equipment
Schick driller C1 device	Schick GmbH	equipment
Ti:Sapphire 2-photon laser scanning microscope	Nikon	equipment
XFe-24 Extracellular Flux Analyzer	Agilent	equipment
Zeiss Laser Scan Microscope 800	Carl Zeiss	equipment