Enucleated eyes were incubated overnight in 5 mg/mL Dispase (Invitrogen) in Dulbecco's Modified Eagle Medium/Nutrient Mixture F-12 (DMEM/F-12) and HEPES (Gibco) at 4°C. The CE was peeled off and total RNA was isolated using the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA was reverse transcribed from 100 µg of total RNA using Invitrogen SuperScript III Reverse Transcriptase and oligo(dT) primers as previously described.
27,29 RT-PCR was performed using a mix of cDNA, SYBR Green reagent (Qiagen), and 10 µM of primers. The sequences of primers for
p63 isoforms were selected using Primer3 Output program technology (Massachusetts Institute of Technology, Cambridge, MA, USA) and were as follows: ΔNp63 forward, 5′-GGAAAACAATGCCCAGACTCA-3′; ΔNp63 reverse, 5′-GTCACGCTATTCTGTGCGTG-3′; TAp63 forward, 5′-CACCCAGACAAGCGAGTTCCT-3′; TAp63 reverse, 5′-CACTGAGGTCTGAGTCTTGCAT-3′; p63α forward, 5′-TCCGACATGCCATCTGGAAG-3′; p63α reverse, 5′-GCATCGATCACACGTTCACC-3′; p63β forward, 5′-TGGCTGGAGACATGAATGGAC-3′; and p63β reverse, 5′-CAGACTTGCCAAATCC. These primers were designed from the reference sequences in the GenBank database, accession numbers AF075439 (ΔNp63α), AF075436 (TAp63α), and AF075435 (TAp63β). Primers for Ets1, Notch1, and Gapdh have been previously published and were as follows: Ets1 forward, 5′-CCCTGGGTAAAGAATGCTTCC-3′; Ets1 reverse, 5′-GCTGATGAAGTAATCCGAGGTG-3′
32; Notch1 forward, 5′-AGTGTGACCCAGACCTTGTGA-3′; Notch1 reverse, 5′-AGTGGCTGGAAAGGGACTTG-3′
33; Hey1 forward, 5′-GCTGAGATCTTGCAGATGAC-3′; Hey1 reverse, 5′-CAACTTCGGCCAGGCATTCC-3′; Hes1 forward, 5′-GTCAACACGACACCGGACAA-3′; Hes-1 reverse, 5′-CCTTCGCCTCTTCTCCATGA-3′; Maml1 forward, 5′-GCACAGCGCGGTCATGGAGC-3′; Maml1 reverse, 5′-GCGCTTGGCCTTGGCCTGGA-3′
27; Gapdh forward, 5′-AGGTCGGTGTGAACGGATTTG-3′; and Gapdh reverse, 5′-GGGGTCGTTGATGGCAACA-3′.
34 The reactions were carried out in an ABI PRISM 7900HT Sequence Detection System (Applied Biosystems, Foster City, CA, USA) using a PCR program consisting of 40 cycles of 95°C for 15 seconds, 55°C for 15 seconds, and 72°C for 30 seconds. Data were analyzed using the 2
-ΔΔCt method, with
Gapdh transcript as a reference.