| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-MAP2 | Synaptic Systems | Cat. #: HS-188 011, RRID: AB_2661868 |
| Anti-vGlut1 | Synaptic Systems | Cat. #: 135 011BT, RRID: AB_2884913 |
| Anti-GFP | Abcam | Cat. #: ab13970, RRID: AB_300798 |
| anti-Synapsin I D12G5 XP | Cell Signaling | Cat. #: 5297, RRID: AB_2616578 |
| Anti- PSD-95 MAGUK scaffolding protein antibody | UC Davis/NIH NeuroMab Facility | Cat. #: K28/43, RRID: AB_2877189 |
| Donkey anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 488 | Thermo Fisher Scientific | Cat. #: A-21202, RRID: AB_141607 |
| Donkey anti-Mouse IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 594 | Thermo Fisher Scientific | Cat. #: A-21203, RRID: AB_141633 |
| Donkey anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody | Thermo Fisher Scientific | Cat. #: A-21206, RRID: AB_2535792 |
| Donkey anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 594 | Thermo Fisher Scientific | Cat. #: A-21207, RRID: AB_141637 |
| Chemicals, peptides, and recombinant proteins | ||
| mTeSR1 Plus | STEMCELL Technologies | Cat. #: 100-0276 |
| ReLeSR | STEMCELL Technologies | Cat. #: 05872 |
| Matrigel matrix | Corning | Cat. #: 354234 |
| Accutase | STEMCELL Technologies | Cat. #: 07920 |
| Neuralbasal Medium | Thermo Fisher Scientific | Cat. #: 21103049 |
| 50x B27 Supplement | Thermo Fisher Scientific | Cat. #: 17504044 |
| 100x Glutamax | Thermo Fisher Scientific | Cat. #: 35050061 |
| Doxycycline | Sigma-Aldrich | Cat. #: D3072-1ML |
| Puromycin | Thermo Fisher Scientific | Cat. #: J67236.8EQ |
| Hygromycin | Millipore | Cat. #: 400053 |
| BDNF | PeproTech | Cat. #: 450-02 |
| GDNF | PeproTech | Cat. #: 450-03 |
| NT-3 | PeproTech | Cat. #: 450-10 |
| Digitonin | Promega | Cat. #: G9441 |
| Blasticidin | Thermo Fisher Scientific | Cat. #: A1113903 |
| Fluor-4 AM | Thermo Fisher Scientific | Cat. #: F14217 |
| ProLong Diamond Antifade Mountant | Thermo Fisher Scientific | Cat. #: P36961 |
| Fugene HD | Promega | Cat. #: E2311 |
| Lipofectamine 3000 | Thermo Fisher Scientific | Cat. #: L3000001 |
| Critical commercial assays | ||
| TaqMan Universal PCR Master Mix | Thermo Fisher Scientific | Cat. #: 4324018 |
| High-Capacity cDNA Reverse Transcription Kit with RNase Inhibitor | Thermo Fisher Scientific | Cat. #: 4374967 |
| RNeasy Plus Mini Kit | Qiagen | Cat. #: 74134 |
| Chromium Next Gem Cell 3’ Kit 3.1 | 10x Genomics | Cat. #: 100269 |
| 24-well MEA plate | Axion BioSystems | Cat. #: M384-tMEA-24W |
| Deposited data | ||
| Code used in the manuscript | This manuscript | DOI: 10.5281/zenodo.8180188 |
| ATAC-seq and RNA-seq data | GSE188491 | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE188491 |
| scRNA-seq data | SRR16919429 | https://dataview.ncbi.nlm.nih.gov/object/SRR16919429 |
| Experimental models: Cell lines | ||
| Human HEK293T cells | ATCC | Cat. #: CRL-3216 RRID: CVCL_0063 |
| Human: iPS cell from sample NG-47827 (F) | Rutgers University Cell and DNA Repository (RUCDR) | Cell ID: 01C08162 |
| Human: iPS cell from sample 92712 (M) | Rutgers University Cell and DNA Repository (RUCDR) | Cell ID: 04C27190 |
| Human: iPS cell from sample 79588 (M) | Rutgers University Cell and DNA Repository (RUCDR) | Cell ID: 04C28905 |
| Human: iPS cell from sample 69153 (M) | Rutgers University Cell and DNA Repository (RUCDR) | Cell ID: 04C37433 |
| Human: iPS cell from sample 18526 (F) | Rutgers University Cell and DNA Repository (RUCDR) | Cell ID: 05C38571 |
| Human: iPS cell from sample 29934 (M) | Rutgers University Cell and DNA Repository (RUCDR) | Cell ID: 05C39664 |
| Human: iPS cell from sample NG-73088 (M) | Rutgers University Cell and DNA Repository (RUCDR) | Cell ID: 05C43356 |
