REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse anti CD68 (used 1:100)	Agilent M0876	RRID:AB_2074844
Rabbit anti P2RY12 (used 1:500)	Sigma-Aldrich HPA014518	RRID:AB_2669027
Rabbit anti Synapsin 1 (used 1:750)	Merck Millipore AB1543P	RRID:AB_90757
Mouse anti synaptophysin (used 1:500)	Abcam ab8049	RRID:AB_2198854
Rabbit anti synaptophysin, direct labeled Alexa Fluor™ 488 (used 1:500)	Abcam ab196379	RRID:AB_2922671
Guinea pig anti PSD-95 (used 1:500)	Synaptic systems 124 014	RRID:AB_2619800
Goat anti Iba1 (used 1:500)	Abcam ab5076	RRID:AB_91676
Rabbit anti TMEM119 (used 1:500)	Abcam ab185333	RRID:AB_2687894
Rabbit anti AW7 (used 1:5,000)	Provided by Dominic Walsh	RRID:AB_2313982
Chicken anti GFAP (used 1:2,000/1:3,000)	Abcam ab53554	RRID:AB_880202
Rabbit anti GAD65/67 (used 1:500)	Abcam ab55412	RRID:AB_880148
Rabbit anti Histone H3 (used 1:1000)	Abcam ab1791	RRID:AB_302613
Rabbit anti PSD-95 (used 1:1000)	Cell Signaling D27E11	RRID:AB_2292883
Mouse anti pan-neurofilament (SMI-312) (used 1:500)	BioLegend 837904	RRID:AB_2566782
Sheep anti MFG-E8 (used 1:500)	R&D Systems AF2767	RRID:AB_10889829
Mouse anti MFG-E8 (used at 10 μg/mL)	Creative Biolabs FAMAB-0225CQ-LowE	N/A
Mouse anti IgG1 (used at 10 μg/mL)	Creative Biolabs MOB-065CQ	N/A
Mouse anti integrin α5β5 (used at 2.5 μg/mL)	R&D Systems MAB2528	RRID:AB_2280706
Mouse anti CD11b-Alexa Fluor™ 594 (used 5 μg/mL)	Biolegend 301340	RRID:AB_2563208
Mouse anti CD45-APC (used 1:20)	Biolegend 304011	RRID:AB_314399
Rat anti CX3CR1-PECy7 (used 0.1 μg/mL)	Biolegend 341611	RRID:AB_2297689
Rat anti CD16/32 (Fc block against mouse) (used 1:1000)	Biolegend 101302	RRID:AB_312801
Human TruStain FcX™ Fc block (Fc block against human) (used 1:1000)	Biolegend 422302	RRID:AB_2818986
Donkey anti mouse Alexa Fluor™ 594 (used 1:500)	Thermo Fisher Scientific A-21203	RRID:AB_141633
Donkey anti rabbit Alexa Fluor™ 488 (used 1:500)	Thermo Fisher Scientific A-21206	RRID:AB_2535792
Donkey anti rabbit Alexa Fluor™ 594 (used 1:500)	Thermo Fisher Scientific A-21207	RRID:AB_141637
Donkey anti rabbit Alexa Fluor™ 647 (used 1:500)	Thermo Fisher Scientific A-31573	RRID:AB_2536183
Donkey anti goat Alexa Fluor™ 647 (used 1:500)	Thermo Fisher Scientific A32849	RRID:AB_2762840
Goat anti chicken Alexa Fluor™ 647 (used 1:500)	Thermo Fisher Scientific A32933	RRID:AB_2762845
Donkey anti chicken Alexa Fluor™ 405 (used 1:500)	Jackson ImmunoResearch 103-475-155	RRID:AB_2337389
Goat anti Guinea pig Alexa Fluor™ 594 (used 1:500)	Thermo Fisher Scientific A-11076	RRID:AB_141930
Goat anti mouse IgM Alexa Fluor™ 594 (used 1:500)	Thermo Fisher Scientific A-21044	RRID:AB_2535713
Rabbit anti-goat HRP (used 1:5000)	Abcam ab6741	RRID:AB_955424
IRDye 680RD Donkey anti-mouse (used 1:5000)	LI-COR 925-68072	RRID:AB_2814912
