Multi-omics Approach Reveals Metabolic Changes in the Heart at Birth
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PROVIDER: PRJNA481787 | ENA |
REPOSITORIES: ENA
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Project description:Multi-omics Approach Reveals Metabolic Changes in the Heart at Birth
| PRJNA481787 | ENA
Project description:During late gestation, the fetal heart relies primarily on glucose and lactate to support rapid growth and development. While numerous studies describe changes in heart metabolism a few weeks after birth to preferentially utilize fatty acids, little is known about metabolic changes of the heart within the first day of life. Therefore, we used the ovine model of pregnancy to investigate metabolic differences between the near-term fetal and the newborn heart. We observed greater abundance of metabolites involved in butanoate and propanoate metabolism, and glycolysis/gluconeogenesis in the term fetal heart (FDR-corrected p<0.10) and differential expression in these pathways were confirmed with single-sample gene set enrichment analysis (ssGSEA) (FDR-corrected p<0.05). Immediately following birth, newborn hearts displayed enrichment in purine, fatty acid, and glycerophospholipid metabolic pathways, as well as oxidative phosphorylation with significant alterations in lipids and metabolites to support transcriptomic findings. While other studies suggest a switch from carbohydrate metabolism to fatty acid metabolism in the neonatal heart in as early as 2 weeks following birth, our data show that this metabolic switch in the heart begins by the first day of postnatal life. A better understanding of metabolic alterations that occur in the heart following birth may improve treatment of neonates at risk for heart failure.
2018-11-01 | GSE117343 | GEO
Project description:Integrated multi-omics approach revealed cellular senescence landscape
| PRJNA865031 | ENA
Project description:Characterizing the Key Metabolic Pathways of the Neonatal Mouse Heart Using a Quantitative Combinatorial Omics Approach
| PRJNA421308 | ENA
Project description:Harnessing HetHydrogel: An Approach to Single-Cell Multi-Omics
| PRJNA1024454 | ENA
Project description:An increasingly common method for predicting gene activity is genome-wide chromatin immunoprecipitation of M-bM-^@M-^XactiveM-bM-^@M-^Y chromatin modifications followed by massively parallel sequencing (ChIP-seq). Using a novel ChIP-seq quantification method (cRPKM), we tested the power of such ChIP-seq strategies to predict relative protein and RNA levels at the pre-pro-B and pro-B differentiation stages in early B cell lymphopoiesis. Using a multi-omics approach that compares promoter chromatin status (ChIP-seq; published in GSE:21978) with ongoing active transcription (GRO-seq; published in GSE:40173), steady state mRNA (RNA-seq), inferred mRNA stability, and relative proteome abundance measurements (iTRAQ), we demonstrate that active chromatin modifications at promoters are a good indicator of transcription and steady state mRNA levels. Moreover, we found that promoters with active chromatin modifications exclusively in one of these cell states frequently predicted differentially expressed proteins. However, we found that many genes whose promoters have non-differential but active chromatin modifications also displayed changes in expression of their cognate proteins. This large class of developmentally and differentially regulated proteins that was uncoupled from chromatin status used mostly post-transcriptional mechanisms. Interestingly, the most differentially expressed protein in our B-cell development system, 2410004B18Rik, was regulated by a post-transcriptional mechanism, which further analyses indicated was mediated by an identified miRNA. These data provide a striking example of how our integrated multi-omics data set can be useful in uncovering regulatory mechanisms. Total RNA from mouse pre-pro-B and pro-B cells, depleted of rRNA and small RNAs, was sequenced using a strand specific, single end sequencing strategy.
2013-11-19 | E-GEOD-52450 | biostudies-arrayexpress
Project description:Developing a single-cell multi-omics technology with mtDNA mutation profiling at its core will enable precise determination of the relationship between mtDNA mutations and cellular phenotypes. To date, the development of permeability-engineered compartmentalization for the isolation and single-cell library preparation of individual cells, which includes Tn5 tagmentation and single-cell barcoding operations in the permeabilized microcapsule format, remains a formidable challenge. Herein, we present a approach for single-cell mitochondrial analysis, harnessing microfluidics to generate heterogeneous hydrogels as artificial membranes. These hydrogels serve to regulate the passage of mitochondrial DNA and nuclear genomes subsequent to the cell lysis step. This approach enables high-throughput mitochondrial DNA genotyping and accessible chromatin profiling at the single-cell level, significantly enhancing the capabilities of permeability-engineered compartmentalization.We conducted a comprehensive evaluation of cell retention and the selective permeability of the capsule reaction system, optimizing conditions for cell lysis, Tn5 tagmentation, and barcode labeling. Validation experiments were performed using Human 293T and Mouse 3T3 cells to assess identification and quantification performance. Our method offers a new strategy for the study of the functions of various mtDNA mutations in biological processes, while also offering a new system for the construction of single-cell multi-omics libraries.
2023-10-10 | GSE244725 | GEO
Project description:Elucidating causes of vaginal symptoms using a multi-omics approach
| PRJNA847316 | ENA
Project description:The heart of new-born mouse has exceptional capacity to regenerate from myocardial injury. However, the mouse heart loses this capacity within the first week of its life. In order to elucidate the molecular mechanisms taking place in the mouse heart during the loss of its regenerative potential, a systematic comparison of 1-day and 7-day-old mouse hearts was performed at the proteomic, metabolomic, and transcriptomic levels.
2018-12-01 | GSE107760 | GEO
Project description:Kids First: Congenital Heart Defects and Laterality Birth Defects
| PRJNA760555 | ENA