Project description:The purpose is to obtain samples for microRNA analysis in human U937 cells infected with Zaire Ebola virus wild-type in the ΔVP30 background and Δmucin virus.
Project description:Analysis of microRNA expression patterns in cytomegalovirus infected human fibroblasts for two cultures with differing sensitivity to the virus
Project description:The purpose is to obtain samples for mRNA analysis in human U937 cells infected with Zaire Ebola virus wild-type in the ΔVP30 background and Δmucin virus.
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:propose: The goals of this study are viral transcript of host cells infected with shaan virus and host cell responses in HEK293, A549 and HRT18 infected with shaan virus. Methods: We infected the virus at an MOI of 0.5 to human tissues-derived cell lines including HEK-293, A549 and HRT18. The infected cells were harvested at 24 hours post infection, and a total RNA was extracted from the harvested cells with Trizol LS reagent. The trimmed reads were mapped to shaan virus genome or GRCh37 human genomic DNA reference. The differentially expressed genes (DEGs) between the virus-infected and mock-infected cells were calculated based on the fold changes of FPKM per each gene. Result: Viral transcripts were expressed differentially depending on the viral genes, it is obvious that the nucleocapsid (N) transcript was most expressed in all infected cells. Gene ontology enrichment analysis based on the DEGs revealed that HEK-293, A549 and HRT18 cells highly expressed the genes related to the antiviral defence system and innate immune response in response to the shaan virus infection. Conclusion: In this study, we describe transcriptome data from the shaan virus-infected cells. The inferred DEGs and their related biological functions can be further investigated to understand the shaanvirus-host interaction.
Project description:The purpose is to obtain samples for mRNA analysis in human U937 cells infected with Zaire Ebola virus wild-type in the deltaVP30 background and delta-mucin virus. Human U937 cells (monocyte-like) expressing the Ebola VP30 protein were infected with Zaire Ebola virus wild-type (wild) in the delta-VP30 background and delta-mucin virus (encodes a GP lacking the mucin domain) (mucin). Infected samples were collected in quintuplet; time-matched mocks were collected in quintuplet in parallel with infected samples. Time points: 0, 8, 18, and 30 h post-infection.
Project description:Analysis of gene expression patterns in cytomegalovirus infected human fibroblasts for two cultures with differing sensitivity to the virus
Project description:RNAseq analysis of human lung tissue explants infected with Influenza B virus Results: Differentially expressed genes after infection Project: Hulu_FluB_2022
