|
Status |
Public on Apr 27, 2024 |
Title |
mock_2 |
Sample type |
SRA |
|
|
Source name |
SH-SY5Y cells
|
Organism |
Homo sapiens |
Characteristics |
cell line: SH-SY5Y cells treatment: mock
|
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).
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|
|
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 |
SAMN32940986 |
SRA |
SRX19199605 |