 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 30, 2022 |
| Title |
High throughput sequencing of MARC145, A549, HEK293, and HRT18 cells infected with Shaan virus |
| Organisms |
Chlorocebus aethiops; Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
Purpose: The goals of this study are to monitor the evolution pattern of Shaan virus in depending host cells by viral transcriptome sequencing analysis of MARC145, A549, HEK293, and HRT18 cells infected with Shaan virus.
Methods: The original isolate of Shaan virus (B16-40, Genbank accession no. MG230624.1) was passaged in MARC-145 cells. Low-passaged virus was obtained from the virus 4 times serially passaged in MARC-145 cells. The shaan virus which was 44 times serially passaged in MARC-145 cells was used for high-passaged virus. The prepared low- (p4) and high passaged shaan virus (p44) in MARC-145 cells were inoculated in triplicate to different host cells, HEK-293, A549, and HRT18 cell lines at M.O.I of 0.5 for 2 hours. The infected cells were incubated with the maintenance medium for each cell line for 24hrs. The infected cell pellets were resuspended to 250µl with fresh medium, to extract RNA for the high-throughput sequencing. The RNA samples were sequenced with illumine TruSeq Strand Total RNA LT kit and illumine NovaSeq6000 plaform form Macrogen, Inc (Seoul, Korea) for high throughput sequencing. The raw reads were trimmed with BBDuk and mapped the isolate Bat-ParaV/B16-40 (Genebank accession number. MG230624.1) with Bowtie 2 using Geneious program 2021.2.2. Transcript expression level in cells infected with shaan virus were calculated based on annotation on a reference shaan virus.
Result: The total reads counts were between 50,285,454 and 76,298,278. The reference mapping of the trimmed reads with a reference genome (Genbank accession no. MG230624.1) showed different coverage values. The mapped reads were normalized and expressed as Transcript per Million (TPM) value. There were no noticeable differences of TPM values of each gene between the cells infected with low- and high-passaged shaan virus. However, the nucleocapsid (N) and matrix (M) gene-associated transcripts were shown to be differently measured among the host cells.
Conclusion: In this regard, we tried to investigate certain selected mutation patterns by host switching using shaan virus isolate in MARC-145 cells. Therefore, this study provided potential evidence for host-specific selective mutation patterns by cell types as well as host of cells for shaan virus evolution.
|
| |
|
| Overall design |
Monitor of mutation pattern of Shaan virus transcript depending on host cells by high throghput sequencing analysis
|
| |
|
| Contributor(s) |
Jang SS, Kim MC, Lim HA, Kim HK |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Apr 22, 2022 |
| Last update date |
Apr 30, 2022 |
| Contact name |
Jiyeong Noh |
| E-mail(s) |
wldud1540@gmail.com
|
| Organization name |
Chungbuk National University
|
| Street address |
Chungdae-ro 1
|
| City |
Cheongju |
| ZIP/Postal code |
28644 |
| Country |
South Korea |
| |
|
| Platforms (2) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
| GPL29682 |
Illumina NovaSeq 6000 (Chlorocebus aethiops) |
|
| Samples (24)
|
|
| Relations |
| BioProject |
PRJNA830904 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE201344_raw_count_A549.xlsx |
11.2 Kb |
(ftp)(http) |
XLSX |
| GSE201344_raw_count_HEK293.xlsx |
11.1 Kb |
(ftp)(http) |
XLSX |
| GSE201344_raw_count_HRT18.xlsx |
12.9 Kb |
(ftp)(http) |
XLSX |
| GSE201344_raw_count_MARC145.xlsx |
13.1 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...