Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10688001_1.fastq.gz | Fastqsanger.gz | |||
| SRR10688001_2.fastq.gz | Fastqsanger.gz | |||
| SRR10688002_1.fastq.gz | Fastqsanger.gz | |||
| SRR10688002_2.fastq.gz | Fastqsanger.gz | |||
| SRR10688003_1.fastq.gz | Fastqsanger.gz |
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Project description:D-galactose orally intake ameliorate DNCB-induced atopic dermatitis by modulating microbiota composition and quorum sensing. The increased abundance of bacteroidetes and decreased abundance of firmicutes was confirmed. By D-galactose treatment, Bacteroides population was increased and prevotella, ruminococcus was decreased which is related to atopic dermatitis.
2022-04-29 | E-MTAB-11632 | biostudies-arrayexpress
Project description:In mammals, DNA methylation occurs mainly at 5mC of CpG dinucleotides. The methylation on the promoter leads to the suppression of gene expression, while the functional role of gene body DNA methylation in highly expressed genes has yet to be clarified. Here, we show that the Dnmt3b-dependent intragenic DNA methylation protects the gene body from RNA Polymerase II (RNA Pol II) spurious entry and cryptic transcription initiation. Using different genome-wide approaches, we demonstrate that loss of Dnmt3b leads to an increase of the RNA Pol II engagement within gene bodies and spurious intragenic transcription initiation events. Furthermore, inhibition of RNA Pol II spurious entry depends on the enzymatic activity of the Dnmt3b recruited by H3K36me3. Thus, elongating RNA Pol II triggers an epigenetic crosstalk that involves SetD2, H3K36me3, Dnmt3b, and DNA methylation to ensure gene transcription initiation fidelity with implications for intragenic hypomethylation in cancer.
2017-02-25 | GSE72853 | GEO
Project description:The characterization of microbial communities based on sequencing and analysis of their genetic information has become a popular approach also referred to as metagenomics; in particular, the recent advances in sequencing technologies have enabled researchers to study even the most complex communities. Metagenome analysis, the assignment of sequences to taxonomic and functional entities, however, remains a tedious task: large amounts of data need to be processed. There are a number of approaches addressing particular aspects, but scientific questions are often too specific to be answered by a general-purpose method.We present MGX, a flexible and extensible client/server-framework for the management and analysis of metagenomic datasets; MGX features a comprehensive set of adaptable workflows required for taxonomic and functional metagenome analysis, combined with an intuitive and easy-to-use graphical user interface offering customizable result visualizations. At the same time, MGX allows to include own data sources and devise custom analysis pipelines, thus enabling researchers to perform basic as well as highly specific analyses within a single application.With MGX, we provide a novel metagenome analysis platform giving researchers access to the most recent analysis tools. MGX covers taxonomic and functional metagenome analysis, statistical evaluation, and a wide range of visualizations easing data interpretation. Its default taxonomic classification pipeline provides equivalent or superior results in comparison to existing tools.
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Project description:In the collective genomes (the metagenome) of the microorganisms inhabiting the Earth's diverse environments is written the history of life on this planet. New molecular tools developed and used for the past 15 years by microbial ecologists are facilitating the extraction, cloning, screening, and sequencing of these genomes. This approach allows microbial ecologists to access and study the full range of microbial diversity, regardless of our ability to culture organisms, and provides an unprecedented access to the breadth of natural products that these genomes encode. However, there is no way that the mere collection of sequences, no matter how expansive, can provide full coverage of the complex world of microbial metagenomes within the foreseeable future. Furthermore, although it is possible to fish out highly informative and useful genes from the sea of gene diversity in the environment, this can be a highly tedious and inefficient procedure. Microbial ecologists must be clever in their pursuit of ecologically relevant, valuable, and niche-defining genomic information within the vast haystack of microbial diversity. In this report, we seek to describe advances and prospects that will help microbial ecologists glean more knowledge from investigations into metagenomes. These include technological advances in sequencing and cloning methodologies, as well as improvements in annotation and comparative sequence analysis. More significant, however, will be ways to focus in on various subsets of the metagenome that may be of particular relevance, either by limiting the target community under study or improving the focus or speed of screening procedures. Lastly, given the cost and infrastructure necessary for large metagenome projects, and the almost inexhaustible amount of data they can produce, trends toward broader use of metagenome data across the research community coupled with the needed investment in bioinformatics infrastructure devoted to metagenomics will no doubt further increase the value of metagenomic studies in various environments.
