Global MicroRNA Expression Profiling of Buffalo (Bubalus bubalis) Embryos at Different Developmental Stages Produced by Somatic Cell Nuclear Transfer and In-Vitro Fertilization Using RNA Sequencing
Abstract
:1. Introduction
2. Materials and Methods
2.1. Production of Pre-Implantation Embryos by Hand-Made Cloning (HMC)
2.2. Production of Pre-Implantation Embryos by IVF
2.3. Extraction of Total RNA for Small-RNA Sequencing
2.4. cDNA Library Preparation and Sequencing
2.5. miRNome Data Analysis
2.6. Validation of RNA-seq Data by qPCR
3. Results
3.1. miRNA Profiling in Bovine Embryos
3.2. Identification of Differentially Expressed miRNAs in Pre-Implantation Embryos
3.3. Identification of Commonly and Uniquely Expressed miRNAs
3.4. Gene Ontology and KEGG Analysis of Cloned vs. IVF Preimplantation Embryos
3.5. Pathway Identification and Network Analysis
3.6. Validation of RNA-seq Data
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Ethics Approval
References
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Parameter | Total Number of Reads | Distinct Number of Reads | Aligned Reads (%) | Unaligned Reads (%) | Maximum Read Length |
---|---|---|---|---|---|
2CC-1 | 17,307,418 | 232,369 | 79.67 | 20.33 | 50 |
2CC-2 | 15,731,948 | 227,625 | 79.82 | 20.18 | 50 |
2CC-3 | 16,309,020 | 392,869 | 81.38 | 18.62 | 50 |
2CI-1 | 13,422,098 | 314,645 | 83.54 | 16.46 | 50 |
2CI-2 | 12,758,526 | 311,976 | 83.66 | 16.34 | 50 |
2CI-3 | 11,893,184 | 225,993 | 85.40 | 14.60 | 50 |
8CC-1 | 17,409,668 | 364,676 | 81.35 | 18.65 | 50 |
8CC-2 | 12,483,044 | 331,093 | 82.16 | 17.84 | 50 |
8CC-3 | 14,840,784 | 351,968 | 81.80 | 18.20 | 50 |
8CI-1 | 13,822,944 | 234,722 | 83.31 | 16.69 | 50 |
8CI-2 | 13,308,848 | 237,288 | 83.49 | 16.51 | 50 |
8CI-3 | 15,839,750 | 366,705 | 83.71 | 16.29 | 50 |
BL-1 | 12,608,590 | 285,577 | 85.59 | 14.41 | 50 |
BL-2 | 10,784,686 | 273,300 | 85.92 | 14.08 | 50 |
BL-3 | 10,875,612 | 276,876 | 84.20 | 15.80 | 50 |
BLI-1 | 12,380,724 | 250,071 | 82.35 | 17.65 | 50 |
BLI-2 | 12,573,252 | 252,929 | 82.39 | 17.61 | 50 |
BLI-3 | 14,146,486 | 355,853 | 83.23 | 16.77 | 50 |
Stages | Total Genes | Annotated Genes in the Wnt Pathway | Log Fold Change | p-Value |
---|---|---|---|---|
2CC-vs-2CI | 2276 | 31 (1.37%) | 1.06 | 6.97 × 10−5 |
8CC-vs-8CI | 1934 | 30 (1.55%) | 1.24 | 2.45 × 10−5 |
BL-vs-BLI | 2631 | 41 (1.56%) | 1.22 | 2.37 × 10−5 |
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Goel, P.; Malpotra, S.; Shyam, S.; Kumar, D.; Singh, M.K.; Palta, P. Global MicroRNA Expression Profiling of Buffalo (Bubalus bubalis) Embryos at Different Developmental Stages Produced by Somatic Cell Nuclear Transfer and In-Vitro Fertilization Using RNA Sequencing. Genes 2022, 13, 453. https://doi.org/10.3390/genes13030453
Goel P, Malpotra S, Shyam S, Kumar D, Singh MK, Palta P. Global MicroRNA Expression Profiling of Buffalo (Bubalus bubalis) Embryos at Different Developmental Stages Produced by Somatic Cell Nuclear Transfer and In-Vitro Fertilization Using RNA Sequencing. Genes. 2022; 13(3):453. https://doi.org/10.3390/genes13030453
Chicago/Turabian StyleGoel, Pallavi, Shivani Malpotra, Songyukta Shyam, Deepak Kumar, Manoj Kumar Singh, and Prabhat Palta. 2022. "Global MicroRNA Expression Profiling of Buffalo (Bubalus bubalis) Embryos at Different Developmental Stages Produced by Somatic Cell Nuclear Transfer and In-Vitro Fertilization Using RNA Sequencing" Genes 13, no. 3: 453. https://doi.org/10.3390/genes13030453