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. 2025 Apr 16;28(5):112446. doi: 10.1016/j.isci.2025.112446
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Anti-SOX2 antibody Abcam Cat# ab97959;
RRID:AB_2341193
Anti-Doublecortin (DCX) antibody Abcam Cat# ab18723; RRID:AB_732011
Neuronal Class III beta-Tubulin (TUJ1) Monoclonal Antibody, Purified BioLegend Cat# 801201; RRID:AB_2313773
GAPDH (6C5) Santa Cruz Biotechnology Cat# sc-32233; RRID:AB_627679
Anti-Nestin, human, clone 10C2 Millipore Cat# MAB5326; RRID:AB_2251134
Human Nestin Phycoerythrin (PE)-conjugated Antibody R&D Systems Cat# IC1259P; RRID:AB_2151147
Cleaved Caspase-3 (Asp175) (5A1E) Rabbit mAb Cell Signaling Technology Cat# 9664; RRID:AB_2070042
Anti-phospho-Histone H2A.X (Ser139) Antibody, clone JBW301 Millipore Cat# 05-636; RRID:AB_309864
Chemicals, peptides, and recombinant proteins
hESC-qualified matrigel Corning Cat# 356277
mTeSR1 StemCell Technologies Cat# 85850
DMEM/F-12, GlutaMAX™ supplement Gibco Cat# 10565018
Neurobasal™ Medium Gibco Cat# 21103049
MEM Non-essential Amino Acid Solution (100×) Merck Cat# M7145
GlutaMAX™ Supplement Gibco Cat# 35050061
Insulin solution human Sigma-Aldrich Cat# I9278
2-Mercaptoethanol Sigma-Aldrich Cat# M3148
Penicillin-Streptomycin (10,000 U/mL) Gibco Cat# 15140122
B-27™ supplement (50X), serum free Gibco Cat# 17504044
N-2 Supplement (100X) Gibco Cat# 17502001
Dorsomorphin dihydrochloride Tocris Cat# 3093
SB 431542 Tocris Cat# 1614
Recombinant Human FGF-basic (154 a.a.) PeproTech Cat# 100-18B
ACCUTASE™ StemCell Technologies Cat# 07922
Recombinant Human/Murine/Rat BDNF PeproTech Cat# 450-02
Recombinant Human GDNF PeproTech Cat# 450-10
Glasgow's MEM (GMEM) Gibco Cat# 11710035
KnockOut™ Serum Replacement Gibco Cat# 10828010
Sodium Pyruvate (100 mM) Gibco Cat# 11360070
endo-IWR 1 Tocris Cat# 3532
Chemically Defined Lipid Concentrate Gibco Cat# 11905031
DPBS Biowest Cat# L0615-500
Tris Duchefa Biochemie Cat# T1501
NaCl Sigma-Aldrich Cat# 9888
NP-40 Sigma-Aldrich Cat# I8896
Sodium deoxycholate Sigma-Aldrich Cat# 264103
SDS Sigma-Aldrich Cat# 62862
Triton™ X-100 Sigma-Aldrich Cat# T9284
BSA assay kit Bio-Rad Cat# 5000006
Tween® 20, Molecular Biology Grade Promega Cat# H5151
Fisher Healthcare Tissue-Plus™ O.C.T. Compound Thermo Fisher Scientific Cat# 23-730-571
Skim Milk Powder MB cell Cat# MB-S1667
Albumin bovine, fraction V, ≥98% MP Biomedicals Cat# 0216006980
Donkey serum Merck Cat# S30-100ML
Glycine Daejung Cat# 4068-4105
Hoechst 33342 Invitrogen Cat# H3570
MitoSOX Invitrogen Cat# M36008
Live-or-Dye™ Fixable Viability Staining Kits Biotium Cat# 32008-T
XF 24 FLUXPAK MINI Agilent Technologies Cat# 102342-100
XF DMEM medium Agilent Technologies Cat# 103573-100
Seahorse XF Glucose Solution Agilent Technologies Cat# 103577-100
Seahorse XF Pyruvate Solution Agilent Technologies Cat# 103578-100
Seahorse XF Glutamine Solution Agilent Technologies Cat# 103579-100