| Human: iPS cell from sample 44414 (F) | Rutgers University Cell and DNA Repository (RUCDR) | Cell ID: 05C43758 |
| Human: iPS cell from sample NG-81739 (M) | Rutgers University Cell and DNA Repository (RUCDR) | Cell ID: 05C45915 |
| Human: iPS cell from sample 81566 (F) | Rutgers University Cell and DNA Repository (RUCDR) | Cell ID: 05C46807 |
| Human: iPS cell from sample 75610 (M) | Rutgers University Cell and DNA Repository (RUCDR) | Cell ID: 05C46837 |
| Human: iPS cell from sample 48181 (M) | Rutgers University Cell and DNA Repository (RUCDR) | Cell ID: 05C48054 |
| Human: iPS cell from sample NG-55047 (F) | Rutgers University Cell and DNA Repository (RUCDR) | Cell ID: 05C49221 |
| Human: iPS cell from sample NG-11293 (M) | Rutgers University Cell and DNA Repository (RUCDR) | Cell ID: 06C52191 |
| Human: iPS cell from sample NG-40965 (M) | Rutgers University Cell and DNA Repository (RUCDR) | Cell ID: 06C52565 |
| Human: iPS cell from sample 16125 (F) | Rutgers University Cell and DNA Repository (RUCDR) | Cell ID: 06C52573 |
| Human: iPS cell from sample NG-77642 (F) | Rutgers University Cell and DNA Repository (RUCDR) | Cell ID: 06C53368 |
| Human: iPS cell from sampleNG-23159 (M) | Rutgers University Cell and DNA Repository (RUCDR) | Cell ID: 06C54426 |
| Human: iPS cell from sample NG-42857 (M) | Rutgers University Cell and DNA Repository (RUCDR) | Cell ID: 07C71166 |
| Human: iPS cell from sample NG-80080 (M) | Rutgers University Cell and DNA Repository (RUCDR) | Cell ID: 07C65853 |
| Oligonucleotides | ||
| See Table S15 | ||
| Recombinant DNA | ||
| Lenti-dCas9-KRAB-blast | Xie et al.29 | RRID: Addgene_89567 |
| pMD2.G | https://www.addgene.org/12259/ | RRID: Addgene_12259 |
| psPAX2 | https://www.addgene.org/12260/ | RRID: Addgene_12260 |
| FUW-M2rtTA | Hockemeyer et al.62 | RRID: Addgene_20342 |
| pTet-O-Ngn2-puro | Zhang et al.19 | RRID: Addgene_52047 |
| CROPseq-Guide-Puro | Datlinger et al.28 | RRID: Addgene_86708 |
| pMDLg/pRRE | Dull et al.63 | RRID: Addgene_12251 |
| pRSV-Rev | Dull et al.63 | RRID: Addgene_12253 |
| Software and algorithms | ||
| MAGMA software and population data | de Leeuw et al.39 | https://ctg.cncr.nl/software/magma |
| H-MAGMA codes and annotation files | Sey et al.39 | https://github.com/thewonlab/H-MAGMA |
| Miniconda | Anaconda Inc. | https://docs.conda.io/en/latest/miniconda.html |
| Pluritest | N/A | https://www.pluritest.com |
| Trimmomatic v 0.32 | Bloger et al.64 | https://github.com/timflutre/trimmomatic |
| Bowtie2 2.4.0 | Langmead et al.65 | https://github.com/BenLangmead/bowtie2 |
| Samtools 1.11.0 | Li et al.66 | https://htslib.org |
| GATK 4.1.8.1 | McKenna et al.67 | https://gatk.broadinstitute.org/ |
| MACS2 2.2.7.1 | Zhang et al.24 | https://github.com/macs3-project/MACS |
| R 4.1.1 | R Core Team | https://cran.r-project.org/ |
| SNPsplit | Kruger et al.68 | https://www.bioinformatics.babraham.ac.uk/projects/SNPsplit/ |
| deepTools 3.5.1 | Ramirez et al.69 | https://deeptools.readthedocs.io/en/develop/ |
| STAR 2.7.0 | Dobin et al.70 | https://github.com/alexdobin/STAR |
| Cell Ranger 4.0 | 10x Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome |
| Seurat 3.2 | Stuart et al.71 | https://satijalab.org/seurat/index.html |
| WebGestalt 2019 | Wang et al.35 | http://www.webgestalt.org/ |
| Synaptic Gene Ontologies (SynGO) | Koopmans et al.31 | https://syngoportal.org/ |
| ImageJ 2 | Schneider et al.72 | https://imagej.nih.gov/ij/download.html |
| NIS-Elements Advanced | Nikon Inc. | N/A |
| GraphPad Prism 9 | GraphPad Inc. | https://www.graphpad.com/ |
| Neural Metrics Analysis Tool | Axion Biosystems | N/A |
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