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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 10, 2022 |
| Title |
miRNAs associated with the pathogenesis of bovine rotavirus |
| Organism |
Macaca mulatta |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Bovine Rotavirus (BRV) causes massive economic losses in the livestock industry worldwide. MA-104 cell line has become a convenient tool for discover BRV–host interactions. Notwithstanding, the role of miRNAs in MA-104 cells during BRV infection is still ambiguous. In our study, we performed Illumina RNA sequencing analysis of miRNA libraries of BRV-infected and mock-infected MA-104 cells (at different time points 0 hpi (just after adsorption time (90 min)), 6 hpi, 12 hpi, 24 hpi, 36 hpi and 48 hpi), and the total clean reads 74701041 and 74184124 were obtained from BRV-infected and uninfected cells, respectively. From these findings, 579 categorized as known miRNAs and 144 as novel miRNAs, 160 differentially expressed (DE) miRNAs in BRV-infected in comparison to uninfected MA-104 cells were successfully investigated, 95 were upregulated and 65 exhibited downregulation. The target mRNAs of DE miRNAs were expected by bioinformatics. The functional annotation of the target genes by GO and KEGG suggested that they were mainly contributed to biological pathways, endocytosis, apoptotic process, trans-Golgi membrane and lysosome, besides, the mTOR, NF-κB , Rap 1, cAMP, TNF, Ras, pathways of cancer and MAPK signaling pathways. What is more, real-time quantitative reverse transcription-polymerase chain reaction verified the expression pictures of ten selected DE miRNAs, which were consistent with the results of the deep sequencing (from 0 hpi up to 48 hpi), and 20 from their corresponding mRNA targets mainly of regulatory pathways of the cellular machinery and immune importance. Our study is the first novel approach which uncover the impact of BRV infection on miRNA expression of MA-104 cells, and it offers clues for identifying potential candidates for antiviral or vaccine strategies.
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| Overall design |
In our study, we performed Illumina RNA sequencing analysis of miRNA libraries of BRV-infected and mock-infected MA-104 cells (at different time points 0 hpi (just after adsorption time (90 min)), 6 hpi, 12 hpi, 24 hpi, 36 hpi and 48 hpi), and the total clean reads 74701041 and 74184124 were obtained from BRV-infected and uninfected cells, respectively. From these findings, 579 categorized as known miRNAs and 144 as novel miRNAs, 160 differentially expressed (DE) miRNAs in BRV-infected in comparison to uninfected MA-104 cells were successfully investigated, 95 were upregulated and 65 exhibited downregulation. The target mRNAs of DE miRNAs were expected by bioinformatics. The functional annotation of the target genes by GO and KEGG suggested that they were mainly contributed to biological pathways, endocytosis, apoptotic process, trans-Golgi membrane and lysosome, besides, the mTOR, NF-κB , Rap 1, cAMP, TNF, Ras, pathways of cancer and MAPK signaling pathways. What is more, real-time quantitative reverse transcription-polymerase chain reaction verified the expression pictures of ten selected DE miRNAs, which were consistent with the results of the deep sequencing (from 0 hpi up to 48 hpi), and 20 from their corresponding mRNA targets mainly of regulatory pathways of the cellular machinery and immune importance. Our study is the first novel approach which uncover the impact of BRV infection on miRNA expression of MA-104 cells, and it offers clues for identifying potential candidates for antiviral or vaccine strategies.
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| Contributor(s) |
Elkady G, Guo A |
| Citation(s) |
35516441 |
| Submission date |
Feb 10, 2022 |
| Last update date |
May 11, 2022 |
| Contact name |
Gehad Elkady |
| E-mail(s) |
gehad.elkady@outlook.com
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| Phone |
15623262168
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| Organization name |
HZAU
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| Department |
Virology
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| Lab |
Virology
|
| Street address |
Huazhong Agricultural University, No.1,Shizishan Street, Hongshan District,Wuhan
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| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
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| Platforms (1) |
| GPL27943 |
Illumina NovaSeq 6000 (Macaca mulatta) |
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| Samples (36)
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| GSM5888844 |
MA-104 cells, Control (0hpi), B1 |
| GSM5888845 |
MA-104 cells, Control (0hpi), B2 |
| GSM5888846 |
MA-104 cells, Control (0hpi), B3 |
| GSM5888847 |
MA-104 cells, Infected (6hpi), C1 |
| GSM5888848 |
MA-104 cells, Infected (6hpi), C2 |
| GSM5888849 |
MA-104 cells, Infected (6hpi), C3 |
| GSM5888850 |
MA-104 cells, Control (6hpi), D1 |
| GSM5888851 |
MA-104 cells, Control (6hpi), D2 |
| GSM5888852 |
MA-104 cells, Control (6hpi), D3 |
| GSM5888853 |
MA-104 cells, Infected (12hpi), E1 |
| GSM5888854 |
MA-104 cells, Infected (12hpi), E2 |
| GSM5888855 |
MA-104 cells, Infected (12hpi), E3 |
| GSM5888856 |
MA-104 cells, Control (12hpi), F1 |
| GSM5888857 |
MA-104 cells, Control (12hpi), F2 |
| GSM5888858 |
MA-104 cells, Control (12hpi), F3 |
| GSM5888859 |
MA-104 cells, Infected (24hpi), G1 |
| GSM5888860 |
MA-104 cells, Infected (24hpi), G2 |
| GSM5888861 |
MA-104 cells, Infected (24hpi), G3 |
| GSM5888862 |
MA-104 cells, Control (24hpi), H1 |
| GSM5888863 |
MA-104 cells, Control (24hpi), H2 |
| GSM5888864 |
MA-104 cells, Control (24hpi), H3 |
| GSM5888865 |
MA-104 cells, Infected (36hpi), I1 |
| GSM5888866 |
MA-104 cells, Infected (36hpi), I2 |
| GSM5888867 |
MA-104 cells, Infected (36hpi), I3 |
| GSM5888868 |
MA-104 cells, Control (36hpi), J1 |
| GSM5888869 |
MA-104 cells, Control (36hpi), J2 |
| GSM5888870 |
MA-104 cells, Control (36hpi), J3 |
| GSM5888871 |
MA-104 cells, Infected (48hpi), K1 |
| GSM5888872 |
MA-104 cells, Infected (48hpi), K2 |
| GSM5888873 |
MA-104 cells, Infected (48hpi), K3 |
| GSM5888874 |
MA-104 cells, Control (48hpi), L1 |
| GSM5888875 |
MA-104 cells, Control (48hpi), L2 |
| GSM5888876 |
MA-104 cells, Control (48hpi), L3 |
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| Relations |
| BioProject |
PRJNA805278 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE196536_10.Readcount_TPM.xls.gz |
200.1 Kb |
(ftp)(http) |
XLS |
| GSE196536_11.TPM_interval.xls.gz |
8.4 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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