E-MTAB-4278
Ontology highlight
ABSTRACT:
TISSUE(S): Fruit, Seed, Pericarp
PROVIDER: E-MTAB-4278 | ExpressionAtlas | 2020-06-22
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-MTAB-4278-analysis-methods.tsv | Tabular | |||
| E-MTAB-4278-atlasExperimentSummary.Rdata | Rdata | |||
| E-MTAB-4278-coexpressions.tsv.gz | Tabular | |||
| E-MTAB-4278-configuration.xml | Xml | |||
| E-MTAB-4278-factors.xml | Xml |
Items per page: 5 1 - 5 of 26 |
Similar Datasets
Project description:MicroRNAs (miRNAs) are a class of non-coding RNA molecules which have significant gene regulation roles in organisms. The advent of new high throughput sequencing technologies has enabled the revelation of novel miRNAs. Although there are two recent reports on high throughput sequencing analysis of small RNA libraries from different organs of two grapevine wine varieties, there were significant divergence in the number and kinds of miRNAs sequenced in these studies. More sequencing of small RNA libraries is still important for the discovery of novel miRNAs in grapevine. Here, we initially constructed a small RNA library of flower and fruit tissues of a table grapevine cultivar ‘Summer Black’ and performed sequencing and analysis of sRNAs using the Illumina Solexa platform, expecting to discover more miRNAs related to the development of grapevine flowers and berries and the formation of dessert quality in grapevine berries. Totally, 130 conserved grapevine miRNA (Vv-miRNA) belonging to 28 Vv-miRNA families were validated, and 92 novel potential grapevine-specific ones representing 80 unique ones were first discovered. Forty-two (48.84%) of the novel miRNAs possessed differential semi-quantitative PCR expression profiles in various grapevine tissues that could further confirm their existence in the grapevine, among which twenty were expressed only in grapevine berries, indicating some fruit-specificity. 130 target genes for 46 novel miRNAs could be predicted. The locations of these potential target genes on grapevine chromosomes and their complementary levels with the corresponding miRNAs were also analyzed.
2013-10-05 | GSE24531 | GEO
Project description:MicroRNAs (miRNAs) are a class of non-coding RNA molecules which have significant gene regulation roles in organisms. The advent of new high throughput sequencing technologies has enabled the revelation of novel miRNAs. Although there are two recent reports on high throughput sequencing analysis of small RNA libraries from different organs of two grapevine wine varieties, there were significant divergence in the number and kinds of miRNAs sequenced in these studies. More sequencing of small RNA libraries is still important for the discovery of novel miRNAs in grapevine. Here, we initially constructed a small RNA library of flower and fruit tissues of a table grapevine cultivar M-bM-^@M-^XSummer BlackM-bM-^@M-^Y and performed sequencing and analysis of sRNAs using the Illumina Solexa platform, expecting to discover more miRNAs related to the development of grapevine flowers and berries and the formation of dessert quality in grapevine berries. Totally, 130 conserved grapevine miRNA (Vv-miRNA) belonging to 28 Vv-miRNA families were validated, and 92 novel potential grapevine-specific ones representing 80 unique ones were first discovered. Forty-two (48.84%) of the novel miRNAs possessed differential semi-quantitative PCR expression profiles in various grapevine tissues that could further confirm their existence in the grapevine, among which twenty were expressed only in grapevine berries, indicating some fruit-specificity. 130 target genes for 46 novel miRNAs could be predicted. The locations of these potential target genes on grapevine chromosomes and their complementary levels with the corresponding miRNAs were also analyzed. Size fractionated small RNAs (16-30 bp) from total RNA extracts was ligated to 5' and 3' adapters, and reverse transcribed. After PCR amplification the sample was subjected to Solexa sequencing. The resultant 35nt sequence data were filtered according to base quality value. The remained sequences were used to trim 5' and 3' adaptors. The clean tags were used for further analysis.
2013-10-05 | E-GEOD-24531 | biostudies-arrayexpress
Project description:Full transcriptomes of the Botrytis cinerea wild-type strain B0510 inoculated on mature grapevine berries (Marselan cultivar) at 16h, 24h, 48h, and in vitro were compared to identify B. cinerea genes diffentially expressed during the infection stages.
