Table 1. Sequences of primers used for PCR, sequencing and Real-Time PCR, followed by sequences of a TaqMan probe, shRNAs, and CRNDEP epitopes used in the present study.
| Primer name | Sequence [5' → 3'] 1 or [NH2 → COOH] |
|---|---|
| L388-SacI PCR primer | CCTGAGCTCCTATGAGAGGATCGCATCAC |
| L388-SmaIv2 PCR primer | GGTCCCGGGCAATTAAGCTTTAGTCTATAAAC |
| L388BglII PCR primer | GGTAGATCTCTATGAGAGGATCGCATCAC |
| L388SmaI PCR primer | GGTCCCGGGCATTAAGCTTTAGTCTATAAAC |
| RedL388F PCR primer | AACCACAACGAGGACTAC |
| RedL388R PCR primer | GGACAAACCACAACTAGAATG |
| L388wewF forward sequencing primer | CTGTACTGGCTATTGGAAGG |
| L388wewR reverse sequencing primer | TAAACCACTCGAGCACTTTG |
| U6prom-F sequencing primer | GACTATCATATGCTTACCGT |
| SV40rev sequencing primer | CATACTTCTGCCTGCTGGG |
| LOCrtF—Real-Time PCR forward primer (universal) | AATTCATCCCAAGGCTGGTC |
| LOCrt35R —Real-Time PCR reverse primer (specific to the CRNDEP-coding transcript, FJ466686) | TTCCAGTGGCATCCTCCTTA |
| LOCrt4wR—Real-Time PCR reverse primer (specific to non-CRNDEP-coding transcripts, e.g., FJ466685) | GCACTCACAATGAGTCATCTG |
| CRNDE-specific TaqMan probe (universal) | CCTTCCAATAGCCAGTACAGTAGCTCC |
| SH1 sense strand 2 | GATCGGGAGCTACTGTACTGGCTATTGGAAGGAGTCAAGAGCTCCTTCCAATAGCCAGTACAGTAGCTCCTTTTTTGA |
| SH1 complementary strand 2 | AGCTTCAAAAAAGGAGCTACTGTACTGGCTATTGGAAGGAGCTCTTGACTCCTTCCAATAGCCAGTACAGTAGCTCCC |
| SH2 sense strand 2 | GATCGAGAAGAAGGTTAAGCTGTATTTGATTGCCTCAAGAGGGCAATCAAATACAGCTTAACCTTCTTCTTTTTTTGA |
| SH2 complementary strand 2 | AGCTTCAAAAAAAGAAGAAGGTTAAGCTGTATTTGATTGCCCTCTTGAGGCAATCAAATACAGCTTAACCTTCTTCTC |
| SH3 sense strand 2 | GATCGGAAGATAAGGAGGATGCCACTGGAAATGTTCAAGAGACATTTCCAGTGGCATCCTCCTTATCTTCTTTTTTGA |
| SH3 complementary strand 2 | AGCTTCAAAAAAGAAGATAAGGAGGATGCCACTGGAAATGTCTCTTGAACATTTCCAGTGGCATCCTCCTTATCTTCC |
| SH SCR (scrambled, negative control) sense strand 2 | GATCGGGAGCAATATCGTGGATGAAACGGTGAAATCAAGAGTTTCACCGTTTCATCCACGATATTGCTCCTTTTTTGA |
| SH SCR (scrambled, negative control) complementary strand 2 | AGCTTCAAAAAAGGAGCAATATCGTGGATGAAACGGTGAAACTCTTGATTTCACCGTTTCATCCACGATATTGCTCCC |
| CRNDEP Epitope 1 | EIHPKAGLQSLQ |
| CRNDEP Epitope 2 | DSEDKEDATGNVEMK |
| CRNDEP Epitope 3 | EWFKYVLGIPVYRL |
1) Restriction enzyme recognition sites inserted in primer overhangs were underlined.
2) shRNA-coding sequences: sense regions were marked with a wavy line, whereas antisense regions were indicated with a double wavy line; sticky ends, specific to BamHI/HindIII digestion, were double-underlined.