Project description:We profiled Sex comb on midleg (Scm), Pc and E(z) in fly embryos and S2 based on BioTAP-XL ChIP-seq. ChIP-seq revealed that Scm is co-localized with PRC1, PRC2, and H3K27me3 in both S2 cells and embryos. Genomic binding/occupancy profiling of Scm, Pc and E(z) by high throughput sequencing
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:Sulfoquinovose (SQ) is a major organosulfonate in nature, and thus plays an important role in the biogeochemical sulfur and carbon cycles. We identified a bacterial anaerobic consortium, enriched from lake Konstanz, which degraded SQ to isethionate as intermediate and further into acetate and sulfide. By a metagenomic analysis we identified Faecalicatena sp. DSM22707 as major SQ-degrader in the consortium. Strain DSM22707 degraded SQ in pure culture into isethionate and small amounts of sulfolactate.
2025-05-07 | PXD055296 | Pride
Project description:Methanotrophic bacteria consortium Targeted loci cultured
Project description:We report the application of chromatin immunoprecipitation sequencing to identify binding sites of the transcription factor serum response factor (SRF) in the cornea of WT and Dstn-corn1 mutant mice Examination of SRF binding sites in WT and Dstn-corn1 mutant cornea
Project description:Septic cardiomyopathy (SCM) is the predominant cause of death in sepsis patients with undefined mechanism to date. Our study analyzed RNA sequencing (RNA-seq) data from rat heart tissue to discover key targets and potential pharmacological actions of the calcitonin gene-related peptide (CGRP) against SCM. A lipopolysaccharide-induced SCM model was established in rats (LPS 10 mg/kg, intraperitoneal (i.p.)). Thereafter, the myocardial tissues from the three groups of rats (Ctrl group, LPS group, and CGRP group) (n=5) were extracted and underwent RNA-seq, followed by bioinformatics analyses. Our findings suggest a basis for finding potential targets for CGRP in the treatment of SCM.
