Table 3.

ASAL-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 ASAL
miR-21a-1-3p	267.99	1.52	0.099	N/A
miR-29b-2-5p	516.80	1.55	0.091	1.47
miR-146a-5p	202688.90	2.01	8.9 × 10−6	1.89
miR-146a-1-2-3p	8503.53	9.06	9.06 × 10−37	5.87
miR-146a-3-3p	12146.14	3.43	2.62 × 10−11	N/A
miR-146d-1-3p	421.43	2.60	2.45 × 10−4	N/A
miR-183-1-3-3p	19.55	4.17	0.018	N/A
miR-183-2-3p	19.24	4.08	0.021	N/A
miR-192a-5p	391.09	6.68	0.016	1.64
miR-194a-5p	82.25	6.68	0.016	1.37
miR-200b-3p	275.30	8.00	0.009	N/A
miR-221-5p	141.35	1.92	0.018	2.23
miR-429ab-3p	11.34	8.40	0.071	N/A
miR-725-5p	26.55	17.15	2.27 × 10−6	1.55
miR-725-3p	163.89	4.63	6.75 × 10−6	N/A
miR-novel-16-5p	1066.67	2.01	1.81 × 10−4	1.09
Down-regulated by ASAL
miR-722-3p	410.45	−2.08	0.021	−1.64
miR-727a-3p	886.63	−1.82	0.085	−1.94

¹ miRNAs with bold font were 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 (ASAL/PBS) was converted from the log₂ fold-change (given by DESeq2 analyses). For down-regulated miRNAs, fold-change values were 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 2^A−B as in Xue et al. [46], where A was the mean of log₂ RQ from ASAL 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.