TABLE 1.

Genes Examined in This Study in the Avian Telencephalon

		Receptors
		Gene	Gene name	Original study	Accession #	Anti/Sense
1	AMPA	GRIA1	Glutamate receptor ionotropic AMPA type 1	Wada et al 2004	AB042749	Sp6/T7
2		GRIA2	Glutamate receptor ionotropic AMPA type 2	Wada et al 2004	AB042750	Sp6/T7
3		GRIA3	Glutamate receptor ionotropic AMPA type 3	Wada et al 2004	AB042751	Sp6/T7
4		GRIA4	Glutamate receptor ionotropic AMPA type 4	Wada et al 2004	AB042752	Sp6/T7
5	Kainate	GRIK1	Glutamate receptor ionotropic kainate type 1	Wada et al 2004	AB107127	T7/Sp6
6		GRIK2	Glutamate receptor ionotropic kainate type 2	Wada et al 2004	AB107128	Sp6/T7
7		GRIK3	Glutamate receptor ionotropic kainate type 3	Wada et al 2004	AB107129	T7/Sp6
8		GRIK4	Glutamate receptor ionotropic kainate type 4	Wada et al 2004	AB107131	Sp6/T7
9		GRIK5	Glutamate receptor ionotropic kainate type 5	Wada et al 2004	AB107131	T7/Sp6
10	NMDA	GRIN1	Glutamate receptor ionotropic NMDA type 1	Wada et al 2004	AB042756	Sp6/T7
11		GRIN2A	Glutamate receptor ionotropic NMDA type 2A	Wada et al 2004	AB042757	Sp6/T7
12		GRIN2B	Glutamate receptor ionotropic NMDA type 2B	Wada et al 2004	AB107125	Sp6/T7
13		GRIN2C	Glutamate receptor ionotropic NMDA type 2C	Wada et al 2004	AB042758	Sp6/T7
14		GRIN2D	Glutamate receptor ionotropic NMDA type 2D	Wada et al 2004	AB042759	Sp6/T7
15		GRIN3A	Glutamate receptor ionotropic NMDA type 3A	Wada et al 2004	AB107126	Sp6/T7
166	Metabotropic	GRM1	Glutamate receptor metabotropic type 1	Wada et al 2004	AB042753	Sp6/T7
17		GRM2	Glutamate receptor metabotropic type 2	Wada et al 2004	AB042754	Sp6/T7
18		GRM3	Glutamate receptor metabotropic type 3	Wada et al 2004	AB107132	Sp6/T7
19		GRM4	Glutamate receptor metabotropic type 4	Wada et al 2004	AB042759	T7/Sp6
20		GRM5	Glutamate receptor metabotropic type 5	Wada et al 2004	AB107133	Sp6/T7
21		GRM8	Glutamate receptor metabotropic type 8	Wada et al 2004	AB107134	Sp6/T7
22	D1	D1A	Dopamine receptor 1A	Kubikova et al 2010	AB372107	Sp6/T7
23		D1B	Dopamine receptor 1B	Kubikova et al 2010	AB372108	T7/Sp6
24		D1C	Dopamine receptor 1C	Kubikova et al 2010	AB372109	T7/Sp6
25	D2	D2	Dopamine receptor 2	Kubikova et al 2010	AB372110	Sp6/T7
26		D3	Dopamine receptor 3	Kubikova et al 2010	AB372111	Sp6/T7
27	other	SEMA6A	Semaphorin-6A	Mello & Lovell 2008	CK308635	T3/T7
28		CB1	Cannabinoid receptor type 1	Soderstorm et al 2004	Anti-CB1 finch	NA
29		ROR-b	RAR-related orphan receptor beta	This study	XM002190956	SP6/T7
		Protein ligands
30		BDNF	Brain derived growth factor	Wada et al 2006	DQ213413	Sp6/T7
31		NRN	Neuritin	This study	AB543000	T3/T7
32		SCUBE1	Signal peptide, CUB domain, EGF-like 1	Mello & Lovell 2008	DV947442	T3/T7
		Transcription factors
33		DLX6	Distal-less homeobox 6	This study	0063P0006H11	T3/T7
34		FOXP1	Forkhead box P1	Haesler et al 2004	AY549152.1	T7/Sp6
35		FOXP2	Forkhead box P2	Haesler et al 2004	AY549150	Sp6/T7
36		ER81	Ets-related protein 81	This study	DV582565	T3/T7
37		COUP-TF2	Chicken ovalbumin upstream promoter-TF2	Yamamoto et al 2005 & this study	AB542998	T7/Sp6
38		LHX8	LIM homeobox 8, zinc finger	This study	EH122589	T3/T7
39		LHX9	LIM homeobox 9, zinc finger	This study	AB542999	SP6/T7
40		NKX2.1	NK2 homeobox 1	This study	HM633194	T7/SP6
41		PAX6	Paired box gene 6	This study	DV580106	T3/T7
42		EGR1	Early growth response gene 1	Wada et al 2006; Feenders et al 2008	JX296528	T7/Sp6
43		C-FOS	Cellular – FBJ osteosarcoma oncogene	Wada et al 2006; Feenders et al 2008	DV571132	T7/Sp6
44		C-JUN	Cellular – jun oncogene	Wada et al 2006	DV573183	Sp6/T7
		Enzymes
45		DUSP1	Dual specificity phosphatase 1	Horita et al 2010, 2012	AB476742	SP6/T7
46		FKBP1A	FK506 binding protein 1A; isomerase	This study	0058P0025C02	T3/T7
47		PPAPDC1A	Phosphatidic acid phosphatase 2 domaincontaining 1A	Mello & Lovell 2008	CK305549	T3/T7
		Other genes
48		ARC	Activity-regulated cytoskeleton protein	Wada et al 2006	0065P0027D05	T3/T7
49		CADPS2	Calcium-dependent secretion activator 2	Mello & Lovell 2008	DV955943	T3/T7
50		ARPP16	cAMP regulated phosphoprotein 16000	This study	0058P0003A02	T3/T7
51		S100B	S100 calcium binding protein B	Mello & Lovell 2008, This study	DV950377	T3/T7
52		TMEM100	Trans membrane protein 100	This study	0064P0009H05	T3/T7
53		MOAB	Monoamine oxidase B	This study		Sp6/T7
54		SP	Substance P	Shimizu & Karten 1990	Anti-SP rat	NA

Listed are the gene family when more than one gene of a family was analyzed, the gene symbol abbreviation, the molecular function/annotated gene name, the original source of the adult brain gene expression pattern if not this study, the NCBI accession no. or clone ID of the cDNA used for in situ hybridization, and the RNA polymerase enzymes used to make the antisense and sense riboprobes. The two genes at the bottom of the list (MOAB and SP) were added for validation at the end of the study. More information on individual nucleotide sequences, insert sizes, and portion of the gene represented in the cDNA clones can be found with a search of the ID# in the NCBI nucleotide (http://www.ncbi.nlm.nih.gov/nucleotide) or songbird transcriptome (http://songbirdtranscriptome.net) databases. Vector clones used were the pFLC1, pBS SK1, or pGEM T-easy vectors, as described in the database files for each clone. Gene nomenclature follows current standards, including revised nomenclature for glutamate receptors.