Project description:This study aims to identify the specific miRNA of mycobacterium tuberculosis (M.tb) infected THP-1 by next-generation sequencing, and further to explore the role of miRNA in innate immunity against M.tb infection.Comprehensive analysis of the next-generation sequencing results showed that the expression of miR-99a-5p was significantly lower in the MTB infected THP-1 cells.
Project description:Primary human monocytes were isolated from four healthy donors. Monocytes were differentiated into macrophages, infected with virulent Mycobacterium tuberculosis (Mtb), strain H37Rv, for 24 or 48 hours, at a multiplicity of infection of 5 or 10. Following infection, infected cells and time-matched uninfected controls were harvested, total RNA including small RNAs was isolated and used for next-generation small RNA sequencing. Small RNA sequencing data was processed using miRge2.0, including a novel miRge2.0-based tRF detection tool. Processed data was used to determine differential expression of microRNAs and differential production of tRNA-derived fragments (tRFs) during infection with Mtb.
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:Mycobacterium tuberculosis (Mtb) causes a wide spectrum of human disease ranging from asymptomatic latent infection to severe host pathology, but it remains unclear how Mtb influence on leukocyte gene expression differs between disease states. We assessed mRNA expression in blood monocytes and granulocytes by next-generation sequencing in healthy controls and patients with active tuberculosis infection. We found genome-wide gene expression changes in granulocyte and monocyte which correlated with disease severity.
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:Detection of low-frequency resistance-mediating SNPs in next-generation sequencing data of Mycobacterium tuberculosis complex strains with binoSNP
Project description:Compare the gene expression difference between MRA_2010 knockout strains and wild-type strains by RNA sequencing in Mycobacterium tuberculosis H37Ra. The goal of this study is that detection cmtR acts as a transcriptional factor and regulates the target genes expression.
Project description:RNA-Seq results accompanying submission of a manuscript: "Cholesterol-dependent transcriptome remodeling reveals new insight into the contribution of cholesterol to Mycobacterium tuberculosis pathogenesis" describing the role of cholesterol and vitamin B12 in shaping the transcriptome of the Mycobacterium tuberculosis H37Rv and M. tuberculosis ∆prpR - propionate regulator (PrpR) mutant. Next generation sequencing results are provided in three independent biological replicates for each strain growing in three different media - minimal medium with glycerol or cholesterol as the sole carbon source and standard 7H9/10% OADC medium. The influence of vitamin B12 on M. tuberculosis transcriptome was analysed on 7H9/10% OADC medium supplemented with B12. The study allowed us to re-establish the list of genes potentially involved in cholesterol metabolism. We further proposed a novel regulatory function of vitamin B12 and PrpR, a propionate regulator, in coordinated cholesterol breakdown metabolite dissipation and virulent phenotype induction. Finally, we demonstrated that a key role of cholesterol in Mtb metabolism is not only providing carbon and energy but also inducing a transcriptome remodeling program that helps in developing tolerance to the unfavorable host cell environment.