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| Status |
Public on Dec 28, 2022 |
| Title |
Skin transcriptomic analysis of rainbow trout infected with infectious hematopoietic necrosis virus |
| Organism |
Oncorhynchus mykiss |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Rainbow trout (Oncorhynchus mykiss), an economically important cold-water fish cultured worldwide, suffers from infectious hematopoietic necrosis virus (IHNV) infection, resulting in huge financial losses. In order to understand the immune response of rainbow trout during virus infection, we explored trout skin transcriptome profiles following IHNV challenge, and identified 6905 differentially expressed genes (DEGs). Transcriptome analysis revealed numerous DEGs involved in immune responses, such as NOD1, NLRC3, NLRC5, TLR3, TLR7/8, TRIM25, DHX58, IFIH1, IRF3/7, STAT1, TRAF3, MX1 and HSP90A1. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that DEGs were significantly enriched in various immune-related terms including immune system process, innate immune response and regulation of immune effector process and pathways of cytokine-cytokine receptor interactions, NOD-like receptor signaling, RIG-I-like receptor signaling, Toll-like receptor signaling, JAK-STAT signaling, Chemokine signaling pathway, and TNF signaling pathway. In addition, protein-protein interaction network (PPI) was used to display highly interactive DEG networks involving immune-related pathways. The expression trends of 16 DEGs were further verified by quantitative real-time PCR, which confirmed the reliability of the transcriptome sequencing results. This study expands our understanding of the immune response of rainbow trout infected with IHNV, and provides valuable resources for future studies on the immune molecular mechanism and disease resistance breeding.
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| Overall design |
In this study, rainbow trout were anesthetized with tricaine methane sulfonate (MS-222, Sigma, USA) at 48 hpi and skin tissues were collected and immediately frozen by liquid nitrogen.We explored rainbow trout skin transcriptome profiles following IHNV challenge, and identified 6905 differentially expressed genes (DEGs).
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| Contributor(s) |
Huang J, Zhao L |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Dec 24, 2022 |
| Last update date |
Dec 28, 2022 |
| Contact name |
lu zhao |
| E-mail(s) |
huangjq@gsau.edu.cn
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| Phone |
0086-931-7631225
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| Organization name |
Gansu Agricultural University
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| Street address |
Yintan Road Street
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| City |
Lanzhou City |
| State/province |
Gansu Province |
| ZIP/Postal code |
730070 |
| Country |
China |
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| Platforms (1) |
| GPL23000 |
Illumina HiSeq 2500 (Oncorhynchus mykiss) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA915612 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE221722_genes_FPKM_expression.txt.gz |
1016.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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