Similar Datasets
Project description:This study aims to study binding events between the Zika virus RNA genome and endogenous transcripts during infection of a human cell line. We develop a novel psolaren-based cross-linking technique to preserve interactions between mRNA and the Zika genome. Interacting RNA molecules are ligated together prior to reversal of the cross-links and selection for Zika-containing fragments. Reverse transcription and paired-end high-throughput sequencing then allow us to identify the interacting transcripts. We generated three batches of libraries, where all samples in each batch were generated from the same pool of RNA. Within each batch, we have the livefire sample, where the protocol was performed as described above; a reverse-control sample, where the protocol was performed by reversing the cross-links prior to ligation; and a no-cross-link control, where the protocol was performed without any cross-linking. The latter two samples represent negative controls where no genuine interactions should be observed.
2018-07-13 | E-MTAB-6427 | biostudies-arrayexpress
Project description:To search for host factors regulating Zika virus infection, we performed a genome-wide loss-of-function CRISPR/Cas9 screen in haploid human ESCs. The regulators were identified by the quantification of enrichment of their mutant clones within a pooled loss-of-function library upon Zika virus infection.
2023-05-31 | E-MTAB-11945 | biostudies-arrayexpress
Project description:Dengue and Zika are closely related members of the Flaviviridae family of positive, single-stranded RNA viruses and are of global clinical importance. These viruses utilize an 11kb RNA genome for translation and replication, and much remains to be learnt about how the entire genome folds to enable virus function. Here, we performed high throughput RNA secondary structure and pair-wise interaction mapping on four dengue serotypes and four Zika strains within their virus particles. We identified structures that are associated with translation pausing, and are evolutionary conserved by integrating synonymous mutation rates into our analysis. Genome-wide interaction mapping revealed alternative structures, as well as extensive long-range RNA interactions – including the known circularization signals– within the virus particles. Many of these long-range interactions are conserved across the viruses and/or clustered into “hubs” that are shown to be functionally important. This comprehensive structural resource of dengue and Zika viruses reveals that viral genome organization is much more complex than previously appreciated and deepens our understanding of the molecular basis for viral pathogenesis.
2019-02-28 | GSE106483 | GEO
Project description:To better understand the critical drivers of Zika virus pathogenicity, we used microarray analysis to evaluate the host responses triggered by Zika virus infection in MRC-5 cells.
2021-03-23 | E-MTAB-10292 | biostudies-arrayexpress
Project description:RNA-seq count data at 3 timepoints was generated for Zika-exposed and Zika-naïve individuals in order to assess associated signatures
2019-04-17 | GSE129882 | GEO
Project description:PolyA+ RNA sequencing of Zika virus-infected human brain organoids at 5 days post-infection.
2017-04-03 | E-MTAB-4811 | biostudies-arrayexpress
Project description:Zika virus (ZIKV) is a mosquito-transmitted positive-sense RNA virus in the family Flaviviridae. Live attenuated vaccines have been successfully used to combat infection by flaviviruses, such as yellow fever and Japanese encephalitis viruses. A Zika virus harboring combined mutations in the envelope protein glycosylation site and in the nonstructural 4B protein amino acid 36 (ZE4B-36) was generated and assessed for stability, attenuation, and protection against infection. To determine the genetic stability of its RNA genome, ZE4B-36 was serially passaged in vitro in Vero cells. Virus harvested from passages (P)1 to P6 was subjected to next generation sequencing and downstream analysis to determine its nucleotide sequence variability. Specifically, single nucleotide variant analysis showed that the ZE4B-36 genome decreased its genetic diversity and resulted in a more stable nucleotide sequence. Thus, in addition to showing attenuation and protection, ZE4B-36 is a stable live attenuated virus that possesses characteristics important for a vaccine to combat Zika disease.
2021-12-31 | E-MTAB-9496 | biostudies-arrayexpress