Gut metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB18118 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR554949_1.fastq.gz | Fastqsanger.gz | |||
| DRR554949_2.fastq.gz | Fastqsanger.gz | |||
| DRR554950_1.fastq.gz | Fastqsanger.gz | |||
| DRR554950_2.fastq.gz | Fastqsanger.gz | |||
| DRR554951_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 24 |
Similar Datasets
Project description:We present InTAC-seq, a method for simultaneous quantification of genome-wide open chromatin and intracellular protein abundance in fixed cells. Using InTAC we directly observe variation in chromatin accessibility and transcription factor motif occupancy driven by differences in transcription factor protein abundance. By purifying bone marrow progenitor cells based on GATA1 protein expression, we establish its role in both functional and epigenetic restriction of erythroid cell identity in human hematopoiesis.
2022-03-10 | GSE167934 | GEO
Project description:Simultaneous epigenomic profiling and regulatory activity measurement using e2MPRA
| PRJDB39977 | ENA
Project description:The paper "Metabolomic Machine Learning Predictor for Diagnosis and Prognosis of Gastric Cancer" addresses the need for non-invasive diagnostic tools for gastric cancer (GC). Traditional methods like endoscopy are invasive and expensive. The authors conducted a targeted metabolomics analysis of 702 plasma samples to develop machine learning models for GC diagnosis and prognosis. The diagnostic model, using 10 metabolites, achieved a sensitivity of 0.905, outperforming conventional protein marker-based methods. The prognostic model effectively stratified patients into risk groups, surpassing traditional clinical models.
I have successfully reproduced the diagnosis model from the paper. This machine learning-based system differentiates GC patients from non-GC controls using metabolomics data from plasma samples analyzed by liquid chromatography-mass spectrometry (LC-MS). The model focuses on 10 metabolites, including succinate, uridine, lactate, and serotonin. Employing LASSO regression and a random forest classifier, the model achieved an AUROC of 0.967, with a sensitivity of 0.854 and specificity of 0.926. This model significantly outperforms traditional diagnostic methods and underscores the potential of integrating machine learning with metabolomics for early GC detection and treatment.
2024-07-23 | MODEL2407230001 | BioModels
Project description:Sudden cardiac death (SCD) associated with heart failure (HF) is a multifactorial problem requiring a systems level approach applied to suitable experimental animal models with features of the human disease. Here we examine key regulatory pathways underlying the transition from compensated hypertrophy (HYP) to decompensated HF and SCD by integrated analysis of the transcriptome, proteome and metabolome. In a guinea pig model of acquired long QT syndrome and HF/SCD, relative protein abundances from sham-operated, HYP and HF hearts were assessed using isobaric tags for relative and absolute quantification (iTRAQ), prior to liquid chromatography and tandem mass spectrometry (LC-MS/MS). Metabolites were quantified by LC-MS/MS or gas chromatography coupled to MS (GC-MS). Transcriptome profiles were obtained using DNA microarrays. The guinea pig HF proteome exhibited classic biosignatures of cardiac HYP, left ventricular dysfunction, fibrosis, cellular degeneration, inflammation and extravasation. Fatty acid metabolism, mitochondrial transcription/translation factors, antioxidant enzymes, and other mitochondrial processes, were downregulated in HF, but not HYP. Proteins upregulated in HF are consistent with extracellular matrix remodeling, cytoskeletal remodeling, and acute phase inflammation markers. Among metabolites, downregulation of acyl-carnitines was observed in HYP, while fatty acids accumulated in HF. Levels of the tricarboxylic acid (TCA) cycle metabolite, citrate, and the potent inhibitor, 2-methylcitrate, increased upon transition from HYP to HF. Correlation of the magnitude of transcript and protein changes in HF is weak (R2=0.23), indicating that targeting transcript/proteome may reveal inform post-transcriptional gene regulation in HF. Proteome/Metabolome integration suggests metabolic bottlenecks in fatty acyl-CoA processing by carnitine palmitoyl transferase (CPT1B) as well as TCA cycle inhibition. We present a model in which hallmarks of acute signaling in HF, including Ca2+ dysregulation and low cAMP levels, are coupled to mitochondrial metabolic and antioxidant defects, through a CREB/PGC1-alpha transcriptional axis.