2015-08-10 | GSE65559 | GEO
Project description:MicroRNAs (miRNAs) play a important part in post-transcriptional gene regulation and have been shown to control many genes involved in various biological and metabolic processes. There have been extensive studies to discover miRNAs and analyze their functions in model plant species, such as Arabidopsis and rice and other plants. However, the number of miRNAs discovered in grape is relatively low and little is known about miRNAs responded gibberellin during fruit germination. In this study, a small RNA library from gibberellin grape fruits was sequenced by the high throughput sequencing technology. A total of 16,033,273 reads were obtained. 812,099 total reads representing 1726 unique sRNAs matched to known grape miRNAs. Further analysis confirmed a total of 149 conserved grapevine miRNA (Vv-miRNA) belonging to 27 Vv-miRNA families were validated, and 74 novel potential grapevine-specific miRNAs and 23 corresponding novel miRNAs* were discovered. Twenty-seven (36.5%) of the novel miRNAs exhibited differential QRT-PCR expression profiles in different development gibberellin-treated grapevine berries that could further confirm their existence in grapevine. QRT-PCR analysis on transcript abundance of 27 conserved miRNA family and the new candidate miRNAs revealed that most of them were differentially regulated by the gibberellin, with most conserved miRNA family and 26 miRNAs being specifically induced by gibberellin exposure. All novel sequences had not been earlier described in other plant species. In addition, 117 target genes for 29 novel miRNAs were successfully predicted. Our results indicated that miRNA-mediated gene expression regulation is present in gibberellin-treated grape berries. This study led to the confirmation of 101 known miRNAs and the discovery of 74 novel miRNAs in grapevine. Identification of miRNAs resulted in significant enrichment of the gibberellin of grapevine miRNAs and provided insights into miRNA regulation of genes expressed in grape berries. GSM604831 is the control for the gibberellin-treated sample. The mixture samples of young berries (one week after flowering) large berries (five week after flowering after flowering), and old berries (nine week after flowering) treated with gibberellin, respectively, were generated by deep sequencing, in triplicate, using Illumina 1G Genome Analyzer.
2013-10-05 | E-GEOD-39734 | biostudies-arrayexpress
Project description:We report the application of Illumina mRNA sequencing technology for high-throughput profiling of the transcriptome of a seeded wine cultivar (wild-type) and its seedless somatic variant (mutant), sampled at three key growth stages of grapevine:Â E-L 15 (single flowers in compact groups), E-L 27 (young berries enlarging) and E-L 38 (berries harvest-ripe). By obtaining over 126 to 143 million and 102 to 127 million reads of 100-bp in length for the wild-type and mutant respectively, we have for the first time provided a holistic view of the transcriptional landscape during seed development in both phenotypes. We found that comparison of differentially expressed (DE) genes, gene patterns and gene enrichment between the wild-type and mutant distinguished transcriptional events in the two lines. For example, differential expression analysis in the pairwise comparison between developmental stages identified DE genes specific to the wild-type background, DE genes specific to the mutant background and DE genes commonly shared in both backgrounds. The analysis of differential expression patterns and functional category enrichment of DE genes highlighted specific and common significant coordination and enrichment of various biological processes during seed development which have lead to the identification of candidate genes for seedlessness that have altered expression in wild-type and mutant. In conclusion, we have shown here a logical approach to identify possible regulators and processes required for normal seed development that may be altered in the seedless phenotype, and highlighted the importance of somatic variants as a resources. Examination of absolute expression count for every gene at three key time-points in a seeded grapevine variety and its seedless somatic variant.
