REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit polyclonal anti-β amyloid	Invitrogen	Cat# 71-5800 RRID: AB_2533989
Rabbit polyclonal anti-IBA1	Wako Chemicals	Cat# 019-19741 RRID: AB_839504
Armenian Hamster monoclonal anti-CD11c	Novus Biologicals	Cat# NB110-97871 RRID: AB_1290725
Rabbit polyclonal anti-P2ry12	Atlas Antibodies	Cat# HPA013796 RRID: AB_1854884
Goat polyclonal anti-lysozyme C	Santa Cruz Biotechnologies	Cat# sc27958 RRID: AB_2138790
Mouse monoclonal anti-CD105	R&D Systems	Cat# MAB1097 RRID: AB_35739
Rabbit monoclonal anti-cleaved caspase 3 (ASP175) (5A1E)	Cell Signaling Technology	Cat# 9664 RRID: AB_2070042
Horse anti-rabbit biotinylated secondary	Vector Laboratories	Cat# BA-1100 RRID: AB_2336201
Goat anti-mouse secondary Alexa Fluor 488	abcam	Cat# ab150113 RRID: AB_2576208
Goat anti-rabbit secondary Alexa fluor 594	Invitrogen	Cat# R37117 RRID: AB_2556545
Goat anti-Armenian hamster secondary Alexa fluor 488	Jackson Immuno-Research Labs	Cat# 127-545-099 RRID: AB_2338996
DAPI	Invitrogen	Cat# 3571 RRID: AB_2307445
Vectastain ABC kit, standard	Vector Laboratories	Cat# PK-6100 RRID: AB_2336819
DAB peroxidase substrate kit, 3,3’-diaminobenzidine	Vector Laboratories	Cat# SK-4100 RRID: AB_2336382
Vectashield hardset antifade mounting medium	Vector Laboratories	Cat# H-1400 RRID: AB_2336787
CD11b microbeads, human & mouse	Miltenyi Biotec	Cat# 130-049-601 RRID: N/A
CD14 microbeads, human	Miltenyi Biotec	Cat# 130-050-201 RRID: AB_2665482
Chemicals, peptides, and recombinant proteins
Formic acid, reagent grade	Sigma Aldrich	F0507
Bovine Serum Albumin	Sigma Aldrich	A7906
Matrigel	BD Biosciences	356234
mTeSR1	StemCell Technologies, Inc.	85851
Accutase	EMD Millipore	SCR005
bFGF	EMD Millipore	01-106
Recombinant human BMP4 protein	R&D Systems	314-BP-010
Recombinant human FLT3 protein	R&D Systems	308-FK-100
Recombinant human GM-CSF protein	R&D Systems	215-GM-050
Recombinant human IL3 protein	R&D Systems	203-IL-010
Recombinant human IL34 protein	R&D Systems	5265-IL-010
Recombinant human M-CSF protein	R&D Systems	216-MC-025
Recombinant human SCF protein	R&D Systems	255-SC-010
Recombinant human VEGF protein	R&D Systems	239-VE-010
Recombinant human thrombopoietin protein	R&D Systems	288-TP-005
StemPro 34 Serum Free Media	Gibco	10639011
RPMI 1640 Media	Gibco	11875093
GlutaMAX Supplement	Gibco	35050061
Cadmium Chloride	Sigma Aldrich	202908
Zinc Chloride	Sigma Aldrich	229997
Critical commercial assays
Neural Tissue Dissociation Kit (P)	Miltenyi Biotec	130-092-628
Direct-zol RNA Miniprep Kit	Zymo Research	R2051
SMART-Seq v4 Ultra Low Input RNA Kit	Takara	091817
Deposited data
Raw data files for RNAseq	NCBI Gene Expression Omnibus	GSE163857
Experimental models: Cell lines
EDi036-A; female, 79 years, E3/E3	iPSC Core, Cedars Sinai Medical Center	EDi036
EDi034-A; female, 79 years, E3/E3	iPSC Core, Cedars Sinai Medical Center	EDi034
EDi035-A; female, 79 years, E3/E3	iPSC Core, Cedars Sinai Medical Center	EDi035
EDi028-A; male, 79 years, E3/E3	iPSC Core, Cedars Sinai Medical Center	EDi028
EDi029-A; male 80 years, E3/E3	iPSC Core, Cedars Sinai Medical Center	EDi029
EDi042-A; female, 79 years, E3/E4	iPSC Core, Cedars Sinai Medical Center	EDi042
EDi044-A; female, 80 years, E3/E4	iPSC Core, Cedars Sinai Medical Center	EDi044
EDi023-A; female, 79 years, E4/E4	iPSC Core, Cedars Sinai Medical Center	EDi023
EDi022-A; male; 79 years, E3/E4	iPSC Core, Cedars Sinai Medical Center	EDi022
CS8FP5iCTR; male, 45 years, E3/E4	iPSC Core, Cedars Sinai Medical Center	CS8FP5iCTR
Experimental models: Organisms/strains
Mouse: APOE-FAD	Generated in the laboratory of Dr. Mary Jo LaDu	N/A
Software and algorithms
Prism 7	GraphPad Software
R statistical software package version 1.1.463	R Foundation
Other
MACS SmartStrainers (70um)	Miltenyi Biotec	130-098-462
MS Columns	Miltenyi Biotec	130-042-201
MACS Separation Buffer	Miltenyi Biotec	130-091-221
OctoMACS Separator	Miltenyi Biotec	130-042-109