Human gut metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1134897 | ENA |
REPOSITORIES: ENA
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Project description:Joint profiling of chromatin accessibility and gene expression from the same single cell provides critical information about cell types in a tissue and cell states during a dynamic process. These emerging multi-omics techniques help the investigation of cell-type resolved gene regulatory mechanisms. Here, we developed in situ SHERRY after ATAC-seq (ISSAAC-seq), a highly sensitive and flexible single cell multi-omics method to interrogate chromatin accessibility and gene expression from the same single cell. We demonstrated that ISSAAC-seq is sensitive and provides high quality data with orders of magnitude more features than existing methods. Using the joint profiles from thousands of nuclei from the mouse cerebral cortex, we uncovered major and rare cell types together with their cell-type specific regulatory elements and expression profiles. Finally, we revealed distinct dynamics and relationships of transcription and chromatin accessibility during an oligodendrocyte maturation trajectory.
2022-06-15 | E-MTAB-11264 | biostudies-arrayexpress
Project description:To further reveal the major cell types of developing pIVC embryos and underlying epigenetic dynamics, the optimized single-cell based multi-omics sequencing method scChaRM-seq was performed (Yan et al., 2021b). 1,862 single cells Bisulfite-seq datasets were further analyzed. We then performed multi-omics profiling analysis using data obtained from9 pIVC embryos at 8 sequential developmental stages.
2023-03-24 | GSE218524 | GEO
Project description:To further reveal the major cell types of developing pIVC embryos and underlying epigenetic dynamics, the optimized single-cell based multi-omics sequencing method scChaRM-seq was performed (Yan et al., 2021b). After stringent filtration, 3,682 single cells RNA-seq datasets were further analyzed We then performed multi-omics profiling analysis using data obtained from9 pIVC embryos at 8 sequential developmental stages.
2023-03-24 | GSE218523 | GEO
Project description:In this study, we analyzed both together the epithelial tissue and the secreted mucus response using a holistic interactome-based multi-omics approach. The effect of the gilthead sea bream (Sparus aurata) skin mucosa to a dietary inclusion of spray-dried porcine plasma (SDPP) was evaluated.
2021-02-24 | GSE162501 | GEO
Project description:During human evolution, lifestyles including dietary choices have had a major impact on shaping of human physiology and health, including aging. However, the underlying mechanisms remain largely unknown. Here, we use a blood nutrient compound library-based screening approach to demonstrate that dietary supplement vanadyl sulfate (VS) selectively induces cell death in senescent cells and ameliorates phenotypes of aging and age-related disorders in vivo. Integrated chemical biology and multi-omics studies reveal that senescent cells are specifically sensitive to VS due to reduced cysteine reactivity with accumulated glutathione disulfide. VS selectively inactivates reactive cysteines on proteins to induce formation of incorrect disulfide bonds in senescent cells with imbalanced cellular redox status, causing aberrant protein misfolding and aggregation and eventual cell death. Our findings uncover a new senolytic mechanism to mitigate age-related disorders and reshape human physiology.
2025-09-22 | GSE243912 | GEO
Project description:Renal ischemia-reperfusion injury (IRI) is a leading cause of acute kidney injury (AKI) and presents significant challenges during kidney transplantation. Due to the detrimental effects of IRI on kidney function and the lack of effective intervention strategies, we conduct a multi-omics study on surgically induced mouse IRI, revealing a modulatory role for the metabolite S-adenosylmethionine (SAM) in AKI development. Our metabolic analysis of clinical samples establishes a link between various AKI conditions and marked elevations in serum SAM, underlying its potential as a biomarker for diagnosis. Furthermore, we find that short-term dietary methionine deprivation, which reduces circulating methionine and kidney SAM levels, effectively enhances renal resilience against IRI. In vivo isotopic tracing demonstrates that this diet preconditions kidney metabolic programs, enhancing glucose and fatty acid oxidation in preparation for IRI. Particularly, the activation of pyruvate dehydrogenase, which produces acetyl-CoA to fuel the tricarboxylic acid (TCA) cycle, highlights an energy-efficient strategy of glucose metabolism that is essential for the protective effects of dietary methionine deprivation.
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Project description:Renal ischemia-reperfusion injury (IRI) is a leading cause of acute kidney injury (AKI) and presents significant challenges during kidney transplantation. Due to the detrimental effects of IRI on kidney function and the lack of effective intervention strategies, we conduct a multi-omics study on surgically induced mouse IRI, revealing a modulatory role for the metabolite S-adenosylmethionine (SAM) in AKI development. Our metabolic analysis of clinical samples establishes a link between various AKI conditions and marked elevations in serum SAM, underlying its potential as a biomarker for diagnosis. Furthermore, we find that short-term dietary methionine deprivation, which reduces circulating methionine and kidney SAM levels, effectively enhances renal resilience against IRI. In vivo isotopic tracing demonstrates that this diet preconditions kidney metabolic programs, enhancing glucose and fatty acid oxidation in preparation for IRI. Particularly, the activation of pyruvate dehydrogenase, which produces acetyl-CoA to fuel the tricarboxylic acid (TCA) cycle, highlights an energy-efficient strategy of glucose metabolism that is essential for the protective effects of dietary methionine deprivation.
2025-12-06 | PXD058530 | Pride
Project description:Meta-analyses suggest that yogurt consumption reduces type 2 diabetes incidence in humans, but the molecular basis of these observations remains unknown. Here we show that dietary yogurt intake preserves whole-body glucose homeostasis and prevents hepatic insulin resistance and liver steatosis in a dietary mouse model of obesity-linked type 2 diabetes. Fecal microbiota transplantation studies reveal that these effects are partly linked to the gut microbiota. We further show that yogurt intake impacts the hepatic metabolome, notably maintaining the levels of branched chain hydroxy acids (BCHA) which correlate with improved metabolic parameters. These metabolites are generated upon milk fermentation and concentrated in yogurt. Remarkably, diet-induced obesity reduces plasma and tissue BCHA levels, and this is partly prevented by dietary yogurt intake. We further show that BCHA improve insulin action on glucose metabolism in liver and muscle cells, identifying BCHA as cell-autonomous metabolic regulators and potential mediators of yogurt's health effects.
2022-02-03 | MTBLS442 | MetaboLights
Project description:Multi-Omics investigation of Bariatric Surgery Outcomes
| PRJEB88699 | ENA