Analysis of MicroRNA Expression Profiles in Weaned Pig Skeletal Muscle after Lipopolysaccharide Challenge
Abstract
:1. Introduction
2. Results and Discussion
2.1. General Analysis of Small RNAs
Classes of Reads | The LPS-Challenged Group | The Saline-Treated Group | ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
L1 Library | L2 Library | L3 Library | L4 Library | L5 Library | L6 Library | |||||||
Total | Unique | Total | Unique | Total | Unique | Total | Unique | Total | Unique | Total | Unique | |
Clean date | 8,166,036 | 424,320 | 8,578,151 | 393,231 | 7,974,032 | 426,707 | 8,261,735 | 532,894 | 7,740,201 | 456,559 | 9,095,380 | 536,545 |
Genome | 7,392,469 | 306,807 | 7,875,613 | 288,075 | 7,280,396 | 316,514 | 7,339,331 | 383,868 | 6,784,012 | 329,527 | 7,966,211 | 395,908 |
miRBase (mature) | 3,979,370 | 7498 | 4,339,317 | 7753 | 3,940,011 | 7770 | 3,609,976 | 7597 | 3,995,522 | 8251 | 5,332,846 | 8842 |
Rfam | 1,972,825 | 71,199 | 2,119,590 | 65,099 | 1,847,538 | 74,226 | 2,269,168 | 81,568 | 1,466,801 | 85,054 | 1,304,709 | 86,567 |
RepBase | 166,565 | 28,787 | 132,226 | 25,094 | 157,402 | 30,124 | 259,354 | 31,758 | 180,018 | 30,089 | 158,490 | 35,920 |
mRNA/EST | 501,200 | 128,735 | 437,848 | 116,045 | 516,196 | 129,355 | 608,415 | 173,253 | 594,752 | 126,662 | 586,024 | 183,958 |
2.2. Identification of Known miRNAs
2.3. Identification of Novel miRNAs by miRDeep2
miRDeep2 Score 1 | Novel miRNAs | Known miRNAs | - | ||||
---|---|---|---|---|---|---|---|
Predicted 2 | False Positives 3 | True Positives 4 | In Species 5 | In Data 6 | Detected 7 | Signal-to-Noise 8 | |
10 | 65 | 3 ± 1 | 62 ± 1 (96% ± 2%) | 411 | 304 | 222 (72%) | 43.7 |
9 | 68 | 3 ± 1 | 65 ± 1 (96% ± 2%) | 411 | 304 | 223 (73%) | 43.5 |
8 | 69 | 3 ± 2 | 66 ± 3 (96% ± 2%) | 411 | 304 | 223 (73%) | 42.7 |
7 | 73 | 3 ± 2 | 70 ± 2 (96% ± 2%) | 411 | 304 | 223 (73%) | 42 |
6 | 78 | 3 ± 2 | 75 ± 3 (96% ± 2%) | 411 | 304 | 223 (73%) | 39.7 |
5 | 126 | 6 ± 2 | 120 ± 3 (95% ± 2%) | 411 | 304 | 256 (83%) | 30.7 |
4 | 156 | 15 ± 4 | 141 ± 4 (90% ± 3%) | 411 | 304 | 259 (84%) | 17.3 |
3 | 170 | 42 ± 6 | 128 ± 5 (75% ± 4%) | 411 | 304 | 261 (85%) | 7.5 |
2 | 206 | 57 ± 7 | 149 ± 6 (72% ± 3%) | 411 | 304 | 265 (86%) | 6.2 |
1 | 300 | 81 ± 8 | 219 ± 7 (73% ± 3%) | 411 | 304 | 278 (91%) | 5.4 |
2.4. Differential Expression Analysis
miRNAs ID | The LPS-Challenged Group | The Saline-Treated Group | FoldChange_Log2 | p-Value | ||||
---|---|---|---|---|---|---|---|---|
L1_TPM | L2_TPM | L3_TPM | L4_TPM | L5_TPM | L6_TPM | |||
ssc-miR-221-5p | 33.69 | 64.15 | 41.10 | 10.94 | 6.95 | 6.59 | 2.50 | 1.65 × 10−11 |
ssc-miR-146a-5p | 2.73 | 14.64 | 50.54 | 2.98 | 13.26 | 4.71 | 1.70 | 1.97 × 10−5 |
ssc-miR-9860-5p | 8.50 | 9.58 | 12.18 | 3.65 | 4.10 | 3.53 | 1.42 | 1.22 × 10−3 |
ssc-miR-148b-3p | 216.10 | 294.41 | 242.05 | 106.78 | 119.34 | 146.86 | 1.01 | 1.73 × 10−5 |
ssc-miR-192 | 191.82 | 104.61 | 123.61 | 545.85 | 142.38 | 183.34 | −1.05 | 1.00 × 10−2 |
4_16129 | 9.41 | 3.46 | 7.92 | 27.19 | 13.58 | 9.41 | −1.27 | 4.33 × 10−2 |
13_5595 | 5.77 | 5.86 | 7.92 | 18.57 | 26.20 | 8.94 | −1.46 | 1.87 × 10−2 |
ssc-miR-215 | 16.09 | 1.06 | 1.83 | 43.11 | 4.74 | 18.12 | −1.80 | 9.43 × 10−4 |
ssc-miR-429 | 0.61 | 0.00 | 0.61 | 3.32 | 2.53 | 0.94 | −2.48 | 1.20 × 10−2 |
2.5. LPS Induces miR-146a-5p and miR-221-5p Expression in C2C12 Myotubes
3. Experimental Section
3.1. Animal and Tissue Collection
3.2. TNF-α Concentration in Plasma Measurements
3.3. Reverse Transcription qPCR
3.4. Small-RNA Library Construction and Deep Sequencing
3.5. Basic Data Processing
3.6. Differential Expression Analysis of miRNAs
3.7. Cell Culture
4. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Zhang, J.; Fu, S.-L.; Liu, Y.; Liu, Y.-L.; Wang, W.-J. Analysis of MicroRNA Expression Profiles in Weaned Pig Skeletal Muscle after Lipopolysaccharide Challenge. Int. J. Mol. Sci. 2015, 16, 22438-22455. https://doi.org/10.3390/ijms160922438
Zhang J, Fu S-L, Liu Y, Liu Y-L, Wang W-J. Analysis of MicroRNA Expression Profiles in Weaned Pig Skeletal Muscle after Lipopolysaccharide Challenge. International Journal of Molecular Sciences. 2015; 16(9):22438-22455. https://doi.org/10.3390/ijms160922438
Chicago/Turabian StyleZhang, Jing, Shu-Lin Fu, Yan Liu, Yu-Lan Liu, and Wen-Jun Wang. 2015. "Analysis of MicroRNA Expression Profiles in Weaned Pig Skeletal Muscle after Lipopolysaccharide Challenge" International Journal of Molecular Sciences 16, no. 9: 22438-22455. https://doi.org/10.3390/ijms160922438