KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
PE-NeuN	Millipore Sigma	Cat # FCMAB317PE; RRID:AB_11212465
GFP	Aves	Cat # GFP-1020: RRID:AB_10000240
Parvalbumin	Swant	Cat # PV27; RRID:AB_2631173
Somatostatin	Peninsula Laboratories	Cat # T-4547; RRID:AB_518618
VIP	Boster Bio	Cat # RP1108
RFP	Abcam	Cat # ab65856; RRID:AB_1141717
GABA	Millipore Sigma	Cat # AB175; RRID:AB_91011
PE-CD9	Thermo Fisher Scientific	Cat # 12-0098-42; RRID:AB_10854122
Bacterial and virus strains
NEB Stable E. coli	New England Biolabs	Cat # C3040I
Stbl3 E. coli	Thermo Fisher Scientific	Cat # C7373-03
Chemicals, peptides, and recombinant proteins
Nextera Tn5 transposase	Illumina	Cat # FC-121-1031
NeuroTrace 500/525	Thermo Fisher Scientific	Cat # N21480
KAPA HiFi HotStart ReadyMix	Roche	Cat # KK2602
Myelin Beads Removal Kit II	Miltenyi Biotec	Cat # 130-096-733
Deposited data
Raw human ATAC-seq and scRNA-seq data	This study	dbGaP:phs2292.v1
Raw mouse snATAC-seq data	Graybuck et al., 2021	https://assets.nemoarchive.org/dat-7qjdj84
ENCODE frontal human cortex DNaseI-HS data	ENCODE consortium	ENCSR000EIK
ENCODE frontal human cortex DNaseI-HS data	ENCODE consortium	ENCSR000EIY
ENCODE human keratinocyte ATAC-seq data	ENCODE consortium	ENCSR356KRQ
Mouse forebrain processed snmC-seq data	Luo et al., 2017	Table S5
Human forebrain processed snmC-seq data	Luo et al., 2017	Table S6
Human and mouse forebrain bulk mC-seq data	Lister et al., 2013	GEO: GSE47966
Human snRNA-seq data	Hodge et al., 2019	dbGaP:phs001790.v1.p1
ENCODE human H1 cell bisulfite sequencing	ENCODE consortium	ENCSR617FKV
ENCODE human H1 cell bisulfite sequencing	ENCODE consortium	ENCSR000AJJ
Experimental models: cell lines
293AAV cell lines	Cell Biolabs	Cat # AAV-100
Experimental models: organisms/strains
C57BL/6J mice	Jackson labs	Stock # 000664
Gad2-T2a-NLS-mCherry mice	Jackson labs	Stock # 023140
Macaca nemestrina animals	Washington National Primate Research Center	N/A
Macaca mulatta animal	Washington National Primate Research Center	N/A
Oligonucleotides
Mouse Slc17a7 mFISH-HCR probe	Molecular Instruments	Accession # NM_182993.2
Mouse Rorb mFISH-HCR probe	Molecular Instruments	Accession # NM_001043354.2
Mouse Lamp5 mFISH-HCR probe	Molecular Instruments	Accession # NM_029530.2
Mouse Sst mFISH-HCR probe	Molecular Instruments	Accession # NM_009215.1
Mouse Pvalb mFISH-HCR probe	Molecular Instruments	Accession # NM_001330686.1
Mouse Gad1 mFISH-HCR probe	Molecular Instruments	Accession # NM_008077.5
Mouse Slc17a7 mFISH-HCR probe	Molecular Instruments	Accession # NM_182993.2
Mouse VIP mFISH-HCR probe	Molecular Instruments	Accession # NM_011702.3
Macaque nemestrina SLC17A7 mFISH-HCR probe	Molecular Instruments	Accession # NM_005589901.2
Macaque nemestrina GAD1 mFISH-HCR probe	Molecular Instruments	Accession # NM_005573441.2