2016-12-02 | GSE78077 | GEO
Project description:<p>The focus of this study was to better understand the effects of cigarette smoking on the vaginal microbiome. There were two phases of the study, cross-sectional and longitudinal, conducted at the Center for Health Behavior Research at the University of Maryland School of Public Health. In the cross-sectional phase, 20 smokers and 20 non-smokers collected mid-vaginal swabs, measured their vaginal pH, prepared a vaginal smear on a slide for Nugent Gram stain analysis, and completed questionnaires about demographics, tobacco use, and reproductive and sexual health history. Smoking status was confirmed through self-report, carbon monoxide exhalation and saliva cotinine measures. Secretions from the mid-vaginal swabs were tested for presence/absence of HPV strains and GC-MS was used to quantify the levels of over 600 metabolites.</p> <p>In the longitudinal phase, 7 participants who were current smokers and motivated to quit smoking were recruited and followed for up to 12 weeks. On a daily basis, participants collected mid-vaginal swabs, measured their vaginal pH, and prepared a mid-vaginal smear on a slide for Nugent Gram stain analysis, and completed daily diaries on tobacco use and reproductive health. Carbon monoxide exhalation and saliva cotinine measures were collected at weekly clinical visits. In addition, participants had weekly behavioral counseling sessions about smoking cessation and used Nicoderm CQ patches to aid in quitting smoking. The self-collected vaginal swabs were used for DNA extractions,16s rRNA sequencing and measurement of metabolites in vaginal fluid.</p>
| phs001386 | dbGaP
Project description:A novel assay based on proximity ligation assay for high-throughput quantification of proteins, protein complexes and mRNA in single cells Here we present proximity-sequencing (Prox-seq), a method for simultaneous measurement of an individual cell’s proteins, protein complexes and mRNA. Prox-seq utilizes deep sequencing and barcoded proximity assays to measure proteins and their complexes from all pairwise combinations of targeted proteins, without any prior knowledge of which proteins can form complexes. The number of measured protein complexes scales quadratically with the number of targeted proteins, allowing for unparalleled multiplexing capacity. We developed a high-throughput experimental and computational pipeline and demonstrated the potential of Prox-Seq for multi-omic analysis with a panel of 13 proximity probes, enabling the measurement of 91 protein complexes, along with thousands of mRNA molecules in single T cells and B cells. Prox-seq is compatible with current single-cell RNA sequencing assays, such as Drop-seq and Smart-seq2. Prox-seq provides access to an untapped yet powerful measurement modality for single-cell phenotyping and has the potential to discover new protein interactions in single-cells.
2020-05-16 | GSE149574 | GEO
Project description:The gut-brain axis is an emerging factor in promoting multiple sclerosis (MS). However, the underlying mechanisms and strategies to target this axis are not established. Here, we investigated how the gut environment influences myelin-specific Th17 cell pathogenicity. We used the adoptive Th17 cell transfer experimental autoimmune encephalomyelitis (EAE) model and antibiotic treatment to modulate the intestinal microbiome. We observed a reduced pathogenic Th17 cell signature in the colon of antibiotics-treated mice. Treatment with fecal filtrates enhanced myelin-specific Th17 cell encephalitogenic properties both in vitro and in vivo. Feces metabolomic profiling identified altered tryptophan-derived metabolites, including indole-3-carboxylate (I3CA). Oral I3CA supplementation accelerated EAE development and I3CA concentration in blood samples from persons with MS (PwMS) was associated with increased disease severity mirrored by increased serum neurofilament light chain levels. Altogether, our study shows that microbiota-derived metabolites play a key role in the intestine during neuroinflammation, offering potential therapeutic insights for PwMS.
2025-07-15 | GSE282316 | GEO
Project description:Regulation of transcript expression in different tolerance classes of rice cultivars in response to high night temperatures (HNT) is investigated. The aim was to identify marker genes which are responsible for HNT tolerance. Addiditionally gene expression data are combined with GC-MS data analysis (primary metabolites) to identify global changes in response to HNT.
2016-12-01 | GSE55341 | GEO
Project description:The hydrolytic deamination of cytosine and 5-methylcytosine drives many of the transition mutations observed in human cancer. The deamination-induced mutagenic intermediates are either uracil or thymine adducts mispaired with guanine. While a substantial array of methods exists to measure other types of DNA adducts, the cytosine deamination adducts pose unusual analytical problems and adequate methods to measure them have not yet been developed. We describe here a novel hybrid thymine DNA glycosylase, hyTDG, which is comprised of a 29-amino acid sequence from human thymine DNA glycosylase linked to a thymine glycosylase found in an archaeal thermophilic bacterium. Using defined-sequence oligonucleotides, we show that hyTDG has robust mispair-selective activity against deaminated U:G and T:G mispairs. We have further developed a method for separating glycosylase-released free bases from oligonucleotides and DNA followed by GC-MS/MS identification and quantification. Using this approach, we have measured for the first time the levels of total Uracil (U), U:G and T:G in calf thymus DNA. The method presented here will allow the measurement of the formation, persistence, and repair of a biologically important class of deaminated cytosine adducts.
2022-02-15 | PXD030459 | Pride