2014-12-31 | E-GEOD-58061 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) play a important part in post-transcriptional gene regulation and have been shown to control many genes involved in various biological and metabolic processes. There have been extensive studies to discover miRNAs and analyze their functions in model plant species, such as Arabidopsis and rice and other plants. However, the number of miRNAs discovered in grape is relatively low and little is known about miRNAs responded gibberellin during fruit germination. In this study, a small RNA library from gibberellin grape fruits was sequenced by the high throughput sequencing technology. A total of 16,033,273 reads were obtained. 812,099 total reads representing 1726 unique sRNAs matched to known grape miRNAs. Further analysis confirmed a total of 149 conserved grapevine miRNA (Vv-miRNA) belonging to 27 Vv-miRNA families were validated, and 74 novel potential grapevine-specific miRNAs and 23 corresponding novel miRNAs* were discovered. Twenty-seven (36.5%) of the novel miRNAs exhibited differential QRT-PCR expression profiles in different development gibberellin-treated grapevine berries that could further confirm their existence in grapevine. QRT-PCR analysis on transcript abundance of 27 conserved miRNA family and the new candidate miRNAs revealed that most of them were differentially regulated by the gibberellin, with most conserved miRNA family and 26 miRNAs being specifically induced by gibberellin exposure. All novel sequences had not been earlier described in other plant species. In addition, 117 target genes for 29 novel miRNAs were successfully predicted. Our results indicated that miRNA-mediated gene expression regulation is present in gibberellin-treated grape berries. This study led to the confirmation of 101 known miRNAs and the discovery of 74 novel miRNAs in grapevine. Identification of miRNAs resulted in significant enrichment of the gibberellin of grapevine miRNAs and provided insights into miRNA regulation of genes expressed in grape berries. GSM604831 is the control for the gibberellin-treated sample.
2013-10-05 | GSE39734 | GEO
Project description:Purpose: High throughput sequencing technologies provide a unique opportunity to deeply investigate the molecular mechanisms involved in plant-pathogen interaction. Botrytis cinerea, is the agent of grapevine grey mould, but in yet uncharacterized environmental conditions, a latent infection can occur determining favourable metabolic and physico-chemical berry modifications which possibly contribute to the typical aromas of “passito” wines (“noble rot”). The present project aims at the identification of the genes deployed by B. cinerea during grape berries colonization in the latent form, in comparison with the saprophytic growth in vitro. Methods: A total of 300 healthy berries have been artificially inoculated one by one with B. cinerea by injecting conidia under berry skin, in controlled conditions, reproducing the pourri plein stage of noble rot. Control samples (300 berries) have been inoculated with water. The saprophytic growth was obtained in liquid nutrient medium in laboratory flasks, and the mycelium collected by filtration. The RNA-sequencing experiments on healthy or infected samples in biological triplicate resulted in 27 data sets to be analyzed (Illumina NextSeq500 paired-end sequencing; 533.779.730 total reads, 150 Gb of data). Conclusions: This work identified important molecular mechanisms involved in Botrytis cinerea colonization of grapevine berries during the noble rot infection.
2019-07-26 | GSE116274 | GEO
Project description:The goal of this project aims to decipher the molecular effects of high temperature on developing Cabernet Sauvignon berries. Using grapevine fruiting cuttings, control and heat-treated berries were sampled to conduct transcriptomic, proteomic and metabolomic analysis.
2020-01-29 | PXD014693 | Pride
Project description:To understand the fruit changes and mechanisms involved in the compatible grapevine-virus interaction, we analyzed the berry transcriptome in two stages of development (veraison and ripening) in the red wine cultivar Cabernet Sauvignon infected with Grapevine leaf-roll-associated virus-3 (GLRaV-3). Analysis of global gene expression patterns indicate incomplete berry maturation in infected berries as compared to uninfected fruit suggesting viral infection interrupts the normal berry maturation process. PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Andrea Vega. The equivalent experiment is VV28 at PLEXdb.
2011-08-26 | GSE31660 | GEO
Project description:Full transcriptomes of the Botrytis cinerea wild-type strain B0510 inoculated on mature grapevine berries (Marselan cultivar) at 16h, 24h, 48h, and in vitro were compared to identify B. cinerea genes diffentially expressed during the infection stages. Grapevine berries were inoculated with Botrytis cinerea conidia and samples were taken at 16h, 24h and 48 hours post-inoculation. An additional control sample corresponding to mycelium growing on static liquid minimal medium was included in the experimental design in order to identify genes that would be differentially expressed between in vitro and in planta growth conditions. 3-4 replicates were performed. The 13 total-RNA samples were used for hybridization on NimbleGen 4plex gene expression arrays (20,885 gene models from Botrytis cinerea with three 60-mer probes per gene).
2015-08-10 | E-GEOD-65559 | biostudies-arrayexpress