|
| Status |
Public on Apr 10, 2024 |
| Title |
PDCoV_virion_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Renal
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: Renal
cell line: LLC-PK1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After completing the proximity-ligated, the RNA was extracted by proteinase K, Trizol and chloroform according to the manufacturer’s instruction.
BioMag®Plus Concanavalin A beads was used to capture virions, 500 μL purified virus was added to the 150 μL washed beads with ConA Binding buffer, and incubated for 10 min at room temperature. The beads was washed with ConA Binding buffer for three times and PBST buffer for once (1 × PBS, 0.1% Tween 20), and resuspended in 1 mL PBST buffer. The final concentration of 1% formaldehyde was used to fix the RNA-RNA interaction, and final concentration 0.125 M glycine was added to quench the formaldehyde.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Data cleaning
Sequence alignment
Identification and visualization of valid chimeric reads
Secondary structure prediction
Assembly: PDCoV CHN-HN-2014 (GenBank accession: KT336560)
Supplementary files format and content: The HIC file displays the interaction matrix of the virus genome structure for different sets of PDCoV data
Supplementary files format and content: The CT file displays the entire genome structure of PDCoV
Library strategy: vRIC-seq
|
| |
|
| Submission date |
Feb 03, 2024 |
| Last update date |
Apr 10, 2024 |
| Contact name |
Dengguo Wei |
| E-mail(s) |
[email protected]
|
| Organization name |
Huazhong Agricultural University
|
| Department |
College of Veterinary Medicine
|
| Lab |
Nucleic acid drug laboratory
|
| Street address |
Huazhong Agricultural University, Hongshan District, Wuhan City, Hubei Province
|
| City |
Wuhan |
| State/province |
Hubei Province |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL22918 |
| Series (1) |
| GSE254992 |
The architecture of the Porcine deltacoronavirus RNA genome inside virions by vRICseq |
|
| Relations |
| BioSample |
SAMN39782884 |
| SRA |
SRX23523148 |
