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Dipterocarpaceae

ABSTRACT: RNAseq for calyx development in Dipterocarpaceae

PROVIDER: PRJDB8182 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR175058_1.fastq.gz	Fastqsanger.gz
	DRR175058_2.fastq.gz	Fastqsanger.gz
	DRR175059_1.fastq.gz	Fastqsanger.gz
	DRR175059_2.fastq.gz	Fastqsanger.gz
	DRR175060_1.fastq.gz	Fastqsanger.gz

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Candidate proteins involved in the calyx abscission process of ‘Kuerlexiangli’ (Pyrus sinkiangensis Yu) identified by iTRAQ analysis

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

Foodomics study on the anti-proliferative activity mechanisms on HT-29 colon cancer cells in response to golden berry (Physalis peruviana L.) calyx extracts

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

Expression profiles of globular bushy cells (GBCs) during maturation

2014-06-24 | GSE49599 | GEO

Transcriptional profiling of calyx abscission zone cells of citrus fruits and adjacent fruit rind cells during ethylene-promoted fruit abscission

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

Expression profiles of globular bushy cells (GBCs) during maturation

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). We identified GBCs by stereotaxic injection of fluorescently labelled retrograde tracer Cholera toxin B into the contralateral MNTB of anesthetized rats. Animals were sacrificed 24h after injection, the brain was taken out and flash frozen. 12um thick brainstem cryosections were prepared and 200 fluorescently labelled GBCs per animal were excised from the VCN using laser microdissection. Cells were collected from 6 animals at P3 (synapse formation), 9 animals at P8 (juvenile synapse) and 5 animals at P21 (mature synapse). RNA was isolated from the collected cells and linearly amplified in order to perform cell-type specific expression profiling.

2014-06-24 | E-GEOD-49599 | biostudies-arrayexpress

Calyx sp. metagenome

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Discodermia

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Dipterocarpaceae NGS