Macaque nemestrina VIP mFISH-HCR probe	Molecular Instruments	Accession # NM_005552161.2
Macaque nemestrina PVALB mFISH-HCR probe	Molecular Instruments	Accession # NM_005567398.2
Macaque nemestrina SST mFISH-HCR probe	Molecular Instruments	Accession # NM_005545442.2
Recombinant DNA
CN1203-scAAV-hDLXI56i-minBG-SYFP2-WPRE3-BGHpA	This study	Addgene # 163492
CN1244-rAAV-hDLXI56i-minBG-SYFP2-WPRE3-BGHpA	This study	Addgene # 163493
CN1390-rAAV-DLX2.0-minBG-SYFP2-WPRE3-BGHpA	This study	Addgene # 163505
CN1402-rAAV-eHGT_058h-minBG-SYFP2-WPRE3-BGHpA	This study	Addgene # 163494
CN1457-rAAV-eHGT_078h-minBG-SYFP2-WPRE3-BGHpA	This study	Addgene # 163495
CN1466-rAAV-eHGT_078m-minBG-SYFP2-WPRE3-BGHpA	This study	Addgene # 163508
CN1253-scAAV-eHGT_017h-minBG-SYFP2-WPRE3-BGHpA	This study	Addgene # 163497
CN1255-scAAV-eHGT_019h-minBG-SYFP2-WPRE3-BGHpA	This study	Addgene # 163496
CN1258-scAAV-eHGT_022h-minBG-SYFP2-WPRE3-BGHpA	This study	Addgene # 163506
CN1259-scAAV-eHGT_023h-minBG-SYFP2-WPRE3-BGHpA	This study	Addgene # 163499
CN1279-scAAV-eHGT_022m-minBG-SYFP2-WPRE3-BGHpA	This study	Addgene # 163507
CN1621-rAAV-hsA2-eHGT_128h-minRho-SYFP2-WPRE3-BGHpA	This study	Addgene # 163498
CN1525-rAAV-hsA2-eHGT_079h-minRho-SYFP2-WPRE3-BGHpA	This study	Addgene # 163501
CN1528-rAAV-hsA2-eHGT_082h-minRho-SYFP2-WPRE3-BGHpA	This study	Addgene # 163502
CN2045-rAAV-3xSP10ins-eHGT_359h-minRho*-SYFP2-WPRE3-BGHpA	This study	Addgene # 163504
CN1408-rAAV-eHGT_064h-minBG-SYFP2-WPRE3-BGHpA	This study	Addgene # 163500
CN1839-rAAV-hSyn 1-SYFP2-10aa-H2B-WPRE3-BGHpA	This study	Addgene # 163509
CN1633-rAAV-hsA2-eHGT_140h-minRho-SYFP2-WPRE3-BGHpA	This study	Addgene # 163503
Software and algorithms
chromVAR	Schep et al. (2017)	https://github.com/GreenleafLab/chromVAR
Cicero	Pliner et al., 2018	https://cole-trapnell-lab.github.io/cicero-release/
methylpy	Luo et al., 2017	https://github.com/yupenghe/methylpy
HOMER	Heinz et al. (2010)	http://homer.ucsd.edu/homer/
ImageJ	Schneider et al., 2012	https://imagej.nih.gov/ij/
Bowtie2	Langmead and Salzberg (2012)	http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
Samtools	Li et al. (2009)	http://samtools.sourceforge.net/
MACS2	Zhang et al. (2008)	https://pypi.org/project/MACS2/
DiffBind	Ross-Innes et al., 2012	https://bioconductor.org/packages/release/bioc/html/DiffBind.html
Lowcat	Graybuck et al., 2021	https://github.com/AllenInstitute/lowcat
scrattch.hicat	Tasic et al. (2018)	https://github.com/AllenInstitute/scrattch.hicat
Bedtools	Quinlan and Hall (2010)	https://bedtools.readthedocs.io/en/latest/#
MEME-CHIP	Bailey et al. (2009)	https://meme-suite.org/
repeatMasker	Smit et al. (2013)	http://www.repeatmasker.org
R	R Core Team (2018)	https://www.r-project.org/
scrattch.hicat	Tasic et al. (2018)	https://github.com/AllenInstitute/scrattch.hicat
LDSC	Bulik-Sullivan et al. (2015)	https://github.com/bulik/ldsc