Table 2. Sequences of miRNAs and probes used in microarray and qRT-PCR.
| miRNA name | miRNA sequence | GCcontent(%) | Agilent | Affymetrix | ||||
| probe sequences | free energy (kcal/mol) | Tm (°C) | probe sequence | free energy (kcal/mol) | Tm (°C) | |||
| mmu-miR-15a | UAGCAGCACAUAAUGGUUUGUG | 40 | CACAAACCATTATGTGCTGCT(A) | (−25.0) | 56.2 | CACAAACCATTATGTGCTGCTA | −25.0 | 56.2 |
| −24.4 | 56.9 | |||||||
| mmu-miR-21 | UAGCUUAUCAGACUGAUGUUGA | 36 | TCAACATCAGTCTGATAAG(C) | (−20.3) | 37.2 | TCAACATCAGTCTGATAAGCTA | −22.7 | 39.9 |
| −17.6 | 32.0 | |||||||
| mmu-miR-34a | UGGCAGUGUCUUAGCUGGUUGU | 50 | ACAACCAGCTAAGACACTG(C) | (−23.2) | 56.9 | ACAACCAGCTAAGACACTGCCA | −27.7 | 60.4 |
| −20.5 | 52.8 | |||||||
| mmu-miR-96 | UUUGGCACUAGCACAUUUUUGCU | 40 | AGCAAAAATGTGCTAGTGCCA(A) | (−24.1) | 39.9 | AGCAAAAATGTGCTAGTGCCAAA | −24.3 | 38.7 |
| −23.9 | 41.2 | |||||||
| mmu-miR-127 | UCGGAUCCGUCUGAGCUUGGCU | 59 | AGCCAAGCTCAGACGGA(T) | (−23.2) | 44.3 | AGCCAAGCTCAGACGGATCCGA | −30.6 | 51.4 |
| −22.3 | 43.9 | |||||||
| mmu-miR-146a | UGAGAACUGAAUUCCAUGGGUU | 40 | AACCCATGGAATTCAGTT(C) | (−21.3) | 55.6 | AACCCATGGAATTCAGTTCTCA | −26.0 | 59.5 |
| −20 | 54.0 | |||||||
| mmu-miR-146b | UGAGAACUGAAUUCCAUAGGCU | 40 | AGCCTATGGAATTCAGTT(C) | (−21.5) | 41.5 | AGCCTATGGAATTCAGTTCTCA | −26.2 | 47.4 |
| −20.2 | 39.2 | |||||||
| mmu-miR-182 | UUUGGCAAUGGUAGAACUCACACCG | 48 | CGGTGTGAGTTCTAC(C) | (−19.9) | 62.9 | CGGTGTGAGTTCTACCATTGCCAAA | −31.9 | 62.9 |
| −17 | 58.8 | |||||||
| mmu-miR-183 | UAUGGCACUGGUAGAAUUCACU | 40 | AGTGAATTCTACCAGTGC(C) | (−23.2) | 44.7 | AGTGAATTCTACCAGTGCCATA | −26.3 | 46.3 |
| −20.3 | 40.0 | |||||||
| mmu-miR-184 | UGGACGGAGAACUGAUAAGGGU | 50 | ACCCTTATCAGTTCTCCGTCC(A) | (−31.9) | 57.0 | ACCCTTATCAGTTCTCCGTCCA | −31.9 | 57.0 |
| −30.3 | 56.2 | |||||||
| mmu-miR-322 | CAGCAGCAAUUCAUGUUUUGGA | 40 | TCCAAAACATGAATTGCTGCTG | −23.1 | 37.7 | TCCAAAACATGAATTGCTGCTG | −23.1 | 37.7 |
| mmu-miR-433 | AUCAUGAUGGGCUCCUCGGUGU | 54 | ACACCGAGGAGCC(C) | (−20.7) | 43.7 | ACACCGAGGAGCCCATCATGAT | −30.3 | 50.9 |
| −17.8 | 38.0 | |||||||
Free energy for the probe-target binding was calculated using the thermodynamic parameters for RNA/DNA hybrid duplexes from Sugimoto et al. [69]. Tm was calculated according to the formula reported in Wei et al. [70] using the thermodynamic parameters for RNA/DNA hybrid duplexes from Sugimoto et al. [69] that consisted of the following parameters: [Na+] = 1 M, Ct (oligonucleotide concentration) = 100 uM, A (helix initiation factor) = −10.8 cal/KM, F (correction term per1% Formamide) = 0.63°C, Formamide concentration = 35%, R (universal gas constant) = 1.987 cal/KM.