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| Status |
Public on Apr 27, 2024 |
| Title |
Discovery of Varicella zoster virus circular RNA with nanopore long-read sequencing |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Varicella-zoster virus (VZV), an alphaherpesvirus, causes chickenpox (varicella) in young children with an annual minimum of 140 million new cases and herpes zoster in senior, a painful and debilitating disease with 3-5‰ incidence. A complex structural transcriptome of VZV, which numerous novel transcripts, transcript isoforms, and unknown splice events are found during cell infection. Circular RNA (circRNA), a newly important component of the transcriptome, is increasing discoveries of circRNA function in mammalian cells. However, VZV encoded circRNA remains unexplored. The code used in this study and extended data are available from the GitHub repository (https://github.com/ShaominYang/VZV_circRNA)
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| Overall design |
Using deep RNA-seq following RNase R treatment, we identified and charactered 35, 076 and 54 human and VZV pOka strain circRNAs respectively from VZV infected neuroblastoma cell (SH-SY5Y). We collected VZV infected human neuroblastoma cell (SH-SY5Y). A deep nanopore long-read sequencing, which combines rolling circular reverse transcription and nanopore sequencing following RNase R treatment was performed.
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| Contributor(s) |
Yang S |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Dec 27, 2023 |
| Last update date |
Apr 29, 2024 |
| Contact name |
SHAO MIN YANG |
| E-mail(s) |
shaominyang@stu2020.jnu.edu.cn
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| Organization name |
Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine
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| Department |
Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center
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| Street address |
Nanshan
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| City |
Shenzhen |
| State/province |
guangdong |
| ZIP/Postal code |
518060 |
| Country |
China |
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| Platforms (1) |
| GPL17303 |
Ion Torrent Proton (Homo sapiens) |
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| Samples (1) |
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| Relations |
| BioProject |
PRJNA1057831 |
