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Transcriptome analysis of epithelioma papulosum cyprini cells after SVCV infection.

Yuan J, Yang Y, Nie H, Li L, Gu W, Lin L, Zou M, Liu X, Wang M, Gu Z - BMC Genomics (2014)

Bottom Line: At 24 h post SVCV infection (1.0 MOI), a total of 623 genes were differentially expressed in EPC cells compared to non-infected cells, including 288 up-regulated genes and 335 down-regulated genes.Our findings demonstrate previously unrecognised changes in gene transcription that are associated with SVCV infection in vitro, and many potential cascades identified in the study clearly warrant further experimental investigation.Our data provide new clues to the mechanism of viral susceptibility in EPC cells.

View Article: PubMed Central - PubMed

Affiliation: Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, People's Republic of China. guzemao@mail.hzau.edu.cn.

ABSTRACT

Background: Spring viraemia of carp virus (SVCV) has been identified as the causative agent of spring viraemia of carp (SVC) and it has caused significant losses in the cultured common carp (Cyprinus carpio) industry. The molecular mechanisms that underlie the pathogenesis of the disease remain poorly understood. In this study, deep RNA sequencing was used to analyse the transcriptome and gene expression profile of EPC cells at progressive times after SVCV infection. This study addressed the complexity of virus-cell interactions and added knowledge that may help to understand SVCV.

Results: A total of 33,849,764 clean data from 36,000,000 sequence reads, with a mean read length 100 bp, were obtained. These raw data were assembled into 88,772 contigs. Of these contigs, 19,642 and 25,966 had significant hits to the NR and Uniprot databases where they matched 17,642 and 13,351 unique protein accessions, respectively. At 24 h post SVCV infection (1.0 MOI), a total of 623 genes were differentially expressed in EPC cells compared to non-infected cells, including 288 up-regulated genes and 335 down-regulated genes. These regulated genes were primarily involved in pathways of apoptosis, oxidative stress and the interferon system, all of which may be involved in viral pathogenesis. In addition, 8 differentially expressed genes (DEGs) were validated by quantitative PCR.

Conclusions: Our findings demonstrate previously unrecognised changes in gene transcription that are associated with SVCV infection in vitro, and many potential cascades identified in the study clearly warrant further experimental investigation. Our data provide new clues to the mechanism of viral susceptibility in EPC cells.

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Related in: MedlinePlus

Assembled contig length distribution of thePimephales promelastranscriptome. The x-axis indicates contig size and the y-axis indicates the number of contigs of each size.
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Fig1: Assembled contig length distribution of thePimephales promelastranscriptome. The x-axis indicates contig size and the y-axis indicates the number of contigs of each size.

Mentions: To obtain an overview of the transcriptome of the EPC cells, cDNA samples from normal EPC cells and from EPC cells at different stages during SVCV infection were mixed and sequenced on an Illumina machine. A total of 33,849,764 clean data from 36,000,000 sequence reads, with a mean read length 100 bp, was obtained. These raw data were assembled into 88,772 contigs. The mean contig size was 831 bp, with lengths ranging from 201 bp to 17,900 bp. The contig size distribution is shown in FigureĀ 1.Figure 1


Transcriptome analysis of epithelioma papulosum cyprini cells after SVCV infection.

Yuan J, Yang Y, Nie H, Li L, Gu W, Lin L, Zou M, Liu X, Wang M, Gu Z - BMC Genomics (2014)

Assembled contig length distribution of thePimephales promelastranscriptome. The x-axis indicates contig size and the y-axis indicates the number of contigs of each size.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4221675&req=5

Fig1: Assembled contig length distribution of thePimephales promelastranscriptome. The x-axis indicates contig size and the y-axis indicates the number of contigs of each size.
Mentions: To obtain an overview of the transcriptome of the EPC cells, cDNA samples from normal EPC cells and from EPC cells at different stages during SVCV infection were mixed and sequenced on an Illumina machine. A total of 33,849,764 clean data from 36,000,000 sequence reads, with a mean read length 100 bp, was obtained. These raw data were assembled into 88,772 contigs. The mean contig size was 831 bp, with lengths ranging from 201 bp to 17,900 bp. The contig size distribution is shown in FigureĀ 1.Figure 1

Bottom Line: At 24 h post SVCV infection (1.0 MOI), a total of 623 genes were differentially expressed in EPC cells compared to non-infected cells, including 288 up-regulated genes and 335 down-regulated genes.Our findings demonstrate previously unrecognised changes in gene transcription that are associated with SVCV infection in vitro, and many potential cascades identified in the study clearly warrant further experimental investigation.Our data provide new clues to the mechanism of viral susceptibility in EPC cells.

View Article: PubMed Central - PubMed

Affiliation: Department of Aquatic Animal Medicine, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, People's Republic of China. guzemao@mail.hzau.edu.cn.

ABSTRACT

Background: Spring viraemia of carp virus (SVCV) has been identified as the causative agent of spring viraemia of carp (SVC) and it has caused significant losses in the cultured common carp (Cyprinus carpio) industry. The molecular mechanisms that underlie the pathogenesis of the disease remain poorly understood. In this study, deep RNA sequencing was used to analyse the transcriptome and gene expression profile of EPC cells at progressive times after SVCV infection. This study addressed the complexity of virus-cell interactions and added knowledge that may help to understand SVCV.

Results: A total of 33,849,764 clean data from 36,000,000 sequence reads, with a mean read length 100 bp, were obtained. These raw data were assembled into 88,772 contigs. Of these contigs, 19,642 and 25,966 had significant hits to the NR and Uniprot databases where they matched 17,642 and 13,351 unique protein accessions, respectively. At 24 h post SVCV infection (1.0 MOI), a total of 623 genes were differentially expressed in EPC cells compared to non-infected cells, including 288 up-regulated genes and 335 down-regulated genes. These regulated genes were primarily involved in pathways of apoptosis, oxidative stress and the interferon system, all of which may be involved in viral pathogenesis. In addition, 8 differentially expressed genes (DEGs) were validated by quantitative PCR.

Conclusions: Our findings demonstrate previously unrecognised changes in gene transcription that are associated with SVCV infection in vitro, and many potential cascades identified in the study clearly warrant further experimental investigation. Our data provide new clues to the mechanism of viral susceptibility in EPC cells.

Show MeSH
Related in: MedlinePlus