Table 1 of Hollborn, Mol Vis 2011; 17:2738-2750.

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).

Hollborn, Mol Vis 2011; 17:2738-2750. http://www.molvis.org/molvis/v17/a296

©2011 Molecular Vision http://www.molvis.org/molvis/

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