REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit polyclonal anti-Tuj1	Sigma	Cat#: T2200; RRID: AB_262133
Mouse monoclonal anti-Tuj1 (clone 2G10)	Abcam	Cat#: ab78078; RRID: AB_2256751
Rabbit polyclonal anti-Sox2	Abcam	Cat#: ab97959; RRID: AB_2341193
Rat monoclonal anti-Ctip2 (clone 25B6)	Abcam	Cat#: ab18465; RRID: AB_2064130
Rabbit polyclonal anti-Satb2	Abcam	Cat#: ab34735; RRID: AB_2301417
Mouse monoclonal anti-GFAP (clone GA5)	Millipore	Cat#: MAB360; RRID: AB_11212597
Goat polyclonal anti-ApoE	Millipore	Cat#: AB947; RRID: AB_2258475
Mouse monoclonal anti-actin (clone AC-74)	Sigma	Cat#: A2228; RRID: AB_476697
Rabbit monoclonal anti-Nanog (clone D73G4)	Cell Signaling Technology	Cat#: 4903 S; RRID: AB_10559205
Mouse monoclonal anti-TRA-1-60 (clone TRA-1-60)	Abcam	Cat#: ab16288; RRID: AB_778563
Mouse monoclonal anti-Nestin (clone 2C1.3A11)	Abcam	Cat#: ab18102; RRID: AB_444246
Mouse monoclonal anti-Sox17 (clone 3B10)	Abcam	Cat#: ab84990; RRID: AB_1861437
Goat polyclonal anti-Brachyury	R&D Systems	Cat#: AF2085; RRID: AB_2200235
Rabbit monoclonal anti-S100β	Abcam	Cat#: ab52642; RRID: AB_882426
Rabbit polyclonal anti-Pax6	BioLegend	Cat#: 901302; RRID: AB_2565003
Rabbit polyclonal anti-Tbr2	Abcam	Cat#: ab23345; RRID: AB_778267
Mouse monoclonal anti-Nkx2.1 (clone 8G7G3/1)	Thermo Fisher Scientific	Cat#: MA5-13961; RRID: AB_10984070
Donkey polyclonal anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor Plus 488	Invitrogen	Cat#: A32790; RRID: AB_2762833
Donkey polyclonal anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor Plus 594	Invitrogen	Cat#: A32754; RRID: AB_2762827
Donkey polyclonal anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor Plus 488	Invitrogen	Cat#: A32766; RRID: AB_2762823
Donkey anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor Plus 594	Invitrogen	Cat#: A32744; RRID: AB_2762826
Donkey anti-Rat IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488	Invitrogen	Cat#: A21208; RRID: AB_2535794
Donkey anti-Rat IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 594	Invitrogen	Cat#: A21209; RRID: AB_2535795
Donkey anti-Goat IgG (H+L) Cross-Adsorbed Secondary Antibody, Alexa Fluor 488	Invitrogen	Cat#: A-11055; RRID: AB_2534102
IRDye 800CW Donkey anti-Goat IgG antibody	LI-COR Biosciences	Cat#: 926-32214; RRID: AB_621846
IRDye 680RD Donkey anti-Mouse IgG secondary antibody	LI-COR Biosciences	Cat#: 926-68072; RRID:AB_10953628
Bacterial and virus strains
DH5α competent cells	Thermo Fisher Scientific	Cat#: 18265017
Chemicals, peptides, and recombinant proteins
FastDigest BbsI	Thermo Fisher Scientific	Cat#: ER1011
FastAP	Thermo Fisher Scientific	Cat#: EF0651
Plasmid-Safe exonuclease	Lucigen	Cat#: E3101K
SOC medium	Thermo Fisher Scientific	Cat#: 15544034
mTeSR1	STEMCELL Technologies	Cat#: 85850
Matrigel hESC-qualified	Corning	Cat#: 354277
Y-27632	STEMCELL Technologies	Cat#: 72304; CAS: 129830-38-2
Dispase	STEMCELL Technologies	Cat#: 07923
Accutase	STEMCELL Technologies	Cat#: 07920
STEMdiff™ Cerebral Organoid Kit	STEMCELL Technologies	Cat#: 08570
DMEM/F-12	Thermo Fisher Scientific	Cat#: 11330-057
Neurobasal	Thermo Fisher Scientific	Cat#: 21103-049
B-27 Supplement	Thermo Fisher Scientific	Cat#: 17504044
N2 supplement	Thermo Fisher Scientific	Cat#: 17502-048
GlutaMAX	Thermo Fisher Scientific	Cat#: 35050061
Nonessential amino acids (NEAA)	Thermo Fisher Scientific	Cat#: 11140076
Ascorbic acid	STEMCELL Technologies	Cat#: 72132; CAS: 50-81-7
DbcAMP	Sigma	Cat#: D0260; CAS: 16980-89-5
Recombinant Human/Murine/Rat BDNF	PeproTech	Cat#: AF-450-02
Animal-Free Recombinant Human GDNF	PeproTech	Cat#: AF-450-10
Sodium pyruvate	Thermo Fisher Scientific	Cat#: 11360070
Normal goat serum	Thermo Fisher Scientific	Cat#: 31872
Bovine serum albumin (BSA)	Sigma	Cat#: A1470
Penicillin-Streptomycin	Thermo Fisher Scientific	Cat#: 15140122
Critical commercial assays
QIAquick® Gel Extraction Kit	QIAGEN	Cat#: 28704
Phusion™ High-Fidelity DNA Polymerase	Thermo Fisher Scientific	Cat#: F530L
Quick Ligation™ Kit	NEB	Cat#: M2200S
Invitrogen Neon™ Transfection System	Thermo Fisher	Cat#: MPK5000
SsoAdvanced Universal SYBR Green Supermix	Bio-Rad	Cat#: 1725274
Quick-DNA genomic extraction kit	Zymo Research	Cat#: D3025
Gel Purification Kit	MACHEREY-NAGEL	Cat#: 740609.250
RNase-Free DNase Set	QIAGEN	Cat#: 79254
RNeasy Mini Kit	QIAGEN	Cat#: 74104
ReverTra Ace® qPCR RT Master Mix	Toyobo	Cat#: FSQ-201
Experimental models: cell lines
MC0192 human iPSC line	(Zhao et al., 2017)	N/A
Oligonucleotides
Primer pairs for qRT-PCR for APOE	(Meyer et al., 2019)	N/A
Primer pairs for qRT-PCR for ACTB	(Zhao et al., 2020)	N/A
Recombinant DNA
PX459 plasmid	(Ran et al., 2013)	Addgene_48139
Software and algorithms
GPP	Broad Institute	https://portals.broadinstitute.org/gpp/public/analysis-tools/sgrna-design
CRISPOR	Broad Institute	http://crispor.tefor.net/
Other
96-Well round-bottom ultra-low attachment plate	Corning	Cat#: 7007
Organoid Embedding Sheet	STEMCELL Technologies	Cat#: 08579