Table 1. Primer pairs used for PCR experiments.
Gene (Accession mRNA/Gene ID) | Primer sequence (5′→3′; numbers indicate the localization with respect to the DNA) | Amplicon (bp/Tm) | ||
---|---|---|---|---|
Forward | Reverse | |||
ACTBNM_001101/ 60 | 2198ATGGCCACGGCTGCTTCCAGC 2218 | 2529CATGGTGGTGCCGCCAGACAG2509 | 237/ 88.0 °C | |
RPLP1NM_213725/ 6076 | 2363GTCAACATTGGGAGCCTCAT2382 | 2678AGACCAAAGCCCATGTCATC2659 | 176/ 88.0 °C | |
HPRTNM_000194/ 3251 | 15049TGCTCGAGATGTGATGAAGG15068 | 26340TCCCCTGTTGACTGGTCATT26321 | 192/ 82.0 °C | |
GAPDHNM_002046/ 2597 | 2619GCAGGGGGGAGCCAAAAGGGT2639 | 3122TGGGTGGCAGTGATGGCATGG3102 | 219/ 86.0 °C | |
Opsin | ||||
OPN2#NM_000539/ 6010 | 3921CACCACACAGAAGGCAGAGA3940 | 4062CATGAAGATGGGACCGAAGT4043 | 142/ 86.0 °C | |
OPN3NM_014322/ 23596 | 373CACCTCCTCCTGGTCAACAT393 | 35928TGTAGGTAATGGCCCTCCAG35909 | 253/ 88.5 °C | |
OPN4NM_033282/ 94233 | 4001GGACCGCTACCTGGTAATCA4020 | 4851GGAGGAAGAACACGAAGCAG4833 | 242 / 89.5 °C | |
OPN5NM_001030051/ 221391 | 26222CTGTGGTGCCAACCCTACTT26241 | 29689TCATGAATTTCCAGCACAGC29670 | 190/ 83.5 °C | |
RRHNM_006583/ 10692 | 14517CCCTTATTCCATCGTGTGCT14536 | 16150TGTCACAGGCATTGTTTGGT16131 | 199/ 82.5 °C | |
OPN1SWNM_001708/ 611 | 1911TCAGCAGCAGGAGTCAGCTA1930 | 3145ATGCAAGCTTGGAACTGCTT2146 | 246/ 86.5 °C | |
OPN1LW+MWNM_020061; NM_000513/ | TCGCTATCATCATGCTCTGC | GCACTTTTGGCAAAGTAGGC (see below) | 247/ 88 °C | |
RGRNM_001012722/ 5995 | 7885CTTCTGGGTTGGGGTCACTA7904 | 9380CACTCTTCCCCAGTTTCTGC 9361 | 181 | |
Phototransduction cascade | ||||
GNAZ#NM_002073/ 2781 | 52660TTCATCAACACCTCACTCATCC52681 | 52842GATCTCCTTGGTCTCCTTGTTG52821 | 183 | |
GNAT1NM_144499/ 2779 | 2591GCTAGTGGAGGACGACGAAG2610 | 3172CTCGTAGGTGTTGGGTCCAT3044 | 193 | |
GNAT2NM_005272/ 2780 | 300GGAAGCCAAGACTGTCAAGC319 | 3043GCACAGCTTGGTTCAGCATA3024 | 216 | |
ARR3NM_004312/ 407 | 9055AGAGACTATGTGCGGCTGGT9074 | 9400GGGTTCTCCGTGGTAGTGAA9380 | 159 | |
SAGNM_000541/ 6295 | 19533GAAGAGCTCCGTGCGATTAC20832 | 21849GGCTCCCCATGGAAATAGAT21831 | 159 | |
Glial marker | ||||
GLULNM_001033056/ 2752 | 6338TGGGAGCAGACAGAGCCTAT6357 | 6780CAGGAATGGGCTTAGGATCA6761 | 240 | |
VIMNM_003380/ 7431 | 6526CCCTCACCTGTGAAGTGGAT6545 | 7116TTCCAGCAGCTTCCTGTAGGT7097 | 241 | |
GFAPNM_002055/ 2670 | 4263ACATCGAGATCGCCACCTAC4282 | 7470ATCTCCACGGTCTTCACCAC7451 | 166 | |
RLBP1NM_000326/ 9617 | 6562ACAAGTATGGCCGAGTGGTC6581 | 9840TCCTCATTCTCCAGCAGCTT9821 | 121 | |
Kir4.1#NM_002241/ 3766 | 27885CAAGGACCTGTGGACAACCT27904 | 28105GGGATTCAAGGGAGAAGAGG28086 | 221 | |
AQP4#NM_001650/ 361 | 3244GGAATTTCTGGCCATGCTTA3263 | 3479AGACTTGGCGATGCTGATCT3450 | 226 | |
SLC1ANM_001166695/ 6507 | 64817CATGCACAGAGAAGGCAAAA64836 | 70641AGAGTCTCCATGGCCTCAGA70622 | 210 | |
Neuronal marker | ||||
NEUNNM_001082575/ 146713 | 380894CAACGGCTGGAAGCTAAATC384751 | 386949GGCTGAGCGTATCTGTAGGC386920 | 264 | |
THY1#NM_006288/ 7070 | 3198CTAGTGGACCAGAGCCTTCG3217 | 3433TGGAGTGCACACGTGTAGGT3414 | 236 | |
MAP2NM_031845/ 4133 | 229258CCAATGGATTCCCATACAGG229277 | 254576CTGCTACAGCCTCAGCAGTG254557 | 180 | |
NEFHNM_021076/ 4744 | 5561GAGGAACACCAAGTGGGAGA5580 | 8721TTCTGGAAGCGAGAAAGGAA8702 | 160 | |
NEUROD1#NM_002500/ 4760 | 1888GTTCTCAGGACGAGGAGCAC1907 | 2040CTTGGGCTTTTGATCGTCAT2021 | 164 | |
Progenitor marker | ||||
NES#NM_006617/ 10763 | 4438GCTCCTCTCTCTCTGCTCCA4457 | 4666CACCGGATTCTCCATCCTTA4647 | 229 | |
PAX6NM_001604/ 5080 | 16055TGCAGATGCAAAAGTCCAAG16074 | 16348TTTCCCAAGCAAAGATGGAC16329 | 200 | |
NOTCH1NM_017617/ 4851 | 37744ACTGTGAGGACCTGGTGGAC37763 | 38456TTGTAGGTGTTGGGGAGGTC38437 | 196 |
Tm represents melting temperature of the PCR product. # represents primer that does not span an intron. Genomic localization for primers: OPN1LW (Gene ID 5956), Forward: 10441–10460, Reverse: 12241- 12222; OPN1MW (Gene ID 2652), Forward: 9211–9230 (4 mismatches), Reverse: 11011–10992 (1 mismatch).