REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Mouse APC anti-human CD43	BioLegend	cat#343205; RRID: AB_2194072
Mouse anti-human Iba1	Thermo Fisher Scientific	GT10312; cat#MA5-27726; RRID: AB_2735228
Alexa Fluor 488 goat anti-mouse	Thermo Fisher Scientific	cat#A-11001; RRID: AB_2534069
Rabbit anti-human TMEM119	Thermo Fisher Scientific	cat#PA5-119902; RRID: AB_2913474
Alexa Fluor 594 goat anti-rabbit	Thermo Fisher Scientific	cat#A-11012; RRID: AB_2534079
Chemicals, peptides, and recombinant proteins
insulin-transferrin-selenium (100X)	Thermo Fisher Scientific	cat#41400045
B27	Thermo Fisher Scientific	cat#17504044
N2	Thermo Fisher Scientific	cat#17502048
glutamax	Thermo Fisher Scientific	cat#35050061
non-essential amino acids	Thermo Fisher Scientific	cat#11140050
monothioglycerol	Sigma	cat#A8960-5G
human insulin	Sigma	cat#I2643-50MG
IL-34	Peprotech	cat#200-34
TGFβ1	Peprotech	cat#100-21
M-CSF	Peprotech	cat#300-25
CD200	Novoprotein	cat#C311
CX3CL1	Peprotech	cat#300-31
Poly(ethyleneimine) solution (PEI)	Milipore Sigma	cat#181978-100g
4% paraformaldehyde	Electron Microscopy Sciences	cat#157-8-100
DPBS	Gibco	cat#14190-144
Goat serum	Abcam	cat#ab7481
Triton-x	Fisher Scientific	cat#AAA16046AE
NucBlue fixed stain ready probes	Thermo Fisher Scientific	cat#R37606
Poly-D-Lysine	Gibco	cat#A38904-10
Tris-HCl pH 7.5	Thermo Fisher Scientific	cat#15567-027
NaCl	Fisher	cat#S271-500
MgCl2	Fisher	cat#bp214-500
nuclease free H2O	Invitrogen	cat#AM9938
NP-40	Thermo Fisher Scientific	cat#85124
Tween-20	Fisher	cat#bp337-500
Digitonin	Promega	cat#G9441
Critical commercial assays
hematopoietic kit	STEMdiff	cat#05310
Nextera DNA library prep kit	Illumina	cat#FC-121-1030
Zymo clean and concentrator kit	Zymo	cat# D4014
QuantiFluor® dsDNA System	Promega	cat#E2671
NextSeq 500/550 150 bp sequencing kit (v2)	Illumina	cat# 20024907
Lonza Human Stem Cell Nucleofector Kit 1	Lonza	cat#VPH-5012
QIAshredder	Qiagen	cat#79654
RNeasy isolation kit	Qiagen	cat#74104
Takara SMARTer Stranded Total RNA-Seq Kit v3 Pico Input Mammalian	Takara Bio	cat#634485
QIAprep Spin Miniprep Kit (250)	Qiagen	cat#27106
QIAquick Gel extraction kit	Qiagen	cat# 28704/28706
Deposited data
raw and analyzed data	this paper	GEO: GSE245524
reanalyzed microglia ATAC-seq and ChIP-seq data	Gosselin et al.11	dbGAP, accession number: phs001373.v1.p1
reanalyzed PLAC-seq data	Nott et al.20	dbGAP, accession number: phs001373.v2.p1
Experimental models: Cell lines
Human iPSCs	ATCC-DYS0100	cat#ACS-1019; RRID:CVCL_X499
Human iPSCs	Synthego	PGP1-SV1
Oligonucleotides
Illumina primer 1 AATGATACGGCGACCACCGA	IDT	N/A
Illumina primer 2 CAAGCAGAAGACGGCATACGA	IDT	N/A
SNCA_guide_1_F caccgGTGAAGGTATCCGTATAATG	this paper	N/A
SNCA_guide_1_R aaacCATTATACGGATACCTTCACc	this paper	N/A
SNCA_guide_2_F caccgCAATGACTTTCGGTATACTG	this paper	N/A
SNCA_guide_2_R aaacCAGTATAccGAAAGTCATTGc	this paper	N/A
Recombinant DNA
pSpCas9(BB)-2A-GFP (PX458)	Addgene Ran et al.72	cat#48138; RRID:Addgene_48138
Software and algorithms
