Ontology highlight
ABSTRACT:
PROVIDER: PRJNA689700 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13378166_1.fastq.gz | Fastqsanger.gz | |||
| SRR13378166_2.fastq.gz | Fastqsanger.gz | |||
| SRR13378167.fastq.gz | Fastqsanger.gz | |||
| SRR13378168.fastq.gz | Fastqsanger.gz | |||
| SRR13378169.fastq.gz | Fastqsanger.gz |
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Project description:The purpose of this study was to quantify the effects of basal leaf removal applied in Sangiovese cultivar at two different phonological stages, pre-bloom and veraison, on berry composition. As very few papers were published about the regulation of gene expression induced by vineyard management techniques, we report the first global transcriptomic analysis (integrated with agronomic and biochemical data) aiming to determine the molecular mechanisms that control Sangiovese berry composition. The comparison of gene expression profiles of defoliated vines at pre-bloom and at veraison with the control, revealed a common transcriptional response at the end of veraison in both treated berries, but also a more extensive transcriptome rearrangement in pre-bloom defoliated ones, which could be linked to the strong biochemical changes detected in the berry after pre-bloom veraison. Total RNA recovered from a pool of berries derived from three control plants (C) was compared to total RNA from a pool of berries derived from three defoliated vines at pre-bloom (PB, JD 147,6 basal leaves and relative laterals removed from each shoot) and three defoliated vines at veraison (V, JD 211,6 basal leaves and relative laterals removed from each shoot) at beginning of veraison (BV), end of veraison (EV) and harvest (H). For each sampling date microarray analyses were conducted for three different biological replicates for treatment.
2013-03-08 | E-GEOD-40487 | biostudies-arrayexpress
Project description:The purpose of this study was to quantify the effects of basal leaf removal applied in Sangiovese cultivar at two different phonological stages, pre-bloom and veraison, on berry composition. As very few papers were published about the regulation of gene expression induced by vineyard management techniques, we report the first global transcriptomic analysis (integrated with agronomic and biochemical data) aiming to determine the molecular mechanisms that control Sangiovese berry composition. The comparison of gene expression profiles of defoliated vines at pre-bloom and at veraison with the control, revealed a common transcriptional response at the end of veraison in both treated berries, but also a more extensive transcriptome rearrangement in pre-bloom defoliated ones, which could be linked to the strong biochemical changes detected in the berry after pre-bloom veraison.
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Project description:Ecological Drivers of Fungal Diversity are Context Specific
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Project description:This dataset was gene expression from natural sockeye salmon populations used to test the preservation of coexpression networks that were found in lake whitefish. Here is the abstract of the manuscript:BackgroundM-BM- : A functional understanding of processes involved in adaptive divergence is one of the awaiting opportunities afforded by high throughput transcriptomic technologies. Functional analysis of co-expressed genes has succeeded in the biomedical field in identifying key drivers of disease pathways. However, in ecology and evolutionary biology, functional interpretation of transcriptomic data is still limited. ResultsM-BM- : Here we used Weighted Gene Co-Expression Network Analysis (WGCNA) to identify modules of co-expressed genes in muscle and brain tissue of a lake whitefish backcross progeny. Modules were connected to gradients of known adaptive traits involved in the ecological speciation process between benthic and limnetic ecotypes. Key drivers, i.e. hub genes of functional modules related to reproduction, growth, and behavior were identified, and module preservation was assessed in natural populations. Using this approach, we identified modules of co-expressed genes involved in phenotypic divergence and their key drivers, and further characterized the underlying regulatory structure governing these complex traits. ConclusionsM-BM- : Functional analysis of transcriptomic data can significantly contribute to the understanding of the mechanisms underlying ecological speciation. Our findings point to BMP and Calcium signaling as common pathways involved in coordinated evolution of trophic behavior, trophic morphology (gill rakers), and reproduction. Results also point to housekeeping pathways implicating hemoglobins and constitutive stress response (HSP70) governing growth in lake whitefish. Here are 49 female sockeye salmon transcriptomes as measured by the 16k cGRASP microarray.
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2008-02-08 | E-GEOD-10119 | biostudies-arrayexpress