Comprehensive Analysis of miRNAs and Target mRNAs between Immature and Mature Testis Tissue in Chinese Red Steppes Cattle
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Animal and Samples
2.3. RNA Extraction and Quality Analysis
2.4. Library Preparation of mRNA and miRNA and Quantification
2.5. Analysis of Differentially Expressed Genes
2.6. GO and KEGG Enrichment Analysis of DEGs
2.7. Analysis of miRNA Profiling and Prediction of Novel miRNA
2.8. miRNA Target Gene Prediction and Annotation Analyses
2.9. Real-Time PCR of DEGs and DERs
3. Results
3.1. Differential Expression of mRNAs in Chinese Red Steppes between Immature and Mature Testicular Tissues
3.2. GO and KEGG Pathway Analyses of DEGs
3.3. Analysis of miRNAs Expression Patterns in Testicular Tissues
3.4. Prediction and Construction of Target Network between DERs and DEGs
3.5. The Comparative Analysis and Verification of the Expression Levels between Real-Time PCR Result and Sequencing Data
4. Discussion
4.1. Mapping and Length Distributions of the miRNAs Sequences
4.2. Gene Expression Patterns and Roles in Testicular Tissues of Cattle
4.3. Target Predictions of DERs and Target Network
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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AccID | Mature | Immature | Log2FC | FDR | Regulate |
---|---|---|---|---|---|
TRIM42 | 1754.37 | 0.00 | 20 | 0.00 | up |
SPACA4 | 879.07 | 0.00 | 20 | 0.00 | up |
FAM187B | 776.40 | 0.00 | 20 | 0.00 | up |
LOC781895 | 693.90 | 0.00 | 20 | 0.00 | up |
PRPS1L1 | 634.28 | 0.00 | 20 | 0.00 | up |
LOC100335845 | 557.42 | 0.00 | 20 | 0.00 | up |
TMIGD3 | 423.84 | 0.00 | 20 | 0.00 | up |
LOC784318 | 405.71 | 0.00 | 20 | 0.00 | up |
CCDC182 | 396.56 | 0.00 | 20 | 0.00 | up |
LOC101904646 | 362.72 | 0.00 | 20 | 0.00 | up |
TMEM239 | 352.87 | 0.00 | 20 | 0.00 | up |
LOC101907601 | 339.97 | 0.00 | 20 | 0.00 | up |
LOC615451 | 280.92 | 0.00 | 20 | 0.00 | up |
LOC516636 | 232.22 | 0.00 | 20 | 0.00 | up |
LOC101906055 | 216.52 | 0.00 | 20 | 0.00 | up |
LOC104976276 | 0.00 | 68.67 | −20 | 0.00 | down |
LOR | 0.00 | 37.29 | −20 | 0.00 | down |
LOC781553 | 0.00 | 34.92 | −20 | 0.00 | down |
PDIA2 | 0.00 | 105.11 | −20 | 0.00 | down |
CHRNA1 | 0.00 | 64.93 | −20 | 0.00 | down |
LOC100847574 | 0.00 | 51.13 | −20 | 0.00 | down |
MMP12 | 0.00 | 29.71 | −20 | 0.00 | down |
LOC107133052 | 0.00 | 28.63 | −20 | 0.00 | down |
MMP7 | 0.00 | 22.75 | −20 | 0.00 | down |
LOC101904303 | 0.00 | 22.03 | −20 | 0.00 | down |
LOC104970370 | 0.00 | 21.73 | −20 | 0.00 | down |
GABRG3 | 0.00 | 16.98 | −20 | 0.00 | down |
LOC104970773 | 0.00 | 16.71 | −20 | 0.00 | down |
CSMD3 | 0.00 | 16.21 | −20 | 0.00 | down |
