Ontology highlight
ABSTRACT:
PROVIDER: PRJNA593234 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10156616_subreads.fastq.gz | Fastqsanger.gz | |||
| SRR21665212_1.fastq.gz | Fastqsanger.gz | |||
| SRR21665212_2.fastq.gz | Fastqsanger.gz | |||
| SRR21665161_1.fastq.gz | Fastqsanger.gz | |||
| SRR21665161_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 22 |
Similar Datasets
Project description:We utilized three ecologically diverse Drosophila species to explore the influence of ecological adaptation on transcriptomic responses to isocaloric diets differing in their relative proportions of protein to sugar. Drosophila melanogaster, a cosmopolitan species that breeds in decaying fruit, exemplifies individuals long exposed to a Western diet higher in sugar, while the natural diet of the cactophilic D. mojavensis, is much lower in carbohydrates. Drosophila arizonae, the sister species of D. mojavensis, is largely cactophilic, but also utilizes rotting fruits that are higher in sugars than cacti. We exposed third instar larvae for 24 hours to diets either (1) high in protein relative to sugar, (2) diets with equal amounts of protein and sugar, and (3) diets low in protein but high in sugar. As we predicted, based upon earlier interspecific studies of development and metabolism, the most extreme differences in gene expression under different dietary conditions were found in D. mojavensis followed by D. arizonae. No differential expression among diets was observed for D. melanogaster, a species that survives well under all three conditions, with little impact on its metabolism. We suggest that these three species together provide a model to examine individual and population differences in vulnerability to lifestyle-associated health problems such as metabolic syndrome and diabetes.
2017-07-20 | GSE101664 | GEO
Project description:In Drosophila, adaptation to xeric environments presents many challenges, greatest among them the maintenance of water balance. Drosophila mojavensis, a cactophilic species from the deserts of North America, is one of the most desiccation-resistant in the genus, surviving low humidity primarily by reducing its metabolic rate. Genetic control of reduced metabolic rate, however, has yet to be elucidated. We utilized the recently sequenced genome of D. mojavensis to create an oligonucleotide microarray in order to pursue the identities of the genes involved in metabolic regulation during desiccation. We observed large differences in gene expression between male and female D. mojavensis as well as both quantitative and qualitative sex differences in their ability to survive xeric conditions. As expected, genes associated with metabolic regulation and carbohydrate metabolism were differentially regulated between stress treatments. Most importantly, we identified four points in central metabolism (Glyceraldehyde 3-phosphate dehydrogenase, transaldolase, alcohol dehydrogenase and phosphoenolpyruvate carboxykinase) that indicate the potential mechanisms controlling metabolic rate reduction associated with desiccation resistance. Furthermore, a large number of genes associated with vision pathways also were differentially expressed between stress treatments, especially in females, that may underlie the initial detection of stressful environments and trigger subsequent metabolic changes. Dataset from Transcriptional regulation of metabolism associated with the increased desiccation resistance of the cactophilic Drosophila mojavensis Matzkin,LM and Markow, MA, Genetics.
2010-05-21 | GSE16234 | GEO
Project description:In Drosophila, adaptation to xeric environments presents many challenges, greatest among them the maintenance of water balance. Drosophila mojavensis, a cactophilic species from the deserts of North America, is one of the most desiccation-resistant in the genus, surviving low humidity primarily by reducing its metabolic rate. Genetic control of reduced metabolic rate, however, has yet to be elucidated. We utilized the recently sequenced genome of D. mojavensis to create an oligonucleotide microarray in order to pursue the identities of the genes involved in metabolic regulation during desiccation. We observed large differences in gene expression between male and female D. mojavensis as well as both quantitative and qualitative sex differences in their ability to survive xeric conditions. As expected, genes associated with metabolic regulation and carbohydrate metabolism were differentially regulated between stress treatments. Most importantly, we identified four points in central metabolism (Glyceraldehyde 3-phosphate dehydrogenase, transaldolase, alcohol dehydrogenase and phosphoenolpyruvate carboxykinase) that indicate the potential mechanisms controlling metabolic rate reduction associated with desiccation resistance. Furthermore, a large number of genes associated with vision pathways also were differentially expressed between stress treatments, especially in females, that may underlie the initial detection of stressful environments and trigger subsequent metabolic changes. Dataset from Transcriptional regulation of metabolism associated with the increased desiccation resistance of the cactophilic Drosophila mojavensis Matzkin,LM and Markow, MA, Genetics. The stock used in this study (15081-1352.22) was the same one utilized for the recently published D. mojavensis genome sequence. Flies were reared using standard Tucson Drosophila Stock Center banana/Opuntia media. The experimental design consisted of two mating status treatments (virgin and mated) and two stress treatments (desiccation and food) for both sexes. There were two replicates per mating status/stress/sex treatment (16 total hybridizations)
2010-05-20 | E-GEOD-16234 | biostudies-arrayexpress
Project description:The model organism Encyclopedia of DNA Elements project (modENCODE) has produced a comprehensive annotation of D. melanogaster transcript models based on an enormous amount of high-throughput experimental data. However, some transcribed elements may not be functional, and technical artifacts may lead to erroneous inference of transcription. Inter-species comparison provides confidence to predicted annotation, since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function. We have performed RNA-Seq and CAGE-Seq experiments on more than 80 samples from multiple tissues and stages of 15 Drosophila species, including 8 previously unsequenced genomes. We have found strikingly conserved sequence, expression, and splicing for the vast majority of transcript models in modENCODE annotation (e.g. 99% exons of coding sequences (CDS), 88% exons of untranslated regions (UTR), and 87% splicing events), indicating that the transcriptome annotation is of very high quality. We also describe dynamic transcriptome evolution within the Drosophila genus, including conserved promoter structure, labile positions of transcription start sites, and rapidly evolving RNA-editing events. We demonstrate how this phylogenetic approach to DNA element validation will prove useful in the annotation of other high priority genomes, especially for genomes that are less compact than Drosophila (e.g. the vast majority of vertebrate genomes). Refer to individual Series (listed below).
2013-02-25 | E-GEOD-44612 | biostudies-arrayexpress
Project description:The model organism Encyclopedia of DNA Elements project (modENCODE) has produced a comprehensive annotation of D. melanogaster transcript models based on an enormous amount of high-throughput experimental data. However, some transcribed elements may not be functional, and technical artifacts may lead to erroneous inference of transcription. Inter-species comparison provides confidence to predicted annotation, since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function. We have performed RNA-Seq and CAGE-Seq experiments on more than 80 samples from multiple tissues and stages of 15 Drosophila species, including 8 previously unsequenced genomes. We have found strikingly conserved sequence, expression, and splicing for the vast majority of transcript models in modENCODE annotation (e.g. 99% exons of coding sequences (CDS), 88% exons of untranslated regions (UTR), and 87% splicing events), indicating that the transcriptome annotation is of very high quality. We also describe dynamic transcriptome evolution within the Drosophila genus, including conserved promoter structure, labile positions of transcription start sites, and rapidly evolving RNA-editing events. We demonstrate how this phylogenetic approach to DNA element validation will prove useful in the annotation of other high priority genomes, especially for genomes that are less compact than Drosophila (e.g. the vast majority of vertebrate genomes).
2013-02-25 | GSE44612 | GEO
Project description:Comparisons of the bacterial communities associated with sympatric cactophilic and generalist Drosophila
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