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Project description:Microbes are increasingly being implicated in autoimmune disease. This calls for a re-evaluation of how these chronic inflammatory illnesses are routinely treated. The standard of care for autoimmune disease remains the use of medications that slow the immune response, while treatments aimed at eradicating microbes seek the exact opposite-stimulation of the innate immune response. Immunostimulation is complicated by a cascade of sequelae, including exacerbated inflammation, which occurs in response to microbial death. Over the past 8 years, we have collaborated with American and international clinical professionals to research a model-based treatment for inflammatory disease. This intervention, designed to stimulate the innate immune response, has required a reevaluation of disease progression and amelioration. Paramount is the inherent conflict between palliation and microbicidal efficacy. Increased microbicidal activity was experienced as immunopathology-a temporary worsening of symptoms. Further studies are needed, but they will require careful planning to manage this immunopathology.
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Project description:Cappable-seq was used to map transcription start sites globally in B. subtilis and E. coli to investigate spurious transcription, and how B. subtilis prevents it.
2022-01-12 | E-MTAB-10777 | biostudies-arrayexpress
Project description:To determine whether the developmental defects of urt1-1 xrn4-3 are linked to the biogenesis of spurious siRNAs, we analyzed small RNA libraries and indeed detected the accumulation of 21 nt siRNAs originating from mRNA loci in urt1-1 xrn4-3.
2020-05-28 | GSE148427 | GEO
Project description:We report the ChIP-seq profiling of a spurious transcriptional factor Sef1 in non-typical model yeast species, Lachancea kluyveri, and show that LkSef1 targets many TCA cycle and many others genes but has very limited regulatory effects to these target genes.
2020-04-08 | GSE148243 | GEO
Project description:The fidelity of signal transmission requires the binding of regulatory molecules to their cognate targets. However, the crowded cell interior risks off-target interactions between proteins that are functionally unrelated. Understanding the constraints this imposes on cell systems evolution requires the fitness cost of spurious interactions to be quantified. Towards this end, we express human tyrosine kinases in the budding yeast S. cerevisiae. Yeast lacks bona fide tyrosine kinases and so the majority of resulting pY sites are functionless and artificial. We express 24 unique tyrosine kinases in total and perform phosphoproteomics in each case, resulting in ~30,000 phosphosites sites mapping to 3500 phosphoproteins. Examination of the fitness costs in each strain reveals a strong correlation between the number of spurious pY sites generated and negative effects on growth. Moreover, the prediction of pY effects on protein structure and on protein function (conservation-based) reveals potential for the widespread perturbation of the yeast proteome. Comparing the spurious pY sites (pre-selection) with native pY sites in human (post-selection) also demonstrates the recurrent modification of proteins and sites with no homology to native substrates. However, examination of these data together (fitness and phosphoproteomics) strongly suggests that a large number of the pY sites generated have a negligible effect on fitness. Finally, we test the hypothesis of pY counter-selection following the emergence of tyrosine kinases in metazoan species, but find no strong evidence for proteome-wide selection against spurious Y phosphorylation.
2024-09-12 | PXD045466 | Pride
Project description:Biofloc technology is increasingly recognised as a sustainable aquaculture method. In this technique, bioflocs are generated as microbial aggregates that play pivotal roles in assimilating toxic nitrogenous substances, thereby ensuring high water quality. Despite the crucial roles of the floc-associated bacterial (FAB) community in pathogen control and animal health, earlier microbiota studies have primarily relied on the metataxonomic approaches. Here, we employed shotgun sequencing on eight biofloc metagenomes from a commercial aquaculture system. This resulted in the generation of 106.6 Gbp, and the reconstruction of 444 metagenome-assembled genomes (MAGs). Among the recovered MAGs, 230 were high-quality (≥90% completeness, ≤5% contamination), and 214 were medium-quality (≥50% completeness, ≤10% contamination). Phylogenetic analysis unveiled Rhodobacteraceae as dominant members of the FAB community. The reported metagenomes and MAGs are crucial for elucidating the roles of diverse microorganisms and their functional genes in key processes such as nitrification, denitrification, and remineralization. This study will contribute to scientific understanding of phylogenetic diversity and metabolic capabilities of microbial taxa in aquaculture environments.
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