Table 2.
Quantitative polymerase chain reaction editing assays used in the study*
| Target | Accession no. | Primers | Probes | % CH |
|---|---|---|---|---|
| GluA2 flip R/G | NM_000826.2 | F-ATGGCATCGCAACACCTAAAG | FAM-TCCTCATTAAGAACCCC | 3.1 |
| R-TCACTGAGTTTCAATACTGCAAGATTT | VIC-CCTCATTAGGAACCCCA | |||
| GluA2 flop R/G | NM_001083619.1 | F-ATGGCATCGCAACACCTAAAG | FAM-ATCCTCATTAAGAAATGCGG | 2.8 |
| R-CATTCAGTTTTAGTACTGCGAGGTTAA | VIC-ATCCTCATTAGGAAATGC | |||
| GluA2 Q/R | NM_000826.3 | F-GGAAGAGAAACACAAAGTAGTGAATCA | FAM-CATCCTTGCTGCATAA | 1.8 |
| R-AGAGAGGGATCTTGGCGAAATAT | VIC-CATCCTTGCCGCATAA | |||
| GluA3 flip R/G | NM_007325.4 | F-TGGTGTGGCAACCCCTAAAG | FAM-CAGCATTAAGAACGCCTG | 4.1 |
| R-CACTGAGTTTCAATACTGCAAGGTTT | VIC-CAGCATTAGGAACGCCT | |||
| GluA3 flop R/G | NM_000828.4 | F-TGGTGTGGCAACCCCTAAAG | FAM-CAGCATTAAGAAATG | 1.4 |
| R-GCCTTGCTCATTCAGTTTTAATACTG | VIC-CAGCATTAGGAAATG | |||
| GluA4 flip R/G | NM_000829.3 | F-CTATGGAGTAGCAACGCCCAA | FAM-ACAGGAGTTCTTAATGAGGA | 1.9 |
| R-TGCCTCACTGAGTTTCAAAACG | VIC-ACAGGAGTTCCTAATGAGGA | |||
| GluA4 flop R/G | NM_001077243.2 | F-CTATGGAGTAGCAACGCCCAA | FAM-CTCATTAAGAAATGCTG | 2.6 |
| R-CAAGAGGCCTTGTTCATTCAGTTT | VIC-CTCATTAGGAAATGCT | |||
| GluK1 Q/R | NM_000830 | F-GACGTGGTGGAAAACAATTTTACTT | FAM-CTCTCATGCAGCAAGGA | 1.0 |
| R-ACTATTCTGGTCGATAGAGCTTTGG | VIC-TCTCATGCGGCAAGGA | |||
| GluK2 Q/R | NM_021956 | F-CTAAATAGTTTCTGGTTTGGAGTTGGA | FAM-TCTCATGCAGCAAGGT | 3.3 |
| R-TCCTGGTGGACAGTGCTTTG | VIC-TCTCATGCGGCAAGGT | |||
| GluK2 I/V | NM_021956 | F-CCTGAATCCTCTCTCCCCTGAT | FAM-TGGATGTATATTCTGCTGGCT | 2.0 |
| R-ACTAAACCTGGCTATGACAAAGAGC | VIC-GATGTATGTTCTGCTGGCT | |||
| GluK2 Y/C | NM_021956 | F-CCTGAATCCTCTCTCCCCTGAT | FAM-TTCTGCTGGCTTACTTGGGTG | 8.0 |
| R-ACTAAACCTGGCTATGACAAAGAGC | VIC-TTCTGCTGGCTTGCTTGGGT |
CH = cross-hybridization; I/V = isoleucine-to-valine site; Q/R = glutamine-to-arginine; R/G = arginine-to-glycine site; Y/C = tyrosine-to-cysteine site.
Each assay consisted of a set of primers (forward [F] and reverse [R]) to amplify both edited and unedited transcripts, and 2 TaqMan probes. One probe was labelled with FAM and was designed to recognize the unedited, genomic base, A. Another probe was labelled with VIC and was designed to recognize the edited base, G, allowing for the edited and unedited transcripts to be measured simultaneously in the same reaction. We show sequences of primers and probes and percentages of cross-hybridization for each assay. Cross-hybridization is determined as the frequency with which a probe hybridizes to its mismatched template (for details, see Wong and colleagues29). Edited base is indicated in boldface type.