Metagenome representing 10 spiked-in bacteria
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA495173 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8135080_1.fastq.gz | Fastqsanger.gz | |||
| SRR8135080_2.fastq.gz | Fastqsanger.gz | |||
| SRR8135090_1.fastq.gz | Fastqsanger.gz | |||
| SRR8135090_2.fastq.gz | Fastqsanger.gz | |||
| SRR8135100_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 105 |
Similar Datasets
Project description:Aim: Test the hypothesis that 5HT receptors (5HTRs) signaling contributes to MVP pathophysiology. Methods and results: MV RNA was used for microarray analysis of MVP patients versus control, highlighting genes that indicate the involvement of 5HTR pathways and extracellular matrix remodeling in MVP. These canine MVP leaflets (N=5/group) showed 5HTR2B upregulation. Conclusion: In humans, MVP is associated with an upregulation in 5HTR2B expression and increased 5HT receptor signaling in the leaflets. 5HTR signaling is involved not only in previously reported 5HTrelated valvulopathies, but it is also involved in the pathological remodeling of MVP.
2018-01-29 | GSE109744 | GEO
Project description:In contrast to mammals, the adult zebrafish hearts can regenerate within a short period. Upregulation of major vault protein (Mvp) expression after ventricle resection. To determine the impact of loss of mvp on transcriptome during heart regeneration, we pursued transcriptome analysis (RNA-Seq) on wild type and mvp mutant zebrafish hearts at 7 day-post-amputation.
2020-09-01 | GSE157170 | GEO
Project description:Increasing concern about pollution of our environment calls for advanced and rapid methods to estimate ecological toxicity. The use of gene expression microarrays in environmental studies can potentially meet this challenge. We present a novel method to examine soil toxicity. We exposed the collembolan Folsomia candida to soil containing an ecologically relevant cadmium concentration, and found a cumulative total of 1586 differentially expressed transcripts across three exposure durations, including transcripts involved in stress response, detoxification, and hypoxia. Additional enrichment analysis of gene ontology (GO) terms revealed that antibiotic biosynthesis is important at all time points examined. Interestingly, genes involved in the "penicillin and cephalosporin biosynthesis pathway" have never been identified in animals before, but are expressed in F. candida’s tissue. The synthesis of antibiotics can possibly be a response to increased cadmium-induced susceptibility to invading pathogens, which might be caused by repression of genes involved in the immune-system (C-type lectins and Toll receptor). This study presents a first global view on the environmental stress response of an arthropod species exposed to contaminated soil,and provides a mechanistic basis for the development of a gene expression soil quality test. Keywords: cadmium, soil, Collembola, environmental genomics
2008-08-08 | GSE11122 | GEO
Project description:The maintained vegetative phase (mvp) mutant has a non-flowering phenotype caused by deletions including, but not limited to, the genes CYS, PHYC and VRN1. However the impact of these deletions on flowering genes and global gene expression is still unknown. In this study, we showed that these deletions caused the up-regulation of several pathogenesis related (PR) and jasmonate responsive genes using microarray analysis. Our results raise the hypothesis that jasmonates may be involved in flowering. To confirm this hypothesis, the methyl-jasmonate (MeJA) and jasmonic acid (JA) content in mvp and wild type plants was measured. The content of JA was comparable in all plants while the content of MeJA was higher in mvp plants. Our transcriptomic and chemical analyses of the mvp mutants plants reveal that the deletion of the major vernalization gene TaVRN1 induces the up-regulation of the major biotic stress related genes and the accumulation of MeJA. In addition, our results demonstrate an important role of MeJA during vernalization and flowering in wheat. A total of 3 biological replicates (R1, R2 and R3) for each condition (wild type (control) and mvp mutant (mutant) ) were used for microarray analyses. Each biological replicate sample was obtained by pooling three wild type plants (control) or five mvp plants (mutant) from different plants harvested randomly. The different biological samples of einkorn spring wheat whole aerial part were ground in dry ice to fine powder and total RNA was extracted with trizol (Invitrogen, Burlington, ON, CA). Total RNA was cleaned using RNeasy plant mini kit (Qiagen) and integrity was determined on agarose gel and on a bioanalyser (Agilent 2100). Synthesized cDNAs were transcribed to cRNAs with the 3M-bM-^@M-^YIVT labelling kit (Santa Clara, CA, USA) and hybridized to the Affymetrix wheat genome array (Santa Clara, Ca, USA) at the McGill University and GM-CM-)nome QuM-CM-)bec Innovation Centre (Montreal, Qc, CA). The experimental design consisted of three biological replicates for each of the two conditions, 1: The einkorn wheat (Triticum monococcum L. 2n = 2x = 14, AmAm) wild type plants (control) and 2: the mvp plants (mutant). Thus, a total of 3 biological samples from each of the two conditions described above were used for hybridizations.
