Molecular Vision: Carr, Mol Vis 2011; 17:1701-1715. Table 1

Table 1. PCR primer sequences used for RT–PCR and Q-PCR.

mRNA	Forward primer (5′-3′)	Reverse primer (5′-3′)	Accession number	Size	Tm-3 °C
RT–PCR
Best1	AGGTCGAATCCGGGACCCTA	GCACAACGAGGTCCAGCTCA	NM_004183.3	226	64
Brn3	CACCCTCCCTGAGCACAAGT	AGGCTAGGGGACAGCAAAGG	NM_006237	101	57
Calb2	GCGGCTACATTGACGAGCAT	GCAGCAGAAGCAGGGTTTGG	NM_001740	232	56
Crx	AGAGGGCAGGGAGCCAAATC	GCCAGTGTGTGGGGAAGAGG	NM_000554	236	58
Gfap	TCTGACCCTCTCCACCCCATA	GCCCTCCCAGTCCCATCTCT	S40719	288	58
Irbp	TGGAGCCCGACATCACTGT	TGCGGTCCTTGGCATTCTC	NM_002900	296	55
Krt8	AAGGATGCCAACGCCAAGTT	CCGCTGGTGGTCTTCGTATG	NM_002273	214	60
Nf-m	TGCTCCCTCCTCAGTCTTTGG	TCGTTTATTGTTTTTGGCTCAGTTG	BC096757	155	55
Nf-h	GCCAAGGTGGAGGTGAAGGA	TGGTCTGTGCTGGAGGATTTTT	NM_021076	271	55
Nse	GCTGCTCCTTGGCTTACCT	AACCCTGACGCTCCCATCAC	M22349	197	58
Nrl	AGAGCGCCTTCTGGTCCTAG	GCATCTCGGATAGAGGTCCT	NM_006177	420	60
Nr2e3	TGGTCCTCTTCAAGCCAGAGA	TTTCACCTCCACCCCCACTA	NM_014249	274	56
Opn1mw/lw	GCCCAGACGTGTTCAGCG	GACCATCACCACCACCAT	NM_000513	211	60
Opn1sw	GGTCACTGGCCTTCCTGG	TGCAGGCCCTCAGGGATG	NM_001708	174	60
Rho	TCAAGCCGGAGGTCAACAAC	TCTTGGACACGGTAGCAGAG	NM_000539	437	50
Opn3	CTCTTCGGGGTCACCTTTAC	AGGAGGAATCGTTGGCATC	NM_014322	330	56
Opn4	GAAGTCCTGAGCTCCCTGTG	TAACTGTTCCAGCGTGCAAA	NM_00100015	2009	52
Opn4 (2)	TGCGAGTTCTATGCCTTCTG	TGCGAGTTCTATGCCTTCTG	NM_00100015	462	53
Rcvrn	GGAAAAGCGAGCCGAGAAGA	CCTGGGGTGGATGTGTGTGT	NM_002903	282	56
Rgr	CAAGGGGGACAGAAACTTCACCAG	CTGCGGTGAGAGGCACTGCCAG	NM_002921	338	60
Rlbp	GCTGCTGGAGAATGAGGAAACTC	GGCTGGTGGATGAAGTGGAT	NM_000326	173	52
Rrh	TCAGCTCGGTGGTGTCTTTG	GTCTCGGATTTCCCAAGCAA	NM_000280	286	54
Rpe65	GCCCAGGAGCAGGACAAAAG	GCGCATCTGCAAGTTAAAACCA	NM_000329	246	52
Sag	CTGCACCTTGCGGTCTCTCT	TTTTTCTTGCGCTTCCTCCA	NM_000541	195	52
Silve	GTGGTCAGCACCCAGCTTAT	GAGGAGGGGGCTATTCTCAC	NM_006928	233	52
Syp	CAGGGTGGGGCTTAGAATGG	GTGTGTGTGGTGGGGTGCTT	NM_003179	264	58
Tbp	GAACCACGGCACTGATTTTC	CCCCACCATATTCTGAATCT	NM_003194	157	52
Thy-1	GACCCACAGCCTCCAAGTCA	CCCGCAGAAGTCCCTGAGAA	NM_006288	178	58
Tubb3	GCGAGATGTACGAAGACGAC	TTTAGACACTGCTGGCTTCG	NM_006086	420	60
Tyr	TGCCAACGATCCTATCTTCC	GACACAGCAAGCTCACAAGC	NM_000372	316	52
Q-PCR
Crx	CCACTATTCTGTCAACGC	CCAAACCTGAACCCTGG	NM_000554	232	60
Krt8	AAGGATGCCAACGCCAAGTT	CCGCTGGTGGTCTTCGTATG	NM_002273	214	60
Opn1mw/lw	GCCCAGACGTGTTCAGCG	GACCATCACCACCACCAT	NM_000513	211	60
Opn3	CTCTTCGGGGTCACCTTTAC	AGGAGGAATCGTTGGCATC	NM_014322	330	56
B2m	TGTTGATGTATCTGAGCAGGTTG	AAGATGTTGATGTTGGATAAGAGAATC	NM_004048	100	60
Gapdh	CCCCACCACACTGAATCTCC	GGTACTTTATTGATGGTACATGACAAG	NM_002046	104	60
Tubb	AATCCCCACCTTTTCTTACTCC	AAAGATGGAGGAGGGTTCCC	NM_178014	119	60

Primer sequences for amplification of human opsins, RPE, retinal and neuronal specific genes: class IV POU domain-containing transcription factor 1 (Brn3), Calbindin2 (Calb2), Cone rod homeobox (Crx), Glial fibrillary acidic protein (Gfap), Interphotoreceptor retinol binding protein (Irbp), Neurofilment medium and heavy chains (Nf-m and Nf-h), Neuron specific enolase (Nse), Neural retinal leucine zipper (Nrl), retinal specific nuclear receptor (Nr2e3), Medium and long wave cone opsin (Opn1mw/lw – primer pair amplifies both medium and long wavelength opsin due to highly conserved sequence), short wave cone opsin (Opn1sw), Rhodopsin (Rho), Encephalopsin (Opn3), Melanopsin (Opn4 – amplified in cells using nested PCR), Recoverin (Rcvrn), Retinal G protein coupled receptor (Rgr), retina arrestin (Sag), Synaptophysin (Syp), Thy-1 cell surface antigen (Thy-1), b-3-tubulin (Tubb3), cytokeratin8 (Krt8), b-2-microglobulin (B2m) and Glyceraldehyde-3- phosphate dehydrogenase (Gapdh). The primer sequences used to amplify Crx for Q-PCR were taken from Peng and Chen 2007 [73].