Gut metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA259602 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:CoMA – an Intuitive and User-friendly Pipeline for Amplicon-Sequencing Data Analysis
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Project description:we developed a low-input and user-friendly pipeline for the simultaneous profiling of five distinct Cys states with regional resolution in the gut of monkeys, including free SH, total Cys oxidation (Sto), sulfenic acid (SOH), S-nitrosylation (SNO), and S-glutathionylation (SSG), shedding light on redox modification stoichiometries and redox signaling of gut aging.Furthermore, redox-modification and proteomic analysis of colonic tissues of calorie-restricted aged mice revealed that CR can reduce oxidative stress and highlight the protective effect of CR on intestinal health.
2024-12-16 | PXD053818 |
Project description:The increasing application of RNA-seq to study non-model species demands easy-to-use and efficient bioinformatics tools to help researchers quickly uncover biological and functional insights. We developed ExpressAnalyst (www.expressanalyst.ca), a web-based tool for processing, analyzing, and interpreting RNA-seq data from any eukaryotic species. ExpressAnalyst contains a series of modules that enable raw data processing and annotation of FASTQ files, and statistical and functional analysis of counts tables and gene lists. All modules are integrated with EcoOmicsDB, an ortholog database that enables comprehensive analysis for species without a reference transcriptome. By coupling ultra-fast read mapping algorithms with high-resolution ortholog databases through a user-friendly web interface, ExpressAnalyst enables researchers to obtain global expression profiles and gene-level insights from raw RNA-seq reads within 24 hours. Here, we present ExpressAnalyst and demonstrate its utility with a case study of RNA-seq data from multiple non-model salamander species, including two that do not have a reference transcriptome.
2023-04-27 | GSE225876 | GEO
Project description:The present work describes a novel search program for the detection of both MS-cleavable and non-cleavable crosslinked peptides and it is the first software program reported with both capacities. The search strategy has been implemented in the computer program MetaMorpheus, which has a user-friendly graphical user interface (GUI). Novel crosslinker molecules can be easily added if desired. A fragment-ion index scheme makes the search computationally efficient. DSSO crosslinked BSA and E.coli ribosome data were used to validate the MS-cleavable crosslink search results.
2018-07-16 | PXD009000 | Pride
Project description:Here, we present ChromSCape, a user-friendly interactive Shiny/R application that processes single-cell epigenomic data to help the biological interpretation of chromatin landscapes within cell populations. ChromSCape successfully analyses the distribution of repressive and active histone modifications as well as chromatin accessibility landscapes from single-cell datasets.
2020-06-16 | GSE152502 | GEO
Project description:Background Single-cell RNA-sequencing (scRNA-seq) experiments typically analyze hundreds or thousands of cells after amplification of the cDNA. The high throughput is made possible by the early introduction of sample-specific bar codes (BCs), and the amplification bias is alleviated by unique molecular identifiers (UMIs). Thus, the ideal analysis pipeline for scRNA-seq data needs to efficiently tabulate reads according to both BC and UMI. Findings zUMIs is a pipeline that can handle both known and random BCs and also efficiently collapse UMIs, either just for exon mapping reads or for both exon and intron mapping reads. If BC annotation is missing, zUMIs can accurately detect intact cells from the distribution of sequencing reads. Another unique feature of zUMIs is the adaptive downsampling function that facilitates dealing with hugely varying library sizes but also allows the user to evaluate whether the library has been sequenced to saturation. To illustrate the utility of zUMIs, we analyzed a single-nucleus RNA-seq dataset and show that more than 35% of all reads map to introns. Also, we show that these intronic reads are informative about expression levels, significantly increasing the number of detected genes and improving the cluster resolution. Conclusions zUMIs flexibility makes if possible to accommodate data generated with any of the major scRNA-seq protocols that use BCs and UMIs and is the most feature-rich, fast, and user-friendly pipeline to process such scRNA-seq data.
2018-06-22 | GSE99822 | GEO
Project description:A user-friendly chromatographic method to purify small regulatory RNAs
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Project description:An Easy Operating Pathogen Microarray (EOPM) was designed to detect almost all known pathogens and related species based on their genomic sequences. For effective identification of pathogens from EOPM data, a statistical enrichment algorithm has been proposed and further implemented in a user-friendly interface.
2013-07-01 | GSE45860 | GEO
Project description:Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is an invaluable tool for mapping chromatin-associated proteins. Processing of samples still remains largely individual and labor-intensive, hindering the assay throughput and comparability across samples. Here we present a novel method for ultra-parallelized high-throughput ChIP-seq for the systematic mapping of histone modifications and transcription factors. The method, called RELACS (Restriction Enzyme-based Labeling of Chromatin in Situ), barcodes chromatin within intact nuclei extracted from different tissutal sources. Barcoded nuclei are pooled and processed within the same ChIP, for maximal comparability and drastical workload reduction. The choice of user-friendly, straightforward, enzymatic steps for chromatin fragmentation and barcoding makes RELACS particularly suitable for implementation in any clinical laboratory settings, for scarce samples, and large-scale studies.
2018-03-06 | GSE111000 | GEO