Project description:We infected DF-1 cells with avian reovirus, and then used high-throughput sequencing to detect changes in miRNA expression profiles. This research provides a more comprehensive understanding of the interaction between viruses and host cells
2022-06-27 | GSE181193 | GEO
Project description:Genome sequencing for novel avian viruses
Project description:With its 2.5 Mb DNA genome packed in amphora-shaped particles of bacterium-like dimension (1.2 µm in length, 0.5 µm in diameter), the Acanthamoeba-infecting Pandoravirus salinus remained the most spectacular and intriguing virus since its description in 2013. Following its isolation from shallow marine sediment off the coast of central Chile, that of its relative Pandoravirus dulcis from a fresh water pond near Melbourne, Australia, suggested that they were the first representatives of an emerging worldwide-distributed family of giant viruses. This was further suggested when P. inopinatum discovered in Germany, was sequenced in 2015. We now report the isolation and genome sequencing of three new strains (P. quercus, P.neocaledonia, P. macleodensis) from France, New Caledonia, and Australia. Using a combination of transcriptomic, proteomic, and bioinformatic analyses, we found that these six viruses share enough distinctive features to justify their classification in a new family, the Pandoraviridae, distinct from that of other large DNA viruses.
Project description:Next-Generation-Sequencing (NGS) technologies have led to important improvement in the detection of new or unrecognized infective agents, related to infectious diseases. In this context, NGS high-throughput technology can be used to achieve a comprehensive and unbiased sequencing of the nucleic acids present in a clinical sample (i.e. tissues). Metagenomic shotgun sequencing has emerged as powerful high-throughput approaches to analyze and survey microbial composition in the field of infectious diseases. By directly sequencing millions of nucleic acid molecules in a sample and matching the sequences to those available in databases, pathogens of an infectious disease can be inferred. Despite the large amount of metagenomic shotgun data produced, there is a lack of a comprehensive and easy-use pipeline for data analysis that avoid annoying and complicated bioinformatics steps. Here we present HOME-BIO, a modular and exhaustive pipeline for analysis of biological entity estimation, specific designed for shotgun sequenced clinical samples. HOME-BIO analysis provides comprehensive taxonomy classification by querying different source database and carry out main steps in metagenomic investigation. HOME-BIO is a powerful tool in the hand of biologist without computational experience, which are focused on metagenomic analysis. Its easy-to-use intrinsic characteristic allows users to simply import raw sequenced reads file and obtain taxonomy profile of their samples.
Project description:To elucidate the potential role of commensal viruses in the etiology of AR, we performed a metagenomic analysis of nasal lavage fluid (NLF) to identify commensal viruses in the nose of mice colonizing in the specific pathogen-free (SPF) circumstances (Vehicle group). To evaluate the potential role of these commensal viruses, we reduced them in the nose of mice by administrating intranasal drops of broad-spectrum antiviral drug ribavirin daily, starting at 4-week-old and lasting for three weeks (Ribavirin group).
Project description:Multiomics of faecal samples collected from individuals in families with multiple cases of type 1 diabetes mellitus (T1DM) over 3 or 4 months. Metagenomic and metatranscriptomic sequencing and metaproteomics were carried out, as well as whole human genome sequencing. Phenotypic data is available.
Project description:To elucidate the potential role of commensal viruses in the etiology of AR, we performed a metagenomic analysis of nasal mucosa to identify commensal viruses in the nose of mice. To evaluate the potential role of these commensal viruses in AR, we reduced them in the nose of mice by administrating intranasal drops of vehicle (Vehicle group) or broad-spectrum antiviral drug ribavirin daily, starting at 4-week-old and lasting for three weeks (Ribavirin group). These mice were also administrated with PBS, OVA, or HDM to induce AR.
Project description:Multiomics of faecal samples collected from individuals in families with multiple cases of type 1 diabetes mellitus (T1DM) over 3 or 4 months. Metagenomic and metatranscriptomic sequencing and metaproteomics were carried out, as well as whole human genome sequencing. Phenotypic data is available.
Project description:We carried out a comparative genomic analysis of 48 avian species to identify avian-specific highly conserved elements (ASHCEs). We performed genome-wide chromatin immunoprecipitation sequencing (ChIP-seq) for three enhancer-associated histone modifications (H3K4me1, H3K27ac, H3K27me3), to investigate dynamic regulatory roles of ASHCEs in chicken development. We found that all three enhancer-associated histone marks are enriched in ASHCEs compared to the whole genome background.