Homo sapiens strain:U2OS
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA244543 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1260866.fastq.gz | Fastqsanger.gz | |||
| SRR1260867.fastq.gz | Fastqsanger.gz | |||
| SRR1260868.fastq.gz | Fastqsanger.gz | |||
| SRR1260869.fastq.gz | Fastqsanger.gz |
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Project description:Crosslinking immunoprecipitation and sequencing was used to characterize nucleocapsid-RNA interactions in Rift Valley fever virus infection. This data set includes illumina HiSeq paired-end reads of Rift Valley fever virus infected HEK293 cells. The sequencing libraries were generated from nucleocapsid-bound RNAs.
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Project description:Rift Valley fever virus (RVFV) is an important human and livestock pathogen. To better understand the molecular virology and mechanisms of pathogenesis in human HEK293 cells during RVFV MP-12 strain infection, we used high-throughput mRNA sequencing technology to identify and analyze differentially expressed genes and mRNA splicing patterns triggered by infection or by expression of RVFV nucleocapsid protein. Here we supply the results of our RNA-seq analysis of RVFV-infected cells and cells transfected with RVFV nucleocapsid protein expressing plasmids. Some of the results were published in: "Transcriptome profiling in Rift Valley fever virus infected cells reveals modified transcriptional and alternative splicing programs" by Katherine E Havranek, Luke Adam White, Jean-Marc Lanchy, J Stephen Lodmell. PLoS One. 2019 May 28;14(5):e0217497. PMID: 31136639 PMCID: PMC6538246.
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Project description:The Rift Valley Fever (RVF) is an arthropod-borne disease present in several countries of Africa and Middle East. It is caused by RVF virus which can infect both humans and animals. In humans, it leads to various manifestations including hepatitis, encephalitis and death, while in domestic animals it usually causes miscarriage in pregnant females and it is often fatal for the newborn. Not all people or animal infected by the virus present the same disease. Some patients exhibit unapparent or moderate febrile reactions, while others develop severe symptoms. This observation suggests that host genetic factors play a role in controlling the outcome of infection. In this work, we compare the response of two different inbred strains of mice, MBT/Pas and BALB/cByJ, to infection with RVF virus. These strains exhibit different profiles of susceptibility to RVF virus infection. Indeed, MBT/Pas mice rapidly develop high viraemia and die soon after infection, while BALB/cByJ mice have a lower viraemia and die later. Interestingly, mouse embryonic fibroblasts (MEFs) obtained from MBT/Pas foetuses allows higher viral production than BALB/cByJ MEFs. Keywords: expression profiling The experiment was designed to include ARN samples from MBT/Pas and BALB/cByJ MEFs infected with the Rift Valley Fever (RVF) virus, and their respective mock-infected controls; each one of those in triplicate. Therefore, we have used 12 different samples for the study, divided as follows: 3 samples of RVF virus-infected BALB/cByJ MEFs, 3 samples of mock-infected BALB/cByJ MEFs, 3 samples of RVF virus-infected MBT/Pas MEFs and 3 samples of mock-infected MBT/Pas MEFs. Each RNA was extracted from a different culture well.
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Project description:Rift Valley fever virus Raw sequence reads
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Project description:Rift Valley Fever Virus (RVFV), a negative-stranded RNA virus, is the etiological agent of the vector-borne zoonotic disease, Rift Valley Fever (RVF). In both humans and livestock, protective immunity can be achieved through vaccination. Earlier and more recent vaccine trials in cattle and sheep demonstrated a strong neutralizing antibody and total IgG response induced by the RVFV vaccine, MP-12. From previous work, protective immunity in sheep and cattle vaccinates normally occurs from 7 to 21 days after inoculation with MP-12. While the serology and protective response induced by MP-12 has been studied, little attention has been paid to the underlying molecular and genetic events occurring prior to the serologic immune response. To address this, we isolated RNA from whole blood from vaccinates over a time course of 21 days before and after inoculation during a recent vaccine trial with MP-12. This RNA time course was deeply sequenced by RNASeq and bioinformatically analyzed. Our results revealed time-dependent activation or repression of numerous gene ontologies and pathways related to immune response and regulation. Additional analyses identified a correlative relationship between specific genes related to immune activity and protective immunity prior to serologic detection of antibody response. These data provide an important proof of concept for identifying molecular and genetic components underlying the immune response to vaccination and protection prior to serologic detection.
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