Table 1.

Selected genes that are downregulated (>1.2‐fold) in NeuroD2 KO vs. WT cortical tissue

Gene symbol	Fold change	P	FDR (Select)	FDR (Total)	Description
Neurod2†‡	−8.81	9.41 × 10−11	1.78 × 10−8	5.25 × 10−6	Neurogenic differentiation factor 2
Grp†‡	−2.48	0.008090833	0.02335726	0.7937901	Gastrin releasing peptide
Kif6	−1.77	0.039458968	0.04267144	0.85842603	Kinesin family member 6
Kcns3	−1.69	0.025873655	0.035351716	0.79384476	Voltage‐gated channel, delayed‐rectifier, subfamily S, member 3
Plxndl†‡	−1.48	0.005626001	0.016380074	0.7004802	Plexin Dl
Kcnd3	−1.42	0.002585986	0.011132563	0.5020108	Voltage‐gated channel, Shal‐related family, member 3
Epha6	−1.42	0.002643762	0.011132563	0.6172144	Eph receptor A6
Nefm†	−1.42	0.007119948	0.02335726	0.7937901	Neurofilament, medium polypeptide
Gabra2†	−1.41	0.032407083	0.03593437	0.79715264	GABA‐A receptor, subunit α2
Kcnt2	−1.39	0.001616994	0.009913773	0.15403655	Potassium channel, subfamily T, member 2
Foxo6	−1.39	0.043240737	0.045719594	0.8979501	Forkhead box O6
Kcnip4	−1.37	0.002442279	0.010243218	0.41595492	Kv channel interacting protein 4
Kcnjll	−1.37	0.034641597	0.038337044	0.8065073	Potassium inwardly rectifying channel, subfamily J, member 11
Stxbp5l	−1.37	0.048574124	0.04882949	0.95340574	Syntaxin binding protein 5‐like
Gabbr2	−1.35	0.006926423	0.019712156	0.7937901	GABA‐B receptor, 2
Dixdcl†‡	−1.35	0.01726422	0.031362873	0.7937901	DIX domain containing 1
Foxol	−1.34	0.002442279	0.010243218	0.49281004	Forkhead box O1
Camk2a†	−1.33	0.042989478	0.045495648	0.8933901	Calcium/calmodulin‐dependent protein kinase II α
Ppplrlb	−1.32	0.00460536	0.012099204	0.63865095	Protein phosphatase 1, regulatory (inhibitor) subunit 1B
Ephb6	−1.32	0.005699302	0.016380074	0.7109885	Eph receptor B6
Kcnk4	−1.31	0.005386524	0.016380074	0.6707512	Potassium channel, subfamily K, member 4
Atp2bl	−1.31	0.007285039	0.02335726	0.7937901	ATPase, Ca2+ transporting, plasma membrane 1
Bok	−1.31	0.021214584	0.034998067	0.7937901	BCL2‐related ovarian killer protein
Sla	−1.3	0.04818842	0.04882949	0.92200255	Src‐like adaptor
Slitrk3	−1.29	0.03366219	0.036189463	0.8025127	SLIT and NTRK‐like family, member 3
Kcncl	−1.29	0.041096598	0.045084268	0.88167274	Potassium voltage‐gated channel, Shaw‐related subfamily, member 1
Cplx2†‡	−1.28	0.008529506	0.02335726	0.7937901	Complexin 2
Ier5	−1.28	0.012563508	0.030142762	0.7937901	Immediate early response 5
Arrdc2	−1.28	0.012955907	0.030538168	0.7937901	Arrestin domain containing 2
Itprl	−1.28	0.013064444	0.0312032	0.7937901	Inositol 1,4,5‐trisphosphate receptor 1
Nrxnl	−1.28	0.024665145	0.035351716	0.7937901	Neurexin I
Grin2c	−1.28	0.03399089	0.036776014	0.8042854	Glutamate receptor, ionotropic, NMDA2C
Mylip	−1.27	0.021410765	0.035166554	0.7937901	Myosin regulatory light chain interacting protein
Ptpn21	−1.26	0.037434865	0.042422105	0.85433745	Protein tyrosine phosphatase, non‐receptor type 21
Camk4†	‐1.25	0.002294663	0.010165026	0.32551256	Calcium/calmodulin‐dependent protein kinase IV
Kcnh3	−1.25	0.004905365	0.012099204	0.6438913	Potassium voltage‐gated channel, subfamily H (eag‐related), member 3
Cacnala	−1.24	0.010805262	0.02335726	0.7937901	Calcium channel, voltage‐dependent, P/Q type, α1A subunit
Klf5	−1.24	0.03539486	0.038420103	0.8133888	Kruppel‐like factor 5
Kcnj9	−1.24	0.03978704	0.044782665	0.8609039	Potassium inwardly rectifying channel, subfamily J, member 9
Slc2a6	−1.23	0.020900369	0.034003094	0.7937901	Solute carrier family 2 (facilitated glucose transporter), member 6
Efna5	−1.23	0.03539486	0.03897731	0.82933736	Ephrin A5
Chka	−1.23	0.036945086	0.040957764	0.8425187	Choline kinase α
Ppp2r5b	−1.22	0.01254365	0.02633919	0.7937901	Protein phosphatase 2, regulatory subunit B
Epha4	−1.22	0.017394949	0.032909703	0.7937901	Eph receptor A4
Phactr2	−1.22	0.027841333	0.035731114	0.79680043	Phosphatase and actin regulator 2
Kcnc3	−1.22	0.046944622	0.047048863	0.91154444	Potassium voltage‐gated channel, Shaw‐related subfamily, member 3
Scnlb	−1.22	0.049731918	0.049957633	0.99979216	Sodium channel, voltage‐gated, type I, β
Pik3r6	−1.21	0.012251093	0.023756737	0.7937901	Phosphoinositide‐3‐kinase, regulatory subunit 6
Npdcl	−1.21	0.03686852	0.03927016	0.8302656	Neural proliferation, differentiation and control gene 1
Stxbp5	−1.21	0.048574124	0.049407627	0.99979216	Syntaxin binding protein 5
Κcnn2†‡	−1.2	9.04 × 10−4	0.005928889	0.068098344	Potassium intermediate/small conductance calcium‐activated channel
Bai2	−1.2	0.006960979	0.021744039	0.7937901	Brain‐specific angiogenesis inhibitor 2
Ppmlf	−1.2	0.036424253	0.03927016	0.8300124	Protein phosphatase 1F
Pddcl	−1.2	0.04594794	0.047048863	0.9028201	Parkinson disease 7 domain containing 1
Lrfn5	−1.2	0.04753913	0.0478091	0.91255474	Leucine rich repeat and fibronectin type III domain containing 5
Gcat	−1.2	0.04825415	0.04882949	0.938082	Glycine C‐acetyltransferase

Over 50 genes were selected, based on their possible involvement in central nervous development from a list of over 600 probes whose expression was decreased in microarray between NeuroD2 WT and KO with a significant fold change larger than 1.2. Seven pairs of WT and KO culture tissues were included in the microarray analysis. ^†Genes whose expression we further assessed by qPCR; ^‡genes whose change in expression was verified by qPCR (6/10).