Characterization of Critical Functions of Long Non-Coding RNAs and mRNAs in Rhabdomyosarcoma Cells and Mouse Skeletal Muscle Infected by Enterovirus 71 Using RNA-Seq
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. EV71 Virus and Cell Treatment
2.3. Animals
2.4. RNA Isolation
2.5. RNA Library Construction and Sequencing
2.6. The Prediction and Classification of New lncRNAs
2.7. Identification of Differentially-Expressed Genes
2.8. Prediction of Target Genes of Differentially-Expressed lncRNAs
2.9. GO Annotations and KEGG Enrichment
2.10. qPCR Confirmation
2.11. Statistical Analysis
3. Results
3.1. In Vitro and In Vivo Models of EV71 Infection
3.2. Identification and Classification of Newly Predicted lncRNAs
3.3. Profiles of Differentially-Expressed lncRNAs and mRNAs
3.4. Prediction of Target Protein-Coding RNA
3.5. GO Annotation and KEGG Pathway Analysis
3.6. qPCR Validation
4. Discussion
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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lncRNA Symbol | Chromosome Location | Primer Sequences (5′-3′) | Products (bp) | |
---|---|---|---|---|
EBLN3P | 9 | Forward | GGACGCGGCCTCCTTACCTC | 189 |
Reverse | GGCACGCGCTAGTTCCACAG | 189 | ||
Gm26945 | 12 | Forward | GGTGGCTCATGTGGATCACTGATG | 87 |
Reverse | ACGATGGACCTCCTGAGTGACAG | 87 | ||
SCARNA2 | 1 | Forward | CTGTGGCGTCGCGTGTGAG | 97 |
Reverse | CGCACGCACTCGCCTAACAC | 97 | ||
LINC01297 | 22 | Forward | ACGTCTCCATCCAGGACTGAGG | 141 |
Reverse | AAGACTGCCATCCAAGGAAGCG | 141 | ||
LINC00847 | 5 | Forward | GGACTTGCCAGCCTTCAGAACTC | 181 |
Reverse | GGTGATTGGATAGTGCCTGCCTAC | 181 | ||
Gm22 | 8 | Forward | GCCACAGCCATCAGCACAGC | 127 |
Reverse | CGCAACACCACTGACATGGAGAG | 127 | ||
4631405K08Rik | 1 | Forward | AGAGTCACTGTCCTCCGCTTATCC | 199 |
Reverse | GCTGGCTCTCCTCTTCAATGAGTG | 199 | ||
β-actin | Forward | AGCGAGCATCCCCCAAAGTT | 285 | |
(Homo sapiens) | Reverse | GGGCACGAAGGCTCATCATT | 285 | |
β-actin | Forward | GTGACGTTGACATCCGTAAAG | 287 | |
(Mus musculus) | Reverse | GTAACAGTCCGCCTAGAAGCAC | 287 |
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Li, Y.; Zhang, C.; Qin, L.; Li, D.; Zhou, G.; Dang, D.; Chen, S.; Sun, T.; Zhang, R.; Wu, W.; et al. Characterization of Critical Functions of Long Non-Coding RNAs and mRNAs in Rhabdomyosarcoma Cells and Mouse Skeletal Muscle Infected by Enterovirus 71 Using RNA-Seq. Viruses 2018, 10, 556. https://doi.org/10.3390/v10100556
Li Y, Zhang C, Qin L, Li D, Zhou G, Dang D, Chen S, Sun T, Zhang R, Wu W, et al. Characterization of Critical Functions of Long Non-Coding RNAs and mRNAs in Rhabdomyosarcoma Cells and Mouse Skeletal Muscle Infected by Enterovirus 71 Using RNA-Seq. Viruses. 2018; 10(10):556. https://doi.org/10.3390/v10100556
Chicago/Turabian StyleLi, Ying, Chao Zhang, Luwei Qin, Dong Li, Guangyuan Zhou, Dejian Dang, Shuaiyin Chen, Tiantian Sun, Rongguang Zhang, Weidong Wu, and et al. 2018. "Characterization of Critical Functions of Long Non-Coding RNAs and mRNAs in Rhabdomyosarcoma Cells and Mouse Skeletal Muscle Infected by Enterovirus 71 Using RNA-Seq" Viruses 10, no. 10: 556. https://doi.org/10.3390/v10100556