Onion WGS sequencing and Assembly
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB29505 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| ERR5263020_1.fastq.gz | Fastqsanger.gz | |||
| ERR5263020_2.fastq.gz | Fastqsanger.gz | |||
| ERR5263190_1.fastq.gz | Fastqsanger.gz | |||
| ERR5263190_2.fastq.gz | Fastqsanger.gz |
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Project description:The goal of this study was to compare differentially expressed transcripts in onion bulbs induced when inoculated with Salmonella using transcriptome profiling (RNA-seq) .Transcriptomic analysis of onion bulb tissue (Variety Don Victor) in response to Salmonella was performed 24 hours and 7 days post-inoculation to identify Differentially Expressed Genes (DEGs) in onion. Within 24 hours of inoculation, 4259 genes were upregulated while 3393 genes were downregulated. After 7 days, 8213 and 6417 genes were up and down-regulated, respectively, as shown below. (FDR<0.05 and Abs (log 2(Y/X) >0)
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Project description:- A de novo onion transcriptome was developed to investigate dormancy transition. Transcriptome and phytohormone changes associated with ethylene-induced onion bulb dormancy
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Project description:This study aimed to compare differentially expressed transcripts in Salmonella recovered from the inoculated onion bulbs using transcriptome profiling (RNA-seq). The Salmonella strains of Salmonella enterica subsp. enterica ser. Newport, isolated from clinical cases affected by the onion-linked outbreak in 2020 (CDC, 2020), was used for the onion bulb inoculation. Transcriptomic analysis of Salmonella was performed 1 day (24 hours) and 7 days post-inoculation to identify Differentially Expressed Genes (DEGs) . 925 and 736 genes were upregulated within 24 hours and seven days after inoculation, while the number of downregulated genes in the same timeframe was 690 and 826, respectively (FDR<0.05 and Abs (log 2(Y/X) >0).
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Project description:Physiological and biochemical changes occur in onion (Allium cepa L.) bulbs during the transition from dormancy to sprout suppression and subsequent sprout growth. These include changes in the concentrations of flavor compounds, carbohydrates, mineral elements and plant growth regulators (PGRs). Detailed analyses of these changes and the impact of different post-harvest techniques, designed to prolong storage life, have not been undertaken. We developed the first onion oligonucleotide microarray to determine differential gene expression in onion during curing and storage, with transcriptional changes supporting biochemical and physiological analyses.
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Project description:Background: Human intestinal tissue samples are barely accessible to study potential health benefits of nutritional compounds. Numbers of animals used in animal trials, however, need to be minimalized. Therefore, in this study we explored the applicability of an in vitro model, namely human intestinal Caco-2 cells, to study the effect of food compounds on (intestinal) health. In vitro digested yellow (YOd) and white onion extracts (WOd) were used as model food compounds and transcriptomics was applied to obtain more insight into their mode of actions in the intestinal cells. Methods: Caco-2 cells were incubated with in vitro digested onion extracts for 6 hours, total RNA was extracted and Affymterix Human Gene 1.1 ST arrays were used to analyze the gene expression profiles. To identify onion-induced gene expression profiles in Caco-2 cells, digested yellow onion and white onion samples were compared to a digest control samples. Results: We found that yellow onion (n=5586, p<0.05) had a more pronounced effect on gene expression than white onion (n=3688, p<0.05). However, a substantial number of genes (n=3281, p<0.05) were affected by both onion variants in the same direction. Pathway analyses revealed that mainly processes related to oxidative stress, and especially the Keap1-Nrf2 pathway, were affected by onions. Our data fit with previous in vivo studies showing that the beneficial effects of onions are mostly linked to their antioxidant properties. Conclusion: our data indicate that the in vitro Caco-2 intestinal model can be used to determine modes of action of nutritional compounds and can thereby reduce the number of animals used in conventional nutritional intervention studies.
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Project description:Physiological and biochemical changes occur in onion (Allium cepa L.) bulbs during the transition from dormancy to sprout suppression and subsequent sprout growth. These include changes in the concentrations of flavor compounds, carbohydrates, mineral elements and plant growth regulators (PGRs). Detailed analyses of these changes and the impact of different post-harvest techniques, designed to prolong storage life, have not been undertaken. We developed the first onion oligonucleotide microarray to determine differential gene expression in onion during curing and storage, with transcriptional changes supporting biochemical and physiological analyses. Samples of RNA were prepared from onions of two cultivars, ‘Wellington’ (brown, long-storing) and ‘Sherpa’ (brown, average-storing), grown according to normal commercial practice at various physiological ages, viz, freshly harvested, cured, pre-sprouting and sprouting. Three biological replicates for each time (harvest, cured, before sprouting, sprouting), curing temperature (20, 28°C) and cultivar (Wellington, Sherpa) combination (n = 42).
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