IRDye 800CW Donkey anti-rabbit (1:5000)	LI-COR 925-32213	RRID:AB_2715510
Biological samples
Human postmortem brain samples (paraffin embedded and fresh-frozen) and live brain samples for cell isolation	MRC Edinburgh Brain Bank	See Tables S1 and S2 for all sample info
Chemicals, peptides, and recombinant proteins
Citrate buffer pH 6	Vector labs	H3300
Autofluorescence eliminator reagent	Merck	2160
TrueVIEW ® Autofluorescence Quenching Kit	Vector labs	SP-8400-15
Triton X-100	Sigma-Aldrich	T8787-100ML
Normal donkey serum	Sigma-Aldrich	D96663
Normal goat serum	Sigma-Aldrich	S26-100ML
DAPI	Sigma-Aldrich	D9542-10MG
Hoechst	ThermoFisher Scientific	H3570
Cellmask deep red	Life technologies	C10046
Thioflavin S	Sigma-Aldrich	T1892
Ponceau S	Sigma-Aldrich	P7170-1L
Immumount	ThermoFisher Scientific	9990402
pHrodo™ Red-SE	ThermoFisher Scientific	P36600
NuPAGE™ buffer	ThermoFisher Scientific	NP0002
Odyssey blocking buffer	LI-COR	927–40000
Protease inhibitors	Merck	11836170001
Phosphatase inhibitors	Merck	524629-1SET
Protease inhibitor cocktail EDTA-free	ThermoFisher Scientific	78447
Western blot molecular weight marker	LI-COR	928–40000
DMEM + GlutaMAX	ThermoFisher Scientific	31966–021
DMEM/F-12	ThermoFisher Scientific	11320033
Astrocyte medium	Caltag Medsystems	SC-1801
Percoll	GE Healthcare	GE17-0891-01
Human mCSF1	R&D Systems	216-MC-010/CF
Mouse mCSF1	R&D Systems	416-ML-010/CF
Recombinant human TGFβ-1	Miltenyi	170-076-166
Low endotoxin BSA	Sigma-Aldrich	A8806
Fetal bovine serum (heat inactivated)	ThermoFisher Scientific	10500064
Penicillin/streptomycin	ThermoFisher Scientific	15070063
Cytochalasin D	Sigma-Aldrich	C8273
K777	Adipogen	AG-CR1-0158
IL-34	Peprotech	20034205
BDNF	Peprotech	45002100
Critical commercial assays
Neural Tissue Dissociation Kit (P)	Miltenyi	130-092-628
Micro BCA kit	ThermoFisher Scientific	23235
CD11b microbeads	Miltenyi	130-093-634
SuperSignal™ West Dura Extended Duration Substrate	ThermoFisher Scientific	34075
Deposited data
All spreadsheets and statistical analysis files can be found at https://doi.org/10.7488/ds/7492	N/A	N/A
All image analysis scripts are available on Github at https://github.com/Spires-Jones-Lab.	N/A	N/A
Experimental models: Cell/mouse lines
Primary human astrocytes	Caltag Medsystems (Sciencell)	SC-1800
BV2 cells
C57Bl/6J mice	Charles River Laboratories	000664
Software and algorithms
R Studio Version 2022.12.0 + 353	GitHub	https://github.com/rstudio/rstudio
R version 4.1.2 GUI 1.77 High Sierra build	https://www.r-project.org/	R 4.1.2 GUI 1.77 High Sierra build
Color scheme for R Studio graphs:	GitHub	https://github.com/asteves/tayloRswift
Prism 9	GraphPad	Prism 9
FIJI Version 2.0.0-rc-54/1.52t	GitHub	FIJI Version 2.0.0-rc-54/1.52t
MATLAB Version R2022a	Mathworks	Version R2022a
Docker Version 4.10.1 (82475)	Docker	Version 4.10.1 (82475)