Unknown,Transcriptomics,Genomics,Proteomics

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RNA-Seq of zebrafish embryos with wdr37 missense variant compared to wild type

ABSTRACT: RNA was extracted from 5-dpf embyros with and without a c.386C>T p.(Ser129Phe) variant in wdr37. Three independent RNA samples were prepared with each sample containing RNA from five individual embryos.

INSTRUMENT(S): HiSeq X Ten

ORGANISM(S): Danio rerio

SUBMITTER: Elena Semina

PROVIDER: E-MTAB-8029 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:RNA-Seq was used to unveil the transcriptional profile of DF-1 cells at the early stage of cell-adapted Infectious Bursal Disease Virus (caIBDV) infection. Total RNAs were extracted from virus-infected cells at 0, 6 and 12 hpi. RNA-Seq datasets of respective samples mapped to 56.5 - 57.6% of isoforms in the reference genome Galgal4.73. At 6 hpi, 23 isoforms underwent an elevated expression, while 128 isoforms were up-regulated and 5 were down-regulated at 12 hpi in the virus-infected group. Besides, 10 isoforms were exclusively expressed in the virus-infected cells. Though no significant change was detected in cytokine and interferon expression levels at the first 12 hours of infection, modulations of the upstream regulators were observed. In addition to the reported regulatory factors including EIF2AK2, MX, OAS*A, GBP7 and IFIT, IBDV infection also triggered a IFIT5-IRF1/3-RSAD5 pathway in the DF-1 cells which potentially restricted the viral replication cycle in the early infection stage. Over-expression of LIPA and CH25H, together with the suppression of STARD4, LSS and AACS genes implied a modulation of membrane fluidity and lipid raft arrangement in the infected cells. Alternative splicing of the EFR3 homolog A gene was also through to be involved in the lipid membrane regulation, and these cumulative responses projected an inhibition of viral endocytosis. Recognition of viral RNA genomes and intermediates was presumably enhanced by the elevated levels of IFIH1, DHX58 and TRIM25 genes which possess properties on detecting viral dsRNA. On the other hand, the caIBDV arrested the host's apoptotic process by inducing the expression of apoptosis inhibitors including NFKBIA/Z, TNFAIP2/3 and ITA at the first 12 hours of infection. In conclusion, the differential expression landscape demonstrated with RNA-Seq provides a comprehensive picture on the molecular interactions between host cells and virus at the early stage of infection. Two sample groups (infected and mock-infected) at three time points (0, 6, 12 hpi) were analysed.

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RNA-Seq of zebrafish embryos with wdr37 missense variant compared to wild type

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