Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1161195 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30687400_1.fastq.gz | Fastqsanger.gz | |||
| SRR30687400_2.fastq.gz | Fastqsanger.gz | |||
| SRR30687401_1.fastq.gz | Fastqsanger.gz | |||
| SRR30687401_2.fastq.gz | Fastqsanger.gz | |||
| SRR30687402_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 192 |
Similar Datasets
Project description:The objective of the work is to explore the pathways and mechanisms driving inflammation and fibrosis in stented ureters. In total, 6 pigs underwent cystoscopic unilateral ureteral stent insertion for 14 days. Ureteral tissue was harvested in 3 pigs, while the remaining 3 pigs had their stents removed, and were recovered for 7 days. Three separate pigs served as controls. Stents cause significant inflammation and fibrosis of ureters. Gene set enrichment analysis confirmed fibrotic changes and tissue proliferation and suggests that epithelial-mesenchymal transition is a driver of fibrosis.
| EGAS00001006855 | EGA
Project description:African swine fever virus (ASFV) is a highly contagious pathogen that primarily affects domestic and wild pigs with specific tropism to porcine alveolar macrophages (PAMs). However, the host receptors involved in ASFV infection remain unknow. Here, we present a multi-omic epigenetic atlas of ASFV-exposed PAMs and profile 3D chromatin architecture and single-nucleus chromatin accessibility landscapes (sn-ATAC)
2025-04-18 | GSE231435 | GEO
Project description:We investigated the fruit development in two plantain banana cultivars from two weeks after bunch emergence till twelve weeks through high-throughput proteomics, major metabolite quantification and metabolic flux analyses. We give for the first time an insight at early stages of starch synthesis and breakdown.
2022-06-01 | PXD029901 | Pride
Project description:Post-translational modifications (PTMs) serve as critical regulatory mechanisms connecting metabolism and protein functions. Following our prior discovery of lysine lactylation (Kla), we herein report the identification and characterization of lysine pyruvylation (Kpy), a previously undescribed PTM driven by the central glycolytic hub metabolite pyruvate. Through integrated biochemical and proteomic strategies, we established the existence and specificity of Kpy. Proteomic profiling revealed Kpy sites across both histones and non-histone proteins, implicating its broad physiological significance. Notably, our investigations demonstrated that Kpy abundance fluctuates in respond to alterations in glycolytic flux and pyruvate concentration, providing a direct mechanism by which metabolic alterations influence protein functions. Additionally, we identified Sirtuin 3 (SIRT3) as the "eraser" enzyme for Kpy removal, while Histone acetyltransferase 1 (HAT1) and p300 (EP300) function as "writer" enzymes responsible for Kpy deposition. Initial mechanistic studies suggested Kpy's regulatory role in transcriptional control. Together, the elucidation of Kpy expands our understanding of metabolite-protein crosstalk through PTMs, providing mechanistic insights into pathophysiological processes and facilitating the development of targeted therapeutic interventions for metabolic disorders.
2025-04-23 | GSE295067 | GEO
Project description:It proves so far difficult to predict the metabolome, even when genome, transcriptome or proteome of a cell are known. In order to globally map enzyme-metabolite relationships, we systematically quantified enzyme expression and metabolite concentrations in Saccharomyces cerevisiae kinase knock-out strains. Enzymes expression changes did account for a major fraction of all differentially expressed proteins, and were non-redundant, implying that kinases act generally yet specifically in metabolic regulation. Differential enzyme expression was found to affect metabolite concentrations through the redistribution of flux control, resulting in a many-to-many relationship between enzyme abundance and the metabolome. Machine learning successfully mapped these relationships, allowing the precise prediction of metabolite concentrations, as well as identifying regulatory genes. Our study reveals that hierarchical metabolic regulation acts predominantly through adjustment of broad enzyme expression patterns rather than over rate-limiting enzymes, and may account for more than half of metabolic regulation.
2018-09-13 | PXD010529 | Pride
Project description:In this study, we used GC-MS analysis in combination with flux analysis and the Affymetrix ATH1 GeneChip to survey the metabolome and transcriptome of Arabidopsis leaves in response to manipulation of the thiol-disulfide status. Feeding low concentrations of the sulfhydryl reagent dithiothreitol (DTT) for one hour at the end of the dark period led to post-translational redox-activation of ADP-glucose pyrophosphorylase and major alterations in leaf carbon partitioning, including an increased flux into major respiratory pathways, starch- cell-wall-, and amino-acid synthesis and a reduced flux to sucrose. This was accompanied by a decrease in the levels of hexose-phosphates, while metabolites in the second half of the TCA cycle and various amino acids increased, indicating a stimulation of anaplerotic fluxes reliant on α-ketoglutarate. There was also an increase in shikimate as a precursor of secondary plant products and marked changes in the levels of the minor sugars involved in ascorbate synthesis and cell wall metabolism. Transcript profiling revealed a relatively small number of changes in the levels of transcripts coding for components of redox-regulation, transport processes and cell wall, protein and amino acid metabolism, while there were no major alterations in transcript levels coding for enzymes involved in central metabolic pathways. These results provide a global picture of the effect of redox and reveal the utility of transcript and metabolite profiling as systemic strategies to uncover the occurrence of redox-modulation in vivo. Experiment Overall Design: Leaf discs were incubated with or without 5mM DTT for one hour to affect the redox status of the cells. The effect of this treatment on global gene expression was analysed using affymetrix ATH1 microarrays. The experiments contains one control (-DTT) and one treatment (+DTT) and is performed with 2 biological replicas.
2008-06-12 | E-GEOD-4021 | biostudies-arrayexpress
Project description:This dataset includes 2*76bp RNA-seq reads from 9 pigs sequenced using Illumina NextSeq500.
| EGAD00001009783 | EGA
Project description:A bile metabolite atlas reveals infection-triggered interorgan mediators of intestinal homeostasis and defense
| PRJNA943516 | ENA
Project description:Pseudomonas species thrive in different nutritional environments and can catabolize divergent carbon substrates. These capabilities have important implications for the role of these species in natural and engineered carbon processing. However, the metabolic phenotypes enabling Pseudomonas to utilize mixed substrates remain poorly understood. This work is part of a multi-omics approach involving stable isotope tracers, metabolomics, fluxomics, and proteomics in Pseudomonas putida KT2440 to investigate the constitutive metabolic network that achieves co-utilization of glucose and benzoate, respectively. The data used to estimate the changes in protein abundance are deposited here and were found to partially predicted the metabolic flux changes in cells grown on the glucose:benzoate mixture versus on glucose alone. Notably, flux magnitude and directionality were also maintained by metabolite levels and regulation of phosphorylation of key metabolic enzymes.
2021-09-08 | PXD013605 | Pride