Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1071110 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27784917_1.fastq.gz | Fastqsanger.gz | |||
| SRR27784917_2.fastq.gz | Fastqsanger.gz | |||
| SRR27784918_1.fastq.gz | Fastqsanger.gz | |||
| SRR27784918_2.fastq.gz | Fastqsanger.gz | |||
| SRR27784919_1.fastq.gz | Fastqsanger.gz |
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Project description:Analysis of the effects of sleep deprivation, recovery sleep, and three time-of-day controls on seven brain regions laser microdissected from mouse brain. The regions include the locus coeruleus, suprachiasmatic nucleus, hypocretin area, tuberomammillary nucleus, orbital cortex, posteromedial cortical amygdala, and entorhinal cortex. In this study, 7 brain regions were collected by laser microdissection from brain tissue of mice from 5 different treatment groups and used for microarray experiments. Four biological replicates were generated for each regionxcondition. Conditions are: SD, sleep deprivation for 6 hours from ZT0 - 6; SDC, time-of-day control for SD at ZT6; RS, recovery sleep for 4 hours following SD; RSC, time-of-day control for RS at ZT10; W, spontaneous waking at ZT18.
2010-08-16 | E-GEOD-23628 | biostudies-arrayexpress
Project description:Sleep Deprivation and Recovery Sleep for 7 Regions of Mouse Brain.
| PRJNA129943 | ENA
Project description:Analysis of the effects of sleep deprivation, recovery sleep, and three time-of-day controls on seven brain regions laser microdissected from mouse brain. The regions include the locus coeruleus, suprachiasmatic nucleus, hypocretin area, tuberomammillary nucleus, orbital cortex, posteromedial cortical amygdala, and entorhinal cortex.
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Project description:This SuperSeries is composed of the following subset Series:; GSE9441: The effect of sleep deprivation on gene expression in the brain and the liver of three inbred mouse strains; GSE9442: Molecular correlates of sleep deprivation in the brain of three inbred mouse strains in an around-the-clock experiment; GSE9443: Gene expression in brain Homer1a-expressing cells after sleep deprivation Experiment Overall Design: Refer to individual Series
2008-06-17 | E-GEOD-9444 | biostudies-arrayexpress
Project description:Micro-RNAs (miRNAs) are key, post-transcriptional regulators of gene expression that have been implicated in a plethora of biological processes. Their role in sleep, however, has received little attention. We first investigated the effects of sleep deprivation on the brain miRNA transcriptome. Sleep deprivation affected 52 miRNAs in the whole brain, and particularly miR-709, an activity-dependent microRNA, enriched in the cerebral cortex.
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Project description:Purpose: To determine the specific effects of 6 hours sleep deprivation after a learning event on the transcriptomes of microglia. Sleep deprivation can generate inflammatory responses in the neuronal environment. In turn, this inflammation increases sleep drive, leading to a rebound in sleep duration. Microglia, a type of support cell found exclusively in the brain, have previously been found to release of inflammatory signals and exhibit altered characteristics in response to sleep deprivation. Together, this suggests microglia may be partially responsible for the brain’s response to sleep deprivation through their inflammatory activity. In this study, we fully and selectively ablated microglia from the mouse brain and assessed resulting sleep, circadian, and sleep deprivation phenotypes. We find microglia are dispensable for both homeostatic sleep and circadian function and the sleep rebound response to sleep deprivation. However, we uncover a phenomenon by which microglia appear to be essential for the protection of synapses and associated memories formed during a period of sleep deprivation, further expanding the list of known functions for microglia in synaptic modulation.
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Project description:To gain insight into the molecular changes of sleep need, this study addresses gene expression changes in a subpopulation of neurons selectively activated by sleep deprivation. Whole brain expression analyses after 6h sleep deprivation clearly indicate that Homer1a is the best index of sleep need, consistently in all mouse strains analyzed. Transgenic mice expressing a FLAG-tagged poly(A)-binding protein (PABP) under the control of Homer1a promoter were generated. Because PABP binds the poly(A) tails of mRNA, affinity purification of FLAG-tagged PABP proteins from whole brain lysates, is expected to co-precipitate all mRNAs from neurons expressing Homer1a. Three other activity-induced genes (Ptgs2, Jph3, and Nptx2) were identified by this technique to be over-expressed after sleep loss. All four genes play a role in recovery from glutamate-induced neuronal hyperactivity. The consistent activation of Homer1a suggests a role for sleep in intracellular calcium homeostasis for protecting and recovering from the neuronal activation imposed by wakefulness. Keywords: sleep deprivation, neuