RNA-Seq Profiling in Chicken Spleen and Thymus Infected with Newcastle Disease Virus of Varying Virulence
Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Animals, Cells, and Viruses
2.2. Virulence Determination
2.3. Animal Experiments
2.4. RNA Detection, Library Construction, and Sequencing
2.5. Screening of Differentially Expressed Genes Between Samples
2.6. Inter-Sample Correlation Analysis
2.7. Functional Enrichment Analysis of Biological Pathways for Differentially Expressed Genes
2.8. Functional Enrichment Analysis of Gene Ontology for Differentially Expressed Genes
2.9. Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR)
2.10. Statistical Analysis
3. Results
3.1. Characterization of the Virulence and Pathogenicity of Model Viruses
3.2. Characterization of mRNA Expression Profile Post-NDV Infection in Chickens
3.3. Identification of Differentially Expressed Genes
3.4. GO Enrichment Analysis of Differentially Expressed Genes
3.5. KEGG Enrichment Analysis of Differentially Expressed Genes
3.6. Validation of RNA-Seq Data by Quantitative Real-Time PCR (qRT-PCR)
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Sample Name | K5500 | Agilent 2200 | Test Summary | Total Reads | Clean Reads | GC(%) | Raw | Clean | ||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
OD260/280 | OD260/230 | RIN | 28S/18S | Q20(%) | Q30(%) | Q20(%) | Q30(%) | |||||
Mukteswar–spleen | 2.03 | 2.27 | 7.9 | 2.1 | A | 14,775,501 | 14,765,073 | 48.55 | 97.35 | 95.03 | 95.10 | 99.79 |
Mukteswar–thymus | 2.01 | 1.82 | 9.9 | 1.6 | A | 16,990,362 | 16,979,110 | 47.69 | 97.31 | 94.95 | 95.10 | 99.83 |
JS/7/05/Ch–spleen | 2.01 | 2.08 | 9.8 | 2.2 | A | 15,433,737 | 15,422,587 | 47.61 | 97.34 | 95.02 | 95.11 | 99.80 |
JS/7/05/Ch–thymus | 2.02 | 2.23 | 10.0 | 2.5 | A | 14,067,476 | 14,056,999 | 46.90 | 97.35 | 95.03 | 95.04 | 99.81 |
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Wang, X.; Lu, X.; Wang, M.; Zhou, Q.; Wang, X.; Yang, W.; Liu, K.; Gao, R.; Liao, T.; Chen, Y.; et al. RNA-Seq Profiling in Chicken Spleen and Thymus Infected with Newcastle Disease Virus of Varying Virulence. Vet. Sci. 2024, 11, 569. https://doi.org/10.3390/vetsci11110569
Wang X, Lu X, Wang M, Zhou Q, Wang X, Yang W, Liu K, Gao R, Liao T, Chen Y, et al. RNA-Seq Profiling in Chicken Spleen and Thymus Infected with Newcastle Disease Virus of Varying Virulence. Veterinary Sciences. 2024; 11(11):569. https://doi.org/10.3390/vetsci11110569
Chicago/Turabian StyleWang, Xiaoquan, Xiaolong Lu, Mingzhu Wang, Qiwen Zhou, Xiyue Wang, Wenhao Yang, Kaituo Liu, Ruyi Gao, Tianxing Liao, Yu Chen, and et al. 2024. "RNA-Seq Profiling in Chicken Spleen and Thymus Infected with Newcastle Disease Virus of Varying Virulence" Veterinary Sciences 11, no. 11: 569. https://doi.org/10.3390/vetsci11110569
APA StyleWang, X., Lu, X., Wang, M., Zhou, Q., Wang, X., Yang, W., Liu, K., Gao, R., Liao, T., Chen, Y., Hu, J., Gu, M., Hu, S., Liu, X., & Liu, X. (2024). RNA-Seq Profiling in Chicken Spleen and Thymus Infected with Newcastle Disease Virus of Varying Virulence. Veterinary Sciences, 11(11), 569. https://doi.org/10.3390/vetsci11110569