Construction of LncRNA-Related ceRNA Networks in Longissimus Dorsi Muscle of Jinfen White Pigs at Different Developmental Stages
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animals and LDM Tissue Collection
2.2. RNA Extraction and cDNA Synthesis
2.3. Construction of cDNA Library and Illumina Sequencing
2.4. Analysis of RNA-Seq Data
2.5. Identification of LncRNAs
2.6. Construction of LncRNA–miRNA–mRNA Networks
2.7. Validation of Sequencing Results Using Quantitative Real-Time PCR (qRT-PCR)
2.8. Statistical Analysis
3. Results
3.1. Landscape of the RNA Transcriptomes
3.2. Differentially Expressed mRNAs
3.3. Genomic Features of LncRNAs
3.4. Differentially Expressed lncRNAs
3.5. Functional Enrichment Analysis
3.6. Construction of LncRNA–miRNA–mRNA Regulatory Networks
3.7. Validation of Sequencing Results via Quantitative Real-Time PCR (qRT-PCR)
3.8. Bioinformatics Predicts Key Nodes of the Network
4. Discussion
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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Samples | Raw Reads | Clean Reads | Q20 (%) | Q30 (%) | GC Content (%) |
---|---|---|---|---|---|
JFW_1d_1 | 92,655,706 | 91,942,766 | 98.62 | 95.72 | 55.62 |
JFW_1d_2 | 107,050,232 | 106,444,968 | 98.64 | 95.78 | 57.33 |
JFW_1d_3 | 104,392,040 | 103,814,406 | 98.58 | 95.45 | 47.55 |
JFW_90d_1 | 96,202,328 | 95,550,798 | 98.08 | 94.20 | 55.77 |
JFW_90d_2 | 106,311,518 | 105,563,842 | 98.56 | 95.75 | 60.57 |
JFW_90d_3 | 95,622,436 | 94,984,938 | 98.67 | 95.89 | 56.13 |
JFW_180 d_1 | 94,853,354 | 94,375,978 | 97.81 | 93.78 | 57.86 |
JFW_180 d_2 | 104,189,042 | 103,407,232 | 98.59 | 95.54 | 54.04 |
JFW_180 d_3 | 107,380,946 | 106,567,824 | 98.40 | 95.04 | 55.09 |
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Wang, S.; Shi, M.; Zhang, Y.; Niu, J.; Li, W.; Yuan, J.; Cai, C.; Yang, Y.; Gao, P.; Guo, X.; et al. Construction of LncRNA-Related ceRNA Networks in Longissimus Dorsi Muscle of Jinfen White Pigs at Different Developmental Stages. Curr. Issues Mol. Biol. 2024, 46, 340-354. https://doi.org/10.3390/cimb46010022
Wang S, Shi M, Zhang Y, Niu J, Li W, Yuan J, Cai C, Yang Y, Gao P, Guo X, et al. Construction of LncRNA-Related ceRNA Networks in Longissimus Dorsi Muscle of Jinfen White Pigs at Different Developmental Stages. Current Issues in Molecular Biology. 2024; 46(1):340-354. https://doi.org/10.3390/cimb46010022
Chicago/Turabian StyleWang, Shouyuan, Mingyue Shi, Yunting Zhang, Jin Niu, Wenxia Li, Jiale Yuan, Chunbo Cai, Yang Yang, Pengfei Gao, Xiaohong Guo, and et al. 2024. "Construction of LncRNA-Related ceRNA Networks in Longissimus Dorsi Muscle of Jinfen White Pigs at Different Developmental Stages" Current Issues in Molecular Biology 46, no. 1: 340-354. https://doi.org/10.3390/cimb46010022
APA StyleWang, S., Shi, M., Zhang, Y., Niu, J., Li, W., Yuan, J., Cai, C., Yang, Y., Gao, P., Guo, X., Li, B., Lu, C., & Cao, G. (2024). Construction of LncRNA-Related ceRNA Networks in Longissimus Dorsi Muscle of Jinfen White Pigs at Different Developmental Stages. Current Issues in Molecular Biology, 46(1), 340-354. https://doi.org/10.3390/cimb46010022