Ontology highlight
ABSTRACT:
PROVIDER: PRJNA588984 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10429264_1.fastq.gz | Fastqsanger.gz | |||
| SRR10429264_2.fastq.gz | Fastqsanger.gz | |||
| SRR10429265_1.fastq.gz | Fastqsanger.gz | |||
| SRR10429265_2.fastq.gz | Fastqsanger.gz | |||
| SRR10429266_1.fastq.gz | Fastqsanger.gz |
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Project description:Our objective was to determine whether gene expression in Drosophila melanogaster selectively bred for long or short night sleep duration changes detectably across generations. To meet this objective, we performed transcriptional profiling of ten pooled whole adult individuals from four selected populations and two control populations across 13 generations. We quantified differential expression among selection scheme (long sleep, short sleep, or unselected control), generation (generation 0; then generations 2-13), and sex for each gene.
2023-07-29 | GSE202600 | GEO
Project description:Artificial selection for long and short sleep duration in Drosophila melanogaster
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Project description:Natural selection maintains genetic variation for sleep in Drosophila melanogaster
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Project description:The mechanisms underlying natural variation in lifespan and ageing rate remain largely unknown. We performed microarray experiment to characterise genome-wide expression patterns of a long-lived, natural variant of Drosophila melanogaster resulting from selection for starvation resistance (SR) and compare it with normal-lived control flies (C).
2012-04-01 | GSE36582 | GEO
Project description:The role natural selection plays in governing the locations and early evolution of copy number mutations remains largely unexplored. Here we employ high-density full-genome tiling arrays to create a fine-scale genomic map of copy number polymorphisms (CNPs) in Drosophila melanogaster. We inferred a total of 2,658 independent CNPs, 56% of which overlap genes. These include CNPs likely to be under positive selection, most notably high frequency duplications encompassing toxin-response genes. The locations and frequencies of CNPs are strongly shaped by purifying selection with deletions under stronger purifying selection than duplications. Among duplications, those overlapping exons or introns and those falling on the X-chromosome seem to be subject to the strongest purifying selection. In order to characterize copy number polymorphisms (CNPs) in Drosophila malanogaster, we applied comparative genome hybridization (CGH) using tiling arrays covering the full euchromatic genome of Drosophila melanogaster. We inferred copy number changes with a Hidden Markov Model (HMM) that returned the posterior probabilities for copy number by comparing DNA hybridization intensities between natural isolates and the reference genome strain. Training data for copy number changes were obtained via hybridization with a line known to contain a ~200kb homozygous duplication and from a set of 52 validated homozygous deletions. The probabilities of mutation were parsed to make CNP calls. Key words: comparative genomic hybridization, CGH, copy number polymorphism, CNP, copy number variation, CNV, duplication, deletion
2008-06-06 | GSE11326 | GEO
Project description:Short sleep duration is associated with adverse metabolic, cardiovascular, and inflammatory effects. Co-twin study methodologies account for familial (e.g., genetics and shared environmental) confounding, allowing assessment of subtle environmental effects, such as the effect of short habitual sleep duration on gene expression. Therefore, we sought to investigate gene expression in monozygotic twins discordant for actigraphically phenotyped habitual sleep duration. Eleven healthy monozygotic twin pairs (82% female; mean age 42.7 years; SD=18.1), selected based on subjective sleep duration discordance, were objectively phenotyped for habitual sleep duration with two-weeks of wrist actigraphy. Peripheral blood leukocyte (PBL) RNA from fasting blood samples was obtained on the final day of actigraphic measurement and hybridized to Illumina humanHT-12 microarrays. Differential gene expression was determined between paired samples and mapped to functional categories using Gene Ontology. Next, a more comprehensive gene set enrichment analysis was performed based on the entire PBL transcriptome. The mean 24 hour sleep duration of the total sample was 439.2 minutes (SD=46.8 minutes; range 325.4 to 521.6 minutes). Mean within-pair sleep duration difference per 24 hours was 64.4 minutes (SD=21.2; range 45.9 to 114.6 minutes). The twin cohort displayed distinctive pathway enrichment based on sleep duration differences. Short sleep was associated with up-regulation of genes involved in transcription, ribosome, translation and oxidative phosphorylation. Unexpectedly, genes down-regulated in short sleep twins were highly enriched in immuno-inflammatory pathways such interleukin signaling and leukocyte activation, as well as developmental programs, coagulation cascade, and cell adhesion. Objectively assessed habitual sleep duration in monozygotic twin pairs appears to be associated with distinct patterns of differential gene expression and pathway enrichment. By accounting for familial confounding and measuring real life sleep duration, our study shows the transcriptomic effects of short sleep on dysregulated immune response and provides a potential link between sleep deprivation and adverse metabolic, cardiovascular and inflammatory outcomes.
