|
| Status |
Public on Apr 27, 2024 |
| Title |
vzv_24h_3 |
| Sample type |
SRA |
| |
|
| Source name |
SH-SY5Y cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SH-SY5Y cells
treatment: Post pOka_WT infected 24 hours
|
| Treatment protocol |
SH-SY5Y cells were seeded at a density of 10^6 in 6-well plate (Corning) prior to inoculation with log106 PFU of pOka.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ribosome-depleted and RNase R-treated RNA samples were used for library preparation and subsequently sequenced using BGISEQ platform in PE150.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
circRNA-seq
RNase R-treated RNA
|
| Data processing |
De novo circRNA identification and reconstruction: Raw reads were aligned with BWA Aligner[25] (BWA-MEM version 0.7.17-R1188) to human, VZV reference genomes: hg38, pOka strain (AB097933.1). Alignment statistics were performed with Qualimap2 (version 2.2.1). CIRI2 (version v2.0.6) vircircRNA, and find_circ were used for circRNA calling. Reconstruction of partial and full length circRNAs was performed with CIRI-full (version 2.0).
|
| |
|
| Submission date |
Jan 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 |
GPL23227 |
| Series (1) |
| GSE223870 |
Discovery of Varicella zoster virus circular RNA with short read sequencing |
|
| Relations |
| BioSample |
SAMN32940982 |
| SRA |
SRX19199609 |
