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| Status |
Public on Feb 02, 2021 |
| Title |
Transcriptome analysis of HEK-293, A549 and HRT18 cells infected with shaan virus |
| Organisms |
Chlorocebus aethiops; Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
propose: The goals of this study are viral transcript of host cells infected with shaan virus and host cell responses in HEK293, A549 and HRT18 infected with shaan virus.
Methods: We infected the virus at an MOI of 0.5 to human tissues-derived cell lines including HEK-293, A549 and HRT18. The infected cells were harvested at 24 hours post infection, and a total RNA was extracted from the harvested cells with Trizol LS reagent. The trimmed reads were mapped to shaan virus genome or GRCh37 human genomic DNA reference. The differentially expressed genes (DEGs) between the virus-infected and mock-infected cells were calculated based on the fold changes of FPKM per each gene.
Result: Viral transcripts were expressed differentially depending on the viral genes, it is obvious that the nucleocapsid (N) transcript was most expressed in all infected cells. Gene ontology enrichment analysis based on the DEGs revealed that HEK-293, A549 and HRT18 cells highly expressed the genes related to the antiviral defence system and innate immune response in response to the shaan virus infection.
Conclusion: In this study, we describe transcriptome data from the shaan virus-infected cells. The inferred DEGs and their related biological functions can be further investigated to understand the shaanvirus-host interaction.
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| Overall design |
transcriptome profile of HEK293, A549, HRT18 and MARC 145 infected with shaan virus
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| Citation(s) |
38076073 |
| |
| Submission date |
Feb 01, 2021 |
| Last update date |
Dec 14, 2023 |
| 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 |
| |
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| Platforms (2) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
| GPL29682 |
Illumina NovaSeq 6000 (Chlorocebus aethiops) |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA698551 |
| SRA |
SRP304116 |
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