Detection of A-to-I RNA Editing in SARS-COV-2
Abstract
:1. Introduction
2. Materials and Methods
2.1. RNAseq Data
2.2. Filtering of RNAseq Raw Data
2.3. Alignment of RNAseq Reads
2.4. Detection of Hyper-Edited Reads
2.5. Detection of RNA Editing at Single-Nucleotide Level
2.6. Gene Expression in Cell Lines
2.7. RNA Editing Enrichment
2.8. Alu Editing Index
2.9. Quantification of Sense and Antisense Viral Strands
2.10. Annotation of A-to-I Editing Events
2.11. Statistical Analysis
3. Results and Discussion
4. 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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BioProject | Run | Source | Virus Load | Depth | RNA Editing (All Events) | % A-to-I | % no A-to-I | % C-to-U | % no C-to-U | # Hyper A-to-I Reads | # Hyper non A-to-I Reads | % Hyper A-to-I Reads |
---|---|---|---|---|---|---|---|---|---|---|---|---|
PRJNA616446 | SRR11454606 | Throat swab | 0.03 | 9.64 | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
PRJNA616446 | SRR11454607 | Faeces | 0.24 | 62.53 | 1 | 100.00 | 0.00 | 0.00 | 100.00 | 0.00 | 0.00 | 0.00 |
PRJNA616446 | SRR11454608 | Throat swab | 3.27 | 610.55 | 21 | 57.14 | 42.86 | 38.10 | 61.90 | 0.00 | 0.00 | 0.00 |
PRJNA616446 | SRR11454612 | Sputum | 0.08 | 13.76 | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
PRJNA616446 | SRR11454613 | BALF | 8.33 | 2256.34 | 1836 | 89.43 | 10.57 | 8.66 | 91.34 | 4.00 | 0.00 | 100.00 |
PRJNA616446 | SRR11454614 | BALF | 18.39 | 4167.78 | 6270 | 84.74 | 15.26 | 13.11 | 86.89 | 2.00 | 0.00 | 100.00 |
PRJNA616446 | SRR11454615 | BALF | 1.21 | 321.73 | 18 | 50.00 | 50.00 | 27.78 | 72.22 | 0.00 | 0.00 | 0.00 |
PRJNA605907 | SRR11059940 | BALF | 95.36 | 21.06 | 1 | 0.00 | 100.00 | 0.00 | 100.00 | 0.00 | 0.00 | 0.00 |
PRJNA605907 | SRR11059941 | BALF | 65.44 | 1.42 | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
PRJNA605907 | SRR11059942 | BALF | 93.56 | 478.34 | 286 | 89.51 | 10.49 | 6.99 | 93.01 | 1.00 | 4.00 | 20.00 |
PRJNA605907 | SRR11059943 | BALF | 87.59 | 39.39 | 5 | 0.00 | 100.00 | 20.00 | 80.00 | 3.00 | 0.00 | 100.00 |
PRJNA605907 | SRR11059944 | BALF | 94.33 | 1904.89 | 2779 | 84.02 | 15.98 | 12.20 | 87.80 | 3.00 | 1.00 | 75.00 |
PRJNA605907 | SRR11059945 | BALF | 99.21 | 267.75 | 0 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 | 0.00 |
PRJNA605907 | SRR11059946 | BALF | 99.05 | 5412.00 | 13,461 | 80.54 | 19.46 | 17.18 | 82.82 | 11.00 | 2.00 | 84.62 |
PRJNA605907 | SRR11059947 | BALF | 94.11 | 7674.39 | 7480 | 76.67 | 23.33 | 21.38 | 78.62 | 59.00 | 14.00 | 80.82 |
PRJNA601736 | SRR10903401 | BALF | 3.12 | 102.80 | 2 | 0.00 | 100.00 | 100.00 | 0.00 | 0.00 | 1.00 | 0.00 |
PRJNA601736 | SRR10903402 | BALF | 9.35 | 429.91 | 13 | 53.85 | 46.15 | 30.77 | 69.23 | 0.00 | 9.00 | 0.00 |
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Picardi, E.; Mansi, L.; Pesole, G. Detection of A-to-I RNA Editing in SARS-COV-2. Genes 2022, 13, 41. https://doi.org/10.3390/genes13010041
Picardi E, Mansi L, Pesole G. Detection of A-to-I RNA Editing in SARS-COV-2. Genes. 2022; 13(1):41. https://doi.org/10.3390/genes13010041
Chicago/Turabian StylePicardi, Ernesto, Luigi Mansi, and Graziano Pesole. 2022. "Detection of A-to-I RNA Editing in SARS-COV-2" Genes 13, no. 1: 41. https://doi.org/10.3390/genes13010041
APA StylePicardi, E., Mansi, L., & Pesole, G. (2022). Detection of A-to-I RNA Editing in SARS-COV-2. Genes, 13(1), 41. https://doi.org/10.3390/genes13010041