2016-09-09 | GSE80612 | GEO
Project description:Sleep is a fundamental physiological function and is essential for all animals, including humans. Sleep has been reported to be affected by diet compositions including protein (P) and carbohydrates (C), but there has not been a systematic investigation of the effect of dietary macronutrient balance on sleep. Here, we used the nutritional geometry framework (NGF) to explore the interactive effects on sleep of protein (P) and carbohydrate (C) in the model organism Drosophila. Our results showed that the combination of low protein and moderate carbohydrate prolonged sleep time and sleep quality, with fewer sleep episodes and longer sleep duration. We further found that the effects of macronutrients on sleep mirrored levels of haemolymph glucose and whole-body glycogen. Moreover, transcriptome analyses revealed that high protein, low carbohydrate diet elevated the gene expression of amino acid metabolic pathways when compared to a diet lacking protein, with the glycine, serine, threonine metabolism pathway being most strongly regulated. However, sleep was not decreased in flies fed on a protein-deficient diet with added glycine, serine and threonine. In summary, our results demonstrate that sleep is affected by the balance of protein and carbohydrates in the diet and that reduced protein coupled with moderate carbohydrate promote sleep duration and quality.
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Project description:In order to investigate the functional relevance of SUR2 (the protein encoded by ABCC9 in humans) for sleep duration, we knocked down the expression of its Drosophila homologue (dSur) in the flies’ nervous system (both central and peripheral). Unlike humans, flies are active predominantly around dawn and dusk and show two large sleep episodes during the day and during the night. Knockdown of dSur dramatically reduced night-sleep, particularly during the first half of the dark period, but had little effect on the flies’ day-sleep. This was true for both elavgal4 UAS-Sur RNAi genotypes compared with their parental control strains. These differences in sleep duration were not due to changes in the circadian clock, as the period of the free-running locomotor activity rhythm in constant darkness was indistinguishable between knockdown flies and controls. Furthermore, no systematic differences in activity levels were found between experimental genotypes and control. Thus, the major effect of knocking down the ABCC9 homologue in flies is shortening nighttime sleep due to a delay of its onset by 3 h.
2018-03-08 | GSE52764 | GEO
Project description:Exploring the intricate link between sleep and brain degeneration holds great promise for the development of effective therapeutics. Here we provide novel insights into the role of TDP-43 and Atx2 in regulating sleep and neurodegeneration using Drosophila. We demonstrate that expression of TDP-43 severely disrupts sleep, resulting in reduced sleep duration of the affected animals. Sleep disruption by TDP-43 is completely rescued by Atx2 knockdown. To unravel the underlying mechanism of TDP43 sleep disruption and Atx2-mediated rescue, we conducted brain RNA sequencing analysis from flies expressing TDP-43 with or without Atx2 knockdown. Among RNAseq changes, we observed upregulation of genes associated with small molecule metabolism with TDP-43 expression, followed by their subsequent downregulation upon Atx2 knockdown. Utilizing these Atx2-regulated genes, we conducted an RNAi screen to identify additional sleep modifiers that interact with TDP-43.
2023-11-17 | GSE234468 | GEO