RNA-Sequencing of onion bulbs exposed to managed stress
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1084777 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28242903_1.fastq.gz | Fastqsanger.gz | |||
| SRR28242903_2.fastq.gz | Fastqsanger.gz | |||
| SRR28242904_1.fastq.gz | Fastqsanger.gz | |||
| SRR28242904_2.fastq.gz | Fastqsanger.gz | |||
| SRR28242905_1.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 in response to managed stress under field conditions using transcriptome profiling (RNA-seq). The clean reads were aligned to the reference genome (a doubled haploid onion line DHCU066619 (https://www.oniongenome.wur.nl/) and the transcriptions assembly. The read count for every transcript was determined from the findings of the mapping process. Genes identified as differentially expressed genes (DEGs) had an adjusted P-value <0.05 and an absolute log2FC ≥0, as determined by DESeq2. Transcriptomic analysis of onion bulb tissue (variety Matahari) in response to nitrogen stress under optimal water identified 3092 and 2204 Differentially Expressed Genes (DEGs) unique genes under optimal nitrogen vs low nitrogen. while under sub-optimal nitrogen, 2770 and 2198 unique genes were identified under optimal nitrogen vs low nitrogen respectively.
2025-03-04 | GSE260985 | GEO
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)
2025-02-28 | GSE260624 | GEO
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.
2012-01-15 | GSE28159 | GEO
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).
2012-01-15 | E-GEOD-28159 | biostudies-arrayexpress
Project description:RNA-Sequencing of onion bulbs inoculated with Salmonella
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Project description:Onion is regarded as non-climacteric. In onion, ethylene can suppress sprouting however, the ethylene binding inhibitor, 1-MCP can also suppress sprout growth although it is unknown how ethylene and 1-MCP elicit the same response. In this study, onion bulbs were treated with 10 μL L-1 ethylene or 1 μL L-1 1-MCP individually or in combination for 24 h at 20°C before or after curing (six weeks) at 20 or 28°C then stored at 1°C. Following curing, a subset of these same onion bulbs was stored separately under continuous air or ethylene (10 μL L-1) at 1°C
2011-06-29 | GSE27132 | GEO
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).
2025-02-28 | GSE260691 | GEO
Project description:Onion is regarded as non-climacteric. In onion, ethylene can suppress sprouting however, the ethylene binding inhibitor, 1-MCP can also suppress sprout growth although it is unknown how ethylene and 1-MCP elicit the same response. In this study, onion bulbs were treated with 10 μL L-1 ethylene or 1 μL L-1 1-MCP individually or in combination for 24 h at 20°C before or after curing (six weeks) at 20 or 28°C then stored at 1°C. Following curing, a subset of these same onion bulbs was stored separately under continuous air or ethylene (10 μL L-1) at 1°C Six treatments were chosen for microarray analysis; four samples were taken before curing immediately after treatment with ethylene or 1-MCP or ethylene and 1-MCP in combination for 24 h at 20°C. The other two samples and two were taken at the end of storage following 6 weeks curing at 28°C andafter 29 weeks cold storage (1°C) in continuous air or continuous ethylene totalling 35 weeks storage. The four pre-curing samples used were untreated (control) or treated with EB, MB or EMB and the two samples after storage were control bulbs stored in continuous ethylene or air at 1°C. There were three biological replicates of each of the six treatments making 18 samples in total.
2011-06-29 | E-GEOD-27132 | biostudies-arrayexpress
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.
2016-09-16 | GSE83893 | GEO
Project description:Rat small intestine precision cut slices were exposed for 6 hours to in vitro digested yellow (YOd) or white onion extracts (WOd) that was followed by transcriptomics analysis. The digestion was performed to mimic the digestion that in vivo takes place in the saliva, stomach and small intestine. A main question was to which extent the outcome of the biological interpretation of the transcription analysis (pathway analysis) depend on the model used. One outcome was that mainly processes related to oxidative stress, and especially the Keap1-Nrf2 pathway, were affected by onions in all three models.
2016-09-29 | E-MTAB-5120 | biostudies-arrayexpress