Table 2.
pIC-responsive miRNAs in the head kidney of fish fed the control diet identified by DESeq2 (n = 3) and confirmed by qPCR (n = 8–9).
| miRNAs 1 | Base Mean 2 | Fold-Change 3 | Adjusted p-Values 4 | qPCR Fold-Change 5 |
|---|---|---|---|---|
| Up-regulated by pIC | ||||
| miR-27d-1-5p 6 | 868.11 | 2.17 | 0.049 | 2.69 |
| miR-27d-2-5p 6 | 861.10 | 2.17 | 0.049 | 2.69 |
| miR-30e-1-2-3p | 404.73 | 2.16 | 0.049 | 2.57 |
| miR-135bd-5p | 52.80 | 14.03 | 0.036 | 1.54 |
| miR-146a-5p | 152066.51 | 1.71 | 0.028 | 1.62 |
| miR-146a-1-2-3p | 6322.03 | 7.94 | 3.85 × 10-4 | 7.89 |
| miR-181a-5-3p | 11080.58 | 1.59 | 0.051 | 1.97 |
| miR-221-5p | 221.52 | 4.44 | 0.036 | 7.55 |
| miR-462a-3p | 1554.09 | 2.69 | 0.098 | 5.72 |
| miR-462b-3p | 941.82 | 5.46 | 8.0 × 10-12 | N/A |
| miR-8159-5p | 97.72 | 9.92 | 0.055 | N/A |
| Down-regulated by pIC | ||||
| miR-106a-3p | 960.11 | −1.93 | 0.036 | N/A |
1 miRNAs with bold font are differentially expressed in both pIC and ASAL groups when compared to the PBS-injected control group. The mature sequences and miRBase identities of each miRNA are given in Supplemental Table S4. 2 The mean of normalized read counts for all of the samples included in the comparison. 3 Fold-change (pIC/PBS) was converted from the log2 fold-change (given by DESeq2 analyses). For the down-regulated miRNA, the fold-change value was inverted (−1/fold-change). 4 Adjusted p-values as determined by DESeq2 analyses. 5 For qPCR fold-change calculation (fish fed the control diet), overall fold up-regulation was calculated as 2A−B as in Xue et al. [46], where A was the mean of log2 RQ from the pIC group, and B was the mean of log2 RQ from PBS group. Underlined qPCR fold-change values indicate statistical significance (p < 0.05). N/A = not applicable. 6 miR-27d-2-5p and miR-27d-1-5p are identical except the length difference (24 vs. 23 nt). Therefore, the qPCR assay was generic to both miRNAs.