Table 2. Differentially expressed miRNAs in the liver between Large White and Erhualian piglets detected with deep sequencing compared to microarray and RT-PCR validation.
| microRNA sequencing | microarray | RT-qPCR | ||||||
| miRNA | RPM (LW) | RPM (EHL) | log2 Ratio (EHL/LW) | log2 Ratio (EHL/LW) | p-value | FDR(%) | log2 Ratio (EHL/LW) | p-value |
| down-regulated miRNAs | ||||||||
| miR-146a | 31 | 19 | −0.71 | # | # | # | −0.30 | 0.380 |
| miR-21* | 22 | 15 | −0.63 | – | – | – | ||
| miR-222 | 1050 | 688 | −0.61 | −0.35 | 0.566 | 35.993 | −0.99 | 0.008 |
| miR-2887 | 49 | 23 | −1.08 | – | – | – | ||
| miR-2904 | 10 | 6 | −0.76 | – | – | – | ||
| miR-2904-3p | 11 | 7 | −0.62 | – | – | – | ||
| miR-375 | 2315 | 1549 | −0.58 | – | – | – | ||
| miR-4332-3p | 319 | 139 | −1.20 | 0.24 | 0.513 | 62.118 | ||
| miR-4332-5p | 25 | 9 | −1.52 | – | – | – | ||
| miR-485-3p | 34 | 18 | −0.93 | – | – | – | ||
| miR-574 | 1072 | 570 | −0.91 | −0.77 | 0.252 | 18.188 | −0.69 | 0.121 |
| miR-652 | 33 | 16 | −1.06 | # | # | # | −1.28 | 0.010 |
| miR-739 | 17 | 10 | −0.77 | – | – | – | ||
| miR-874 | 297 | 189 | −0.65 | – | – | – | ||
| miR-874* | 19 | 12 | −0.65 | – | – | – | ||
| up-regulated miRNAs | ||||||||
| miR-100 | 746 | 1170 | 0.65 | 0.13 | 0.737 | 62.17 | 0.42 | 0.379 |
| miR-129 | 12 | 22 | 0.87 | # | # | # | ||
| miR-133a | 67 | 129 | 0.95 | # | # | # | 1.58 | 0.020 |
| miR-1343 | 14 | 21 | 0.60 | – | – | – | ||
| miR-140 | 427 | 666 | 0.64 | 0.8 | 0.19 | 34.194 | ||
| miR-144 | 41 | 86 | 1.07 | – | – | – | ||
| miR-155 | 133 | 585 | 2.14 | # | # | # | ||
| miR-184 | 21 | 59 | 1.48 | 1.71 | 0.009 | 0 | ||
| miR-188-5p | 69 | 141 | 1.03 | – | – | – | ||
| miR-190 | 69 | 124 | 0.84 | – | – | – | ||
| miR-193a-3p | 13 | 32 | 1.24 | # | # | # | ||
| miR-193a-5p | 13 | 24 | 0.83 | 1.13 | 0.032 | 6.839 | ||
| miR-193b* | 6 | 10 | 0.64 | – | – | – | ||
| miR-19a | 64 | 97 | 0.59 | # | # | # | ||
| miR-210 | 16 | 31 | 0.96 | # | # | # | ||
| miR-216 | 3 | 19 | 2.71 | # | # | # | 1.31 | 0.000 |
| miR-335 | 41 | 67 | 0.72 | # | # | # | ||
| miR-335* | 32 | 49 | 0.62 | – | – | – | ||
| miR-362 | 83 | 143 | 0.79 | # | # | # | ||
| miR-451 | 2056 | 3165 | 0.62 | 0.12 | 0.713 | 40.884 | ||
| miR-582-3p | 5 | 13 | 1.48 | – | – | – | ||
| miR-582-5p | 12 | 33 | 1.42 | – | – | – | 1.01 | 0.060 |
| miR-590 | 65 | 106 | 0.70 | – | – | – | ||
| miR-660 | 335 | 509 | 0.60 | – | – | – | ||
| miR-802 | 12 | 21 | 0.81 | – | – | – | ||
The miRNA expression in the liver of Erhualian piglets was compared with that of Large White. miRNAs with fold change >1.5 and average RPM >10 are shown. “#" means that this miRNA could not be detected by microarray due to low fluorescence, while “–" means that the probe for the miRNA is missing on the microarray.