REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-cleaved-caspase-3	Cell Signaling Technology	#9661; RRID:AB_2341188
Anti-GAD67	Millipore	#MAB5406; RRID:AB_2278725
Anti-Chx10	Santa Cruz	#sc-21690; discontinued
Anti-FoxP2	Sigma-Aldrich	#HPA000382; RRID:AB_1078908
Anti-pan axonal-neurofilament (SMI312)	Covance	#SMI312; discontinued
Guinea pig anti-PcdhγCR antibody	produced by CBSN, Hasegawa et al. (2016)	N/A
Anti-β-actin	Sigma-Aldrich	#A5441; RRID:AB_476744
Anti-digoxigenin-AP Fab fragments antibody	Sigma-Aldrich	#11093274910; RRID:AB_2734716
Goat anti-mouse IgG Alexa Fluor Plus 488	ThermoFisher	#A32723; RRID:AB_2633275
Goat anti-rabbit IgG Alexa Fluor Plus 594	ThermoFisher	#A32740; RRID:AB_2762824
Donkey anti-goat IgG Alexa Fluor 594	ThermoFisher	#A11058; RRID:AB_2534105
Donkey anti-rabbit IgG Alexa Fluor 488	ThermoFisher	#A21206; RRID:AB_2535792
Chemicals, peptides, and recombinant proteins
TRIzol reagent	ThermoFisher	Cat#15596018
DNaseI (RNase-free)	TaKaRa Bio, Inc.	Cat#2270A
Superscript III reverse transcriptase	ThermoFisher	Cat#18080093
SYBR Premix Ex Taq	TaKaRa Bio, Inc.	Cat#RR420A, discontinued
ECL Select	Cytiva	Cat#RPN2235
Diethyl pyrocarbonate	Nacalai Tesque, Inc.	Cat#12311-86
Ribonuclease inhibitor (porcine liver)	TaKaRa Bio, Inc.	Cat#2311A
T7 RNA polymerase	Promega	Cat#PR-P2075
T3 RNA polymerase	Promega	Cat#PR-P2083
DIG RNA labeling mix	Sigma-Aldrich	Cat#11277073910
ProtectRNA RNase inhibitor	Sigma-Aldrich	Cat#R-7397
Formamide, deionized, nuclease and protease tested	Nacalai Tesque, Inc.	Cat#16345-65
4-Nitro blue tetrazolium chloride	Roche	Cat#11383213001
5-Bromo-4-chloro-3-indoyl-phosphate	Roche	Cat#11383221001
Paraformaldehyde	Nacalai Tesque, Inc.	Cat#02890-45
Low melting temperature gelatin	Nippi	Cat#MAX-F
Tissue-Tek O.C.T. compound	Sakura Finetek	N/A
Immunoselect antifading mounting medium	Dianova	Cat#SCR-038447
Proteinase K	Nacalai Tesque, Inc.	Cat#29442-85
Experimental models: Organisms/strains
Mouse: C57BL/6 PcdhabgTC/+:TGTaf7	This study	RIKEN BRC, RBRC09813
Mouse: C57BL/6 Pcdhabgdel/+:TGTaf7	Hasegawa et al. (2016)	RIKEN BRC, RBRC04820
Mouse: C57BL/6 Pcdhgdel/+:TGTaf7	Hasegawa et al. (2016)	RIKEN BRC, RBRC04821
Mouse: C57BL/6 TGTaf7	Hasegawa et al. (2016)	RIKEN BRC, RBRC04822
Oligonucleotides
For Southern blot probe A, B sequence, see Table S1	This study	N/A
For genotyping PcdhabgTC allele, see Table S1	This study	N/A
For genotyping TGTaf7 allele, see Table S1	This study	N/A
For RT-PCR/real-time RT-PCR, see Table S1	This study	N/A
For amplifying in situ hybridization RNA probes, see Table S1	This study	N/A
Software and algorithms
ImageJ ver1.53	NIH	N/A
PRISM 7.05	GraphPad	N/A
Other
ImageQuant LAS-4000	Cytiva	LAS-4000
ABI 7900HT Fast Real-Time PCR System	Applied Biosystems	7900HT
Leica CM3050 cryostat	Leica	CM3050
DS-Qi1Mc digital camera	Nikon	DS-Qi1Mc
BIOREVO BZ-9000 All-in-one Fluorescence Microscope	Keyence Corp.	BZ-9000
Dragonfly	Andor, Oxford Instruments, Belfast, Northern Ireland	https://andor.oxinst.com/products/dragonfly-confocal-microscope-system