LOC100139712 | 0.00 | 15.90 | −20 | 0.00 | down |
AccID | Mature | Immature | Log2FC | FDR | Style |
---|---|---|---|---|---|
bta-miR-449a | 10,427.15 | 14.20 | 9.52 | 0.00 | up |
bta-miR-449b | 326.43 | 1.49 | 7.77 | 0.00 | up |
bta-miR-34b | 4001.49 | 35.13 | 6.83 | 0.00 | up |
bta-miR-34c | 75,119.87 | 561.35 | 7.06 | 0.00 | up |
bta-miR-449c | 151.18 | 1.49 | 6.66 | 0.00 | up |
bta-miR-146a | 379.95 | 8.22 | 5.53 | 0.00 | up |
bta-miR-375 | 671.60 | 20.18 | 5.06 | 0.00 | up |
bta-miR-544b | 28.09 | 0.00 | 20.00 | 0.01 | up |
bta-miR-2384 | 64.22 | 2.24 | 4.84 | 0.02 | up |
bta-miR-151-5p | 13,120.22 | 488.10 | 4.75 | 0.02 | up |
bta-miR-2284s | 17.39 | 0.00 | 20.00 | 0.04 | up |
bta-miR-493 | 1.34 | 290.77 | −7.76 | 0.00 | down |
bta-miR-409b | 2.68 | 224.24 | −6.39 | 0.01 | down |
bta-miR-409a | 0.00 | 94.93 | −20.00 | 0.01 | down |
bta-miR-495 | 16.05 | 964.99 | −5.91 | 0.01 | down |
bta-miR-487b | 5.35 | 327.39 | −5.94 | 0.01 | down |
bta-miR-376e | 4.01 | 238.44 | −5.89 | 0.01 | down |
bta-miR-411c-5p | 6.69 | 346.08 | −5.69 | 0.01 | down |
bta-miR-196b | 0.00 | 69.51 | −20.00 | 0.02 | down |
bta-miR-376b | 1.34 | 92.69 | −6.11 | 0.02 | down |
bta-miR-433 | 13.38 | 469.41 | −5.13 | 0.03 | down |
bta-miR-3956 | 0.00 | 50.08 | −20.00 | 0.03 | down |
bta-miR-432 | 255.53 | 13391.71 | −5.71 | 0.03 | down |
bta-miR-541 | 0.00 | 44.85 | −20.00 | 0.03 | down |
bta-miR-369-3p | 9.36 | 284.79 | −4.93 | 0.03 | down |
bta-miR-665 | 10.70 | 307.21 | −4.84 | 0.04 | down |
bta-miR-496 | 0.00 | 38.87 | −20.00 | 0.04 | down |
bta-miR-3578 | 16.05 | 417.84 | −4.70 | 0.04 | down |
bta-miR-543 | 20.07 | 504.54 | −4.65 | 0.05 | down |
bta-miR-382 | 17.39 | 419.33 | −4.59 | 0.05 | down |
bta-miR-485 | 17.39 | 418.58 | −4.59 | 0.05 | down |
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Fang, X.; Qin, L.; Yu, H.; Jiang, P.; Xia, L.; Gao, Z.; Yang, R.; Zhao, Y.; Yu, X.; Zhao, Z. Comprehensive Analysis of miRNAs and Target mRNAs between Immature and Mature Testis Tissue in Chinese Red Steppes Cattle. Animals 2021, 11, 3024. https://doi.org/10.3390/ani11113024
Fang X, Qin L, Yu H, Jiang P, Xia L, Gao Z, Yang R, Zhao Y, Yu X, Zhao Z. Comprehensive Analysis of miRNAs and Target mRNAs between Immature and Mature Testis Tissue in Chinese Red Steppes Cattle. Animals. 2021; 11(11):3024. https://doi.org/10.3390/ani11113024
Chicago/Turabian StyleFang, Xibi, Lihong Qin, Haibin Yu, Ping Jiang, Lixin Xia, Zhen Gao, Runjun Yang, Yumin Zhao, Xianzhong Yu, and Zhihui Zhao. 2021. "Comprehensive Analysis of miRNAs and Target mRNAs between Immature and Mature Testis Tissue in Chinese Red Steppes Cattle" Animals 11, no. 11: 3024. https://doi.org/10.3390/ani11113024