2014-05-02 | E-GEOD-50882 | biostudies-arrayexpress
Project description:Using mouse genetic studies and systematic assessments of brain neuroanatomical phenotypes, we set out to identify which of the 30 genes causes brain defects at the autism-associated 16p11.2 locus. We show that multiple genes mapping to this region interact to regulate brain anatomy, with female mice exhibiting far fewer brain neuroanatomical phenotypes. In male mice, among the 13 genes associated with neuroanatomical defects (Mvp, Ppp4c, Zg16, Taok2, Slx1b, Maz, Fam57b, Bola2, Tbx6, Qprt, Spn, Hirip3 and Doc2a), Mvp is the top driver implicated in phenotypes pertaining to brain, cortex, hippocampus, ventricles and corpus callosum sizes. The major vault protein (MVP), the main component of the vault organelle, is a conserved protein found in eukaryotic cells, yet its function is not understood. Here, we find MVP expression highly specific to the limbic system and show that Mvp regulates neuronal morphology, postnatally and specifically in males. We also recapitulate a previously reported genetic interaction and show that Mvp+/-;Mapk3+/- mice exhibit behavioral deficits, notably decreased anxiety-like traits detected in the elevated plus maze and open field paradigms. Our study highlights multiple gene drivers in neuroanatomical phenotypes, interacting with each other through complex relationships. It also provides the first evidence for the involvement of the major vault protein in the regulation of brain size and neuroanatomy, specifically in male mice.
2023-09-15 | GSE243261 | GEO
Project description:Gut microbiome research is rapidly moving towards the functional characterization of the microbiota by means of shotgun meta-omics. Here, we selected a cohort of healthy subjects from an indigenous and monitored Sardinian population to analyze their gut microbiota using both shotgun metagenomics and shotgun metaproteomics. We found a considerable divergence between genetic potential and functional activity of the human healthy gut microbiota, in spite of a quite comparable taxonomic structure revealed by the two approaches. Investigation of inter-individual variability of taxonomic features revealed Bacteroides and Akkermansia as remarkably conserved and variable in abundance within the population, respectively. Firmicutes-driven butyrogenesis (mainly due to Faecalibacterium spp.) was shown to be the functional activity with the higher expression rate and the lower inter-individual variability in the study cohort, highlighting the key importance of the biosynthesis of this microbial by-product for the gut homeostasis. The taxon-specific contribution to functional activities and metabolic tasks was also examined, giving insights into the peculiar role of several gut microbiota members in carbohydrate metabolism (including polysaccharide degradation, glycan transport, glycolysis and short-chain fatty acid production). In conclusion, our results provide useful indications regarding the main functions actively exerted by the gut microbiota members of a healthy human cohort, and support metaproteomics as a valuable approach to investigate the functional role of the gut microbiota in health and disease.
2017-07-19 | PXD005780 | Pride
Project description:SREBP2 controls the expression of enzymes involved in the mevalonate pathway (MVP), a biosynthetic process that drives the synthesis of dolichol, heme A, ubiquinone and cholesterol but also provides substrates for protein prenylation, and that is frequently deregulated in cancer. We show here that SREBP2 is a novel substrate for the deubiquitinating enzyme USP28 and that USP28 regulates SREBP2 stability independent of FBXW7. Inhibition of USP28 reduces MVP activity and renders cancer cells highly sensitive to MVP inhibition by statins. Moreover, statin sensitivity of USP28 depleted cells was rescued by the addition of geranyl-geranyl-pyrophosphate, a substrate for protein prenylation. We also provide evidence that SREBP2 participates in the regulation of gene expression signature associated with squamous cell carcinoma (SCC) and that SREBP2 and enzymes of the MVP are overexpressed in SCC from different tissue origins. Finally, deletion of SREBP2 attenuated tumour growth in a mouse model of lung cancer. Our findings suggest that SREBP2 is a novel substrate for USP28 and that combinatorial targeting of the MVP together with USP28 inhibition could be a therapeutic strategy for the treatment of squamous cell carcinomas.
2023-05-16 | GSE204703 | GEO
Project description:This project contains raw data, intermediate files and results is a re-analysis of the publicly available dataset from the PRIDE dataset PXD005780. The RAW files were processed using ThermoRawFileParser, SearchGUI and PeptideShaker through standard settings (see ‘Data Processing Protocol’). This reanalysis work is part of the MetaPUF (MetaProteomics with Unknown Function) project, which is a collaboration between EMBL-EBI and the University of Luxembourg. The dataset was selected with the following conditions: 1. It has been made publicly available in PRIDE and focuses on metaproteomics of the human gut; 2. The corresponding metagenomics assemblies were also available from ENA (European Nucleotide Archive) or MGnify. The processed peptide reports for each sample are available to view at the contig level on the MGnify website. In total, the reanalysis identified 15,417 unique proteins from 15 samples.
2022-05-04 | PXD032303 | Pride
Project description:The maintained vegetative phase (mvp) mutant has a non-flowering phenotype caused by deletions including, but not limited to, the genes CYS, PHYC and VRN1. However the impact of these deletions on flowering genes and global gene expression is still unknown. In this study, we showed that these deletions caused the up-regulation of several pathogenesis related (PR) and jasmonate responsive genes using microarray analysis. Our results raise the hypothesis that jasmonates may be involved in flowering. To confirm this hypothesis, the methyl-jasmonate (MeJA) and jasmonic acid (JA) content in mvp and wild type plants was measured. The content of JA was comparable in all plants while the content of MeJA was higher in mvp plants. Our transcriptomic and chemical analyses of the mvp mutants plants reveal that the deletion of the major vernalization gene TaVRN1 induces the up-regulation of the major biotic stress related genes and the accumulation of MeJA. In addition, our results demonstrate an important role of MeJA during vernalization and flowering in wheat.
2014-05-02 | GSE50882 | GEO