Oligomycin Sigma-Aldrich Cat# 75351
2-Deoxy-D-glucose Sigma-Aldrich Cat# 8375
FCCP [carbonyl cyanide 4-(trifluoromethoxy)-phenylhydrazone] Sigma-Aldrich Cat# C2920
Rotenone Sigma-Aldrich Cat# R8875
Critical commercial assays
Click-iT™ EdU Cell Proliferation Kit for Imaging, Alexa Fluor™ 594 dye EdU Invitrogen Cat# C10339
P3 Primary Cell 4D-Nucleofector Kit Lonza Cat# V4XP-3024
Deposited data
scRNA-seq from human prefrontal cortex at gestation weeks 8-26 Zhong et al.20 GEO: GSE274912
RNA-seq data from NPCs and Neurons In this study GEO: GSE104276
Original western blot images In this study https://doi.org/10.17632/zjcy22ztjr.1 (Mendeley Data)
Experimental models: Cell lines
Human iPSC line from a healthy control (APOE3) Coriell Cat# AG09173
APOE4 isogenic line from #AG09173 Tsai Laboratory12 N/A
APPswe isogenic line from #AG09713 In this study N/A
Oligonucleotides
APP sgRNA oligomer pair (Forward):
5’–CACCGCAGAATTCCGACATGACTC-3’		 This paper N/A
APP sgRNA oligomer pair (Reverse):
5’–AAACGAGTCATGTCGGAATTCTGC-3’		 This paper N/A
ssODN for APP → APPswe
5'-AAACTAATTGGTTGTCCTGCATACT
TTAATTATGATGTAATACAGGTTCTGG
GTTGACAAATATCAAGACGGAGGAGA
TCTCTGAAGTGAATCTCGATGCAGAAT
TCCGACATGACTCAGGATATGAAGTT
CATCATCAAAAATTGGTACGTAAAAT
AATTTACCTCTTTCCACTACTGT-3'		 This paper N/A
Primer for APP (Forward):
5’-GCCAACCTCTCAACCAGGAT-3’		 This paper N/A
Primer for APP (Reverse):
5’-GCACAGGATGAACCAGAGTT-3’		 This paper N/A
Primer for Off-target #1 (Forward):
5’-GATGACTAAGTAGAGTTGGGGAGC-3’		 This paper N/A
Primer for Off-target #1 (Reverse):
5’-GACAATAGCGGTTTTGATGG-3’		 This paper N/A
Primer for Off-target #2 (Forward):
5’-AGGAACAGCCTGCACATAGC-3’		 This paper N/A
Primer for Off-target #2 (Reverse):
5’-GGTGTGGATCTCAGTGGCTC-3’		 This paper N/A
Primer for Off-target #3 (Forward):
5’-AAGCACCAGTAGCCTTGACC-3’		 This paper N/A
Primer for Off-target #3 (Reverse):
5’-TGGCCAGAAGGACATAAGCC-3’		 This paper N/A
Primer for Off-target #4 (Forward):
5’-CCTGACTGGGGGATTAGGGA-3’		 This paper N/A
Primer for Off-target #4 (Reverse):
5’-GGTGCCATTCTTGGCTCTCT-3’		 This paper N/A
Primer for Off-target #5 (Forward):
5’-GGTTCCTGCTCCATCGTTCC-3’		 This paper N/A
Primer for Off-target #5 (Reverse):
5’-CGTTCATCCGTTACTGTCCAC-3’		 This paper N/A
Recombinant DNA
pSpCas9(BB)-2A-GFP (PX458) Addgene Cat#43138, RRID:Addgene_48138
Software and algorithms
AxIS https://www.axionbiosystems.com/products/axis-software RRID:SCR_016308
Neural Module https://www.axionbiosystems.com/products/software/neural-module RRID:SCR_019270
Sony Biotechnology SH800S Cell Sorter https://www.sonybiotechnology.com/us/instruments/sh800s-cell-sorter/ RRID:SCR_018066
GraphPad Prism http://www.graphpad.com/ RRID:SCR_002798
Seahorse Wave Agilent Technologies RRID:SCR_014526
STAR (v.2.4.0) Dobin et al.40 N/A
featureCounts Liao et al.41 N/A
DESeq2 (v1.26.0) Love et al.42 N/A
ToppGene Suite Chen et al.43 N/A
SynGO Koopmans et al.19 N/A
HOMER Heinz et al.44 N/A
PANTHER Mi et al.45 N/A