Table 1. List of primer pairs used for analyses of ECM glycoprotein and CSPG mRNA expression in control (CO) and ischemic (I/R) rat retinae and optic nerves by qRT-PCR.
| Gene | Primer sequence | Amplicon size | Primer efficiency (retina/optic nerve) | Reference |
|---|---|---|---|---|
| β-Actin_for | CCCGCGAGTACAACCTTCT | 72 bp | 1.000/− | 52 |
| β-Actin_rev | CGTCATCCATGGCGAACT | |||
| Aggrecan_for | TGGCTGCAGGACCAGACT | 97 bp | 1.000/1.000 | This study |
| Aggrecan_rev | CGCCATAGGTCCTGACTCC | |||
| Brevican_for | AGCAGAACCGCTTCAATGTC | 61 bp | 0.825/0.838 | This study |
| Brevican_rev | TCAGAGAAGGCAGAGGGATG | |||
| Cyclophilin_for | TGCTGGACCAAACACAAATG | 88 bp | −/0.939 | 52 |
| Cyclophilin_rev | CTTCCCAAAGACCACATGCT | |||
| Fibronectin_for | CAGCCCCTGATTGGAGTC | 73 bp | 0.909/0.775 | This study |
| Fibronectin_rev | TGGGTGACACCTGAGTGAAC | |||
| α1-Laminin_for | CCCTGGGATGAAGAAGCA | 101 bp | 0.894/0.752 | This study |
| α1-Laminin_rev | CAGGGCTGCTGATGGAAG | |||
| RPTPβ/ζ CA_for | AACCATCCTTGGAAAACACG | 66 bp | 1.000/0.757 | 52 |
| RPTPβ/ζ CA_rev | CATTGGTGAGATTTATTTCCACTGT | |||
| RPTPβ/ζ PTP1_for | CCTCGTGGAGAAAGGAAGAAG | 77 bp | 0.953/0.739 | 52 |
| RPTPβ/ζ PTP1_rev | CCAGGAAGCTCCCGTATTCT | |||
| Tenascin-C_for | GCTCTCCTATGGCATCAAGG | 60 bp | 0.805/1.000 | 52 |
| Tenascin-C_rev | TCATGTGTGAGGTCGATGGT | |||
| Tenascin-R_for | TCATCTCCATTACTGCTGAGAGG | 93 bp | 0.769/0.779 | This study |
| Tenascin-R_rev | AGTGCAAGTGGGAGATAGGG |
For relative quantification of mRNA levels in the retinae and optic nerves the genes β-actin and cyclophilin served as housekeeping genes, respectively. The primer sequence, the predicted amplicon size, primer efficiency for retinae and optic nerves and the reference are indicated. Abbreviations: bp = base pairs, for = forward, rev = reverse.