Genome-Wide Landscape of mRNAs, lncRNAs, and circRNAs during Testicular Development of Yak
Abstract
:1. Introduction
2. Results
2.1. Overview of the Sequencing Data
2.2. Predictions and Properties of ncRNAs in the Yak Testis
2.3. Differential Expression Analysis of mRNAs, lncRNAs, and circRNA
2.4. Gene ontology (GO) Analysis of DE Genes between M30 and M6
2.5. Gene Ontology (GO) Analysis of DE Genes between M18 and M6
2.6. Gene Ontology (GO) Analysis of DE Genes between M30 and M18
2.7. Function Analysis of Common DE Genes during Testicular Development
2.8. Construction of the lncRNA-mRNA Co-Expression Network
2.9. Validation of DE Genes by qRT-PCR
3. Discussion
4. Materials and Methods
4.1. Ethics Statement
4.2. Animals
4.3. RNA-Sequencing Data Analysis
4.4. Identification of lncRNA and circRNA
4.5. Analysis of Differentially Expressed (DE) Genes
4.6. Functional Enrichment Analysis
4.7. Co-Expression Network Construction
4.8. Gene Expression Validation by Quantitative Real-Time PCR
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
DE | differentially expressed |
GO | Gene ontology |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
qRT-PCR | Quantitative real-time PCR |
M6 | 6-month-old |
M18 | 18-month-old |
M30 | 30-month-old |
FPKM | fragments per kilobase of transcript per million reads mapped |
SRPBM | spliced reads per billion mappings |
LncRNAs | long non-coding RNAs |
CircRNAs | circular RNAs |
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Sample | Raw Reads | Clean Reads | Q30 (%) | GC Content (%) | Mapped Reads | Uniquely Mapped |
---|---|---|---|---|---|---|
M18-1 | 101.07M | 99.83M | 95.11 | 48.28 | 89.95M (94.48%) | 80.21M (84.26%) |
M18-2 | 91.07M | 89.98M | 95.09 | 48.33 | 81.17M (94.60%) | 72.12M (84.05%) |
M18-4 | 97.24M | 96.07M | 95.14 | 48.87 | 86.66M (94.59%) | 76.68M (83.69%) |
M6-2 | 88.87M | 87.66M | 94.89 | 47.93 | 78.59M (94.01%) | 70.38M (84.19%) |
M6-3 | 91.57M | 90.39M | 94.83 | 46.47 | 81.29M (94.31%) | 74.12M (85.98%) |
M6-4 | 97.52M | 96.20M | 94.68 | 47.49 | 86.61M (94.41%) | 78.23M (85.27%) |
M30-1 | 100.51M | 99.26M | 94.96 | 48.20 | 89.58M (94.63%) | 79.83M (84.34%) |
M30-2 | 103.01M | 101.81M | 95.06 | 48.13 | 92.03M (94.78%) | 81.81M (84.25%) |
M30-3 | 99.81M | 98.60M | 95.05 | 48.06 | 89.03M (94.67%) | 79.24M (84.27%) |
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La, Y.; Ma, X.; Bao, P.; Chu, M.; Yan, P.; Liang, C.; Guo, X. Genome-Wide Landscape of mRNAs, lncRNAs, and circRNAs during Testicular Development of Yak. Int. J. Mol. Sci. 2023, 24, 4420. https://doi.org/10.3390/ijms24054420
La Y, Ma X, Bao P, Chu M, Yan P, Liang C, Guo X. Genome-Wide Landscape of mRNAs, lncRNAs, and circRNAs during Testicular Development of Yak. International Journal of Molecular Sciences. 2023; 24(5):4420. https://doi.org/10.3390/ijms24054420
Chicago/Turabian StyleLa, Yongfu, Xiaoming Ma, Pengjia Bao, Min Chu, Ping Yan, Chunnian Liang, and Xian Guo. 2023. "Genome-Wide Landscape of mRNAs, lncRNAs, and circRNAs during Testicular Development of Yak" International Journal of Molecular Sciences 24, no. 5: 4420. https://doi.org/10.3390/ijms24054420