Ontology highlight
ABSTRACT:
PROVIDER: PRJNA986224 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Physalis angulata is a medicinal plant with a high pharmaceutical value that is widely cultivated in East Asia. Lysine succinylation, a newly identified post-translational modification, is associated with various cellular processes. However, the regulatory mechanism underlying the metabolism of P. angulata is largely unknown. Here, liquid chromatography tandem-mass spectrometry combined with a high-efficiency succinyl-lysine antibody was used to identify the succinylated peptides in P. angulata. In total, 422 lysine succinylation sites in 242 proteins were identified.
2019-11-08 | PXD006778 | Pride
Project description:Different research works have described goldenberry calyx as a source of bioactive compounds, but limited information is available about its effects at the transcriptome and metabolome levels To apply a Foodomics approach to study the effects of a goldenberry calyx PLE-extract on the transcriptome and metabolome of HT-29 colon cancer cells.
2022-05-24 | GSE132855 | GEO
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of plants. The goals of this study are to compare omparatively evaluated both sequence variation and gene expression at the transcriptomic level between two species. Methods: Pooled total RNA of P. floridana flower buds and young fruits, in triplicate, using Illumina HiSeqTM 2000. The sequence reads remove reads with adaptors or unknown nucleotides larger than 5% and low-quality reads using . qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: Sequencing the Physalis transcriptome revealed 147,118 unigenes. When aligned to the tomato genome, we estimated that around 30,121 genes were expressed in the Physalis floral-fruit transcriptome, and 10,498 orthologous gene pairs were identified between P. floridana and S. pimpinellifolium.with a fold change ≥1.5 and FER value <0.001, 0.68% of the unigenes in the Physalis floral-fruit transcriptome were developmentally regulated at the floral-fruit transition, and Altered expression of 15 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Conclusions: Our study represents the first detailed analysis of floral-fruit transcriptomes, with biologic replicates, generated by RNA-seq technology.The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a organ or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
2018-12-29 | GSE92998 | GEO
Project description:‘Kuerlexiangli’ (Pyrus sinkiangensis Yu) is an important market pear in China. The shape and quality of the fruit is negatively affected by the presence of a persistent calyx. Here, to explore the molecular mechanism of calyx abscission, we designed an experiment to compare protein expression at two critical stages of the calyx abscission process under three treatments: a calyx abscising treatment (6000 × Flusilazole + 300 × PBO), a calyx persisting treatment (50 mg L−1 GA3), and a water control. We investigated the collected protein fragments using isobaric tags for relative and absolute protein quantitation (iTRAQ) to identify candidate proteins and perform relative quantification. We identified 378,078 spectra and 3,873 proteins, of which there were 2,371 differentially abundant proteins (DAPs) having Gene Ontology terms and associating with 124 defined pathways from the Kyoto Encyclopedia of Genes and Genomes. The DAPs that were correlated with calyx abscission were mainly those known to be involved in photosynthesis, plant hormone signal transduction, cell-wall modification, and carbohydrate metabolism. Quantitative real-time PCR was used to confirm the results of the digital transcript abundance measurements. Among the isolated candidate proteins, polygalacturonase and chitinase appear to play key roles during the process of calyx abscission. We identified candidate proteins that exhibit highly dynamic expression changes during the calyx abscission progress. These proteins are potential targets for future functional identification and should be valuable to explore the mechanism of the calyx abscission, and finally for the development of a method for inducing calyx abscission in fruit production based on the use of small molecules.
2020-06-17 | PXD012499 | Pride
Project description:The aim of this study was to gain insight into the molecular mechanisms of intraspecies difference of copper accumulation in Crassostrea angulata. In this attempt, we have performed a comprehensive analysis of the transcriptome of oyster (gill and mantle). Digital gene expression (DGE) technology was applied to analyze the relationships between gene expression and differential Cu body burden.
2016-06-30 | GSE65653 | GEO
Project description:Calyx of Held giant presynaptic terminals in the medial nucleus of the trapezoid body of the auditory brainstem form axosomatic synapses that have advanced to one of the best-studied synaptic system of the mammalian brain. As the auditory system matures and adjusts to high fidelity synaptic transmission, the calyx undergoes extensive structural and functional changes: it is formed around postnatal day 3 (P3), achieves immature function until hearing onset around P10 and can be considered mature from P21 onwards. This setting provides the unique opportunity to examine the repertoire of genes driving synaptic structure and function. We performed cell type-specific gene expression profiling of globular bushy cells (GBCs), the neurons giving rise to the calyx of Held, at different maturational stages (P3, P8 and P21).
2014-06-24 | GSE49599 | GEO
Project description:The aim of this study was to gain insight into the molecular mechanisms of intraspecies difference of copper accumulation in Crassostrea angulata. In this attempt, we have performed a comprehensive analysis of the transcriptome of oyster (gill and mantle). Digital gene expression (DGE) technology was applied to analyze the relationships between gene expression and differential Cu body burden. Digital gene expression (DGE) technology was applied to analyze the relationships between gene expression and differential Cu body burden
2016-06-30 | E-GEOD-65653 | biostudies-arrayexpress
Project description:Magallana angulata Transcriptome or Gene expression
| PRJNA695413 | ENA
Project description:Magallana angulata Transcriptome or Gene expression
| PRJNA80349 | ENA
Project description:Abscission is a cell separation process that takes place in particular positions of the plant body named abscission zones. In citrus, maturing fruits are shed through the calix abscission zone, which is composed by 10-15 cell layers located at the boundary between the calyx button and the fruit rind. In order to gain further insight into the molecular mechanisms involved in citrus fruit abscission, we used laser microdissection combined with microarray analysis to compare the global expression profiles of calyx abscission zone cells and adjacent fruit rind cells (control cells) at 0, 12 and 24 hours after the activation of the process with ethylene. Thus, this study allowed identifying a set of abscission zone-specifically expressed genes potentially involved in citrus fruit abscission.
2017-02-08 | E-MTAB-4538 | biostudies-arrayexpress