|
| Status |
Public on Apr 27, 2024 |
| Title |
circRNA long reads sequencing |
| Sample type |
SRA |
| |
|
| Source name |
SH-SY5Y cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SH-SY5Y cells
genotype: VZV
|
| Treatment protocol |
SH-SY5Y or ARPER-19 cells were seeded at a density of 106 in 6-well plate (Corning) 12 h prior to inoculation with log106 PFU of pOka.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested at 24 and 48 h post-infection with TRIzol RNA Isolation Reagents (Invitrogen, USA, Catalog number: 15596026). Chloroform extraction and isopropanol precipitation methods were used to isolate RNA from samples.
Ribosome-depleted and RNase R-treated RNA samples were used for library preparation and nanopore long-read sequencing, which combines rolling circular reverse transcription and nanopore sequencing.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
RNase R-treated RNA
nanopore long-read sequencing, which combines rolling circular reverse transcription and nanopore sequencing
|
| Data processing |
de novo circRNA identification and reconstruction: Raw reads were aligned with minimap2, VZV reference genomes. CIRI-long was used for circRNA calling.
Assembly: VZV pOka strain, containing GFP and luciferase coding genes
Supplementary files format and content: 1,The ID of human or VZV circRNAs, 2 The number of circRNA juction reads
|
| |
|
| Submission date |
Dec 27, 2023 |
| Last update date |
Apr 27, 2024 |
| Contact name |
SHAO MIN YANG |
| E-mail(s) |
shaominyang@stu2020.jnu.edu.cn
|
| Organization name |
Department of Pain Medicine and Shenzhen Municipal Key Laboratory for Pain Medicine
|
| Department |
Shenzhen Nanshan People's Hospital and the 6th Affiliated Hospital of Shenzhen University Health Science Center
|
| Street address |
Nanshan
|
| City |
Shenzhen |
| State/province |
guangdong |
| ZIP/Postal code |
518060 |
| Country |
China |
| |
|
| Platform ID |
GPL17303 |
| Series (1) |
| GSE252124 |
Discovery of Varicella zoster virus circular RNA with nanopore long-read sequencing |
|
| Relations |
| BioSample |
SAMN39153145 |
| SRA |
SRX23045362 |
