Table 2.
Details of TaqMan® real-time PCR assays
| Gene | Oligo | Sequence | Amplicon size (bp) |
Genomic position (exon) | Genomic (bp) |
Detection gDNA | Pseudo-gene |
|---|---|---|---|---|---|---|---|
| ABL | Forward | TGTGGCGAGTGGTGATAATACAC | 83 | 2 | ~12,000 7 | No | No |
| Probe | CAGCATCACTAAAGGTGAAAAGCTACGAGTCCTT 2 | 2/3 | |||||
| Reverse | TCCACTCACCATTCTGGTTGTAA | 3 | |||||
| ACTB | Forward | CAACCGTGAGAAGATGACTCAGA | 127 | 3/4 | 410 8 | (Yes) 11 | Yes |
| Probe | TCTCTGTACGCTTCTGGCCGCACC 3 | 4 | |||||
| Reverse | CCCAGAGTCCATGACAATACCA | 4 | |||||
| B2M | Forward | CGCGTTTTGTGGTCTTGGT | 84 | 1 | 3,270 7 | No | No |
| Probe | CGGACTGCTCTATCTGTCCCACCTGGA 2 | 1 | |||||
| Reverse | AAACCTGAACCTTTGGAGAATGC | 1/2 | |||||
| GAPDH | Forward | GCCATCAATGACCCCTTCAT | 82 | 1 | NA | (Yes) 11,12 | Yes |
| Probe | CTCAACTACATGGTCTACATGTTCCAGTATGATTCCA 4 | 1/2 | |||||
| Reverse | GCCGTGGAATTTGCCGT | 2 | |||||
| GUSB | Forward | CTACATCGATGACATCACCATCAG | 80 | 4 | 532 9 | Yes | No |
| Probe | ACCAGCGTGAACCAAGACACTGGGC 3 | 4/5 | |||||
| Reverse | CGCCTTCAACAAAAATCTGGTAA | 5 | |||||
| HMBS | Forward | TGGCAGTGCTGAAAGCCTTA | 94 | 3 | 554 7 | No | No |
| Probe | TTGAAATCGTTGCTATGTCCACCACAGG 2 | 3/4 | |||||
| Reverse | TTAGAGAGCGCAGTATCAAGAATCTT | 4 | |||||
| HPRT | Forward | AACTGGAAAGAATGTCTTGATTGTTG | 100 | 4/5 | >90,000 7 | (Yes) 11 | Yes |
| Probe | CACTGGCAAAACAATGCAAACCTTGCTTT 3 | 6 | |||||
| Reverse | GACCATCTTTGGATTATACTGCTTGA | 6 | |||||
| RPS7 | Forward | GTCCCAGAAGCCGCACTTT | 74 | 4/5 | ~2,200 10 | (Yes) 11 | Yes |
| Probe | CGCCGTGCACGACGCGA 5 | 5 | |||||
| Reverse | CACAATCTCGCTCGGGAAAA | 5 | |||||
| YWHAZ | Forward | ACAAAGACAGCACGCTAATAATGC | 84 | 4 | 2,878 7 | (Yes) 11 | Yes |
| Probe | CGATGTCCACAATGTCAAGTTGTCTCTCAGTAAT 3 | 4/5 | |||||
| Reverse | CTTCAGCTTCATCTCCTTGGGTAT | 5 | |||||
| 18S rRNA 1 | Forward | CGGCTACCACATCCAAGGAA | NA | NA | NA | NT | NT |
| Probe | TGCTGGCACCAGACTTGCCCTC 6 | NA | |||||
| Reverse | GCTGGAATTACCGCGGCT | NA |
1 TaqMan® Gene Expression Assay (Applied Biosystems); 2 5' FAM/3' BHQ-1; 3 5' Yakima Yellow/3' BHQ-1; 4 5' FAM/3' TAMRA; 5 5' TET/3' TAMRA; 6 5' VIC/3' MGB; 7 Ensembl; 8 For ACTB, the PCR product was sequenced [GenBank: GQ848333]; it showed the highest identity to the human actin isoform gamma 1 [GenBank: NG_011433]. 9 According to the Genome Annotation Resource Fields (GARFIELD) http://lgd.abcc.ncifcrf.gov[25]; 10 According to Penning et al. [13]; 11 Amplification of processed pseudogene; 12 According to Leutenegger et al. [26]; NA = Not available; NT = Not tested