Illumina NextSeq Control Software (NCS) v2.0	Illumina	https://support.illumina.com/sequencing/sequencing_instruments/nextseq-500/downloads.html
Illumina Bcl2fastq v1.9.0	Illumina	https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software/downloads.html
Trimgalore	Felix Krueger, Babraham Institute	https://github.com/FelixKrueger/TrimGalore
BWA v0.7.17	Li et al.60	https://anaconda.org/bioconda/bwa; RRID:SCR_010910
Multiqc v1.0	Ewels et al.61	https://anaconda.org/bioconda/multiqc; RRID:SCR_014982
Samblaster v0.1.24	Faust et al.62	https://anaconda.org/bioconda/samblaster; RRID:SCR_000468
Samtools v1.9	Danecek et al.73	https://anaconda.org/bioconda/samtools, RRID:SCR_002105
MACS2 v2.1.1	Zhang et al.64	https://anaconda.org/bioconda/macs2; RRID:SCR_013291
GenomicRanges v3.11	Lawrence et al.65	https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html; RRID:SCR_000025
Bedtools v2.29.0	Quinlan et al.66	https://anaconda.org/bioconda/bedtools; RRID:SCR_006646
Benchling	N/A	https://www.benchling.com/RRID:SCR_013955
IGV v2.16.2	Robinson et al.74	https://igv.org/doc/desktop/#DownloadPage/; RRID:SCR_011793
ChIPseeker v3.11	Wang et al.75 Yu et al.67	https://bioconductor.org/packages/release/bioc/html/ChIPseeker.html; RRID:SCR_021322
STAR v2.5.4b	Dobin et al.70	https://anaconda.org/bioconda/star;
edgeR v3.18	Robinson et al.76	https://bioconductor.org/packages/release/bioc/html/edgeR.html; RRID:SCR_012802
Graphpad Prism v10.0.3	N/A	https://www.graphpad.com; RRID:SCR_002798
UCSC Genome Browser PLAC-seq, H3K27ac ChIP-seq, and ATAC-seq session	Nott et al.20	https://genome.ucsc.edu/s/nottalexi/glassLab_BrainCellTypes_hg19
UCSC Genome Browser	Nassar et al.77	https://genome.ucsc.edu; RRID:SCR_005780
Other
StemFlex medium	ThermoFisher	cat#A3349401
Geltrex LDEV-free reduced growth factor basement membrane	ThermoFisher	cat#A1413201
iMatrix	Matrixome	cat#892012
ReLeSR	STEMCELL Technologies	cat#05872
Cell Staining Buffer	BioLegend	cat#420201
TruStain FcX (Fc Receptor Blocking Solution)	BioLegend	cat#422301
12x75mm round bottom tubes	Fisherbrand	cat#14-965-3C
DMEM/F12, HEPES, no phenol red	ThermoFisher	cat#11039021
8-well chamber slides	Ibidi	cat#80841
EverBright Hardset Mounting Medium	Biotium	cat#23003
TD Buffer (part of kit)	Illumina	cat#FC-121-1030
ATM (part of kit)	Illumina	cat#FC-121-1030
NT buffer (part of kit)	Illumina	cat#FC-121-1030
Illumina Nextera DNA unique Dual Indexes	Illumina	cat#20027214
NEBNext High-Fidelity 2X PCR Master Mix	NEB	cat#M0541L
KAPA Pure beads	Roche	cat#KK8001
Agilent DNA High Sensitivity chip	Agilent Technologies	cat#5067-4626
T4 Kinase (PNK)	Thermo Fisher Scientific	cat#EK3001
BbsI	NEB	cat#R0539S/R0539L
Cut Smart Buffer	NEB	cat#B7204
T4 ligase buffer	Thermo Fisher Scientific	cat#B69
T4 DNA ligase	Thermo Fisher Scientific	cat# EL0011
PlasmidSafe ATP-dependent DNase	Lucigen	cat#E3101K
PlasmidSafe buffer	Lucigen	not available
25 mM ATP solution	Lucigen	not available
One Shot Top10 E. Coli	Thermo Fisher Scientific	cat#C404003
S.O.C.	Thermo Fisher Scientific	cat#15544034
Revitacell	Thermo Fisher Scientific	cat#A2644501