Table 3.

The expression of Brn3a target genes: ISH and RNASeq results comparison

Gene	Known function	GCL P3	GCL P0-P22	Brn3a target P3	Brn3a target any age	Postnatal GCL Expression			GCL Sparse	Brn3a-independ. Transcripts	Brn3a-regulation Gene level
						Onset	Peak	Offset
Transcriptional and translational regulators
Foxp2	TF	yes	no	no	yes	P0	P7	no	no	no	yes
Tshz2	TF	yes	yes	yes	yes	P3	P7	no	no	no	yes
Rbfox1	Splicing of neuronal genes	yes	no	no	no	P0	P14	no	no	yes	no
Intracellular signaling and cytoskeleton-associated genes
Eml1	Microtubule-binding protein	yes	no	no	no	P0	P7	no	no	yes	no
Hpca	Calcium sensor	yes	yes	no	yes	P0	P7-P14	no	no	yes	no
Plppr3	Neurite growth and regeneration	yes	yes	no	yes	P0	P0	no	no	no	no
Mapk10	Axonal growth and neuronal survival	yes	yes	no	yes	P0	P7-P14	no	yes	yes	no
Pip5kl1	Cell morphology and adhesion	no	no	no	no	P3	P7	no	no	no	no
Pak6	Signaling kinase	no	no	no	no	no	no	no	no	no	na
Vesicle-associated proteins
Ankrd13b	Caveolin- mediated endosomal traffick	yes	yes	no	no	P0	P7	no	no	no	no
Pick1	Glutamate receptor trafficking	yes	no	no	no	P0	no	no	no	yes	no
Snap91	Clathrin-mediated endocytosis	yes	yes	yes	yes	P0	P7-P14	no	yes	yes	no
Tusc5	Insulin-stimulated glucose transport	yes	yes	yes	yes	P3	P14	no	yes	no	yes
Synapse-associated proteins
Elfn1	Synaptic adhesion protein	yes	no	no	yes	P3	P7	no	yes	no	yes
Gabra1	GABA receptor alpha1 subunit	no	no	no	yes	P3	no	no	yes	no	yes
Grm4	Metabotropic glutamate receptor	yes	no	no	no	P0	P7	no	no	no	yes
Ntrk1	Neurotrophin receptor	yes	no	no	no	P0	P14-P22	no	no	no	yes
Pnkd	Synaptic vesicle release	no	yes	no	no	P0	P7-P14	no	yes	yes	no
Rims1	Synaptic vesicle release & recycling	yes	yes	no	yes	P0	P0-P3	no	yes	no	no
Secreted proteins
Fam19a4	Unknown	no	no	no	no	P3	P3-P7	P7	no	no	yes
Nptx1	Trans-synaptic, excitatory synapse	yes	yes	no	yes	P0	P14	no	yes	no	yes
Nptx2	Trans-synaptic, excitatory synapse	yes	no	no	no	P3	P7-P14	no	yes	no	yes
Sez6l2	Synapse formation	yes	yes	no	yes	P3	P7	no	no	yes	no
Adhesion molecules and other transmembrane proteins
Cdh4	Cell adhesion molecule	yes	no	yes	yes	P0	no	no	yes	no	yes
Pcdh20	Cell adhesion molecule	no	no	no	yes	P14	no	no	no	no	yes
Rtn4rl2	Axon guidance molecule	yes	yes	no	yes	P0	no	P22	no	no	no
Tmem25	Unknown	no	no	no	no	P0	P7-P14	no	no	no	no
Tmem91	Unknown	no	no	no	yes	P0	P7-P14	no	no	yes	no

Column 1 represents gene name, column 2 – known function of the gene, column 3 – GCL enrichment at P3, column 4 – consistent GCL enrichment (at least at 4 out of 5 ages) from P0-P22. Fifth column shows whether the gene is regulated by Brn3a at P3, 6th – regulated by Brn3a at any of 5 studied ages. Columns 7, 8 and 9 represent the onset, the peak and the offset respectively of postnatal gene expression in the GCL. Column 10 shows whether the gene is highly and sparsely expressed in the GCL at any of studied ages. Columns 11 and 12 identify the genes that had unregulated transcripts or exhibited gene level regulation by RNASeq