Virus Dataset Detail

> Detail information for each sample

Dataset Information
Accession GSE133086
Status 2020/3/26
Title Dual RNA-Seq characterization of host and pathogen gene expression in liver cells infected with Crimean-Congo Hemorrhagic Fever Virus
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne virus that can cause a hemorrhagic fever in humans, with a case fatality rate of up to 50%. Cases of CCHFV have been reported in Africa, Asia, and southern Europe; and recently, due to the expanding range of its vector, autochthonous cases have been reported in Spain. Although it was discovered over 70 years ago, our understanding of the pathogenesis of this virus remains limited. We used RNA-Seq in two human liver cell lines (HepG2 and Huh7) infected with CCHFV (strain Ib 10200), to examine kinetic changes in host expression and viral replication simultaneously at 24 and 72 hours post infection. Through this, numerous host pathways were identified that were modulated by the virus including: antiviral response and endothelial cell leakage. Notably, DDX60, a cytosolic component of the RIG-I signalling pathway and OAS2 were both shown to be dysregulated. Interestingly, the PTPRR gene was induced in Huh7 cells. This has been associated with the TLR9 signalling cascade, and polymorphisms in the TLR9 gene have been associated with poor outcomes in patients. Additionally, we whole-genome sequenced CCHFV to assess viral diversity over time, and its relationship to the host response. As a result, we have demonstrated that through next-generation mRNA deep-sequencing it is possible to not only examine mRNA gene expression, but also to examine viral evolution. This demonstrates a proof-of-principle that specimens can be analyzed to identify both the virus, and host biomarkers that may have implications for prognosis.
Samples
GSM ID Sample info Characteristics Description
GSM3899584 huh7_ctrl_d1_rep1 cell line:Huh7; cell origin:hepatocellular carcinoma derived liver cells; infection:control; time:d1 -
GSM3899585 huh7_ctrl_d1_rep2 cell line:Huh7; cell origin:hepatocellular carcinoma derived liver cells; infection:control; time:d1 -
GSM3899586 huh7_ctrl_d1_rep3 cell line:Huh7; cell origin:hepatocellular carcinoma derived liver cells; infection:control; time:d1 -
GSM3899587 huh7_infected_d1_rep1 cell line:Huh7; cell origin:hepatocellular carcinoma derived liver cells; infection:CCHFV; time:d1 -
GSM3899588 huh7_infected_d1_rep2 cell line:Huh7; cell origin:hepatocellular carcinoma derived liver cells; infection:CCHFV; time:d1 -
GSM3899589 huh7_infected_d1_rep3 cell line:Huh7; cell origin:hepatocellular carcinoma derived liver cells; infection:CCHFV; time:d1 -
GSM3899590 huh7_ctrl_d3_rep1 cell line:Huh7; cell origin:hepatocellular carcinoma derived liver cells; infection:control; time:d3 -
GSM3899591 huh7_ctrl_d3_rep2 cell line:Huh7; cell origin:hepatocellular carcinoma derived liver cells; infection:control; time:d3 -
GSM3899592 huh7_ctrl_d3_rep3 cell line:Huh7; cell origin:hepatocellular carcinoma derived liver cells; infection:control; time:d3 -
GSM3899593 huh7_infected_d3_rep1 cell line:Huh7; cell origin:hepatocellular carcinoma derived liver cells; infection:CCHFV; time:d3 -
GSM3899594 huh7_infected_d3_rep2 cell line:Huh7; cell origin:hepatocellular carcinoma derived liver cells; infection:CCHFV; time:d3 -
GSM3899595 huh7_infected_d3_rep3 cell line:Huh7; cell origin:hepatocellular carcinoma derived liver cells; infection:CCHFV; time:d3 -
GSM3899596 hepg2_ctrl_d1_rep1 cell line:HepG2; cell origin:hepatocellular carcinoma derived liver cells; infection:control; time:d1 -
GSM3899597 hepg2_ctrl_d1_rep2 cell line:HepG2; cell origin:hepatocellular carcinoma derived liver cells; infection:control; time:d1 -
GSM3899598 hepg2_ctrl_d1_rep3 cell line:HepG2; cell origin:hepatocellular carcinoma derived liver cells; infection:control; time:d1 -
GSM3899599 hepg2_infected_d1_rep1 cell line:HepG2; cell origin:hepatocellular carcinoma derived liver cells; infection:CCHFV; time:d1 -
GSM3899600 hepg2_infected_d1_rep2 cell line:HepG2; cell origin:hepatocellular carcinoma derived liver cells; infection:CCHFV; time:d1 -
GSM3899601 hepg2_infected_d1_rep3 cell line:HepG2; cell origin:hepatocellular carcinoma derived liver cells; infection:CCHFV; time:d1 -
GSM3899602 hepg2_ctrl_d3_rep1 cell line:HepG2; cell origin:hepatocellular carcinoma derived liver cells; infection:control; time:d3 -
GSM3899603 hepg2_ctrl_d3_rep2 cell line:HepG2; cell origin:hepatocellular carcinoma derived liver cells; infection:control; time:d3 -
GSM3899604 hepg2_ctrl_d3_rep3 cell line:HepG2; cell origin:hepatocellular carcinoma derived liver cells; infection:control; time:d3 -
GSM3899605 hepg2_infected_d3_rep1 cell line:HepG2; cell origin:hepatocellular carcinoma derived liver cells; infection:CCHFV; time:d3 -
GSM3899606 hepg2_infected_d3_rep2 cell line:HepG2; cell origin:hepatocellular carcinoma derived liver cells; infection:CCHFV; time:d3 -
GSM3899607 hepg2_infected_d3_rep3 cell line:HepG2; cell origin:hepatocellular carcinoma derived liver cells; infection:CCHFV; time:d3 -
Platform GPL20301  : Illumina HiSeq 4000 (Homo sapiens)
Literature 32251473  
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xCell Plot
* p<0.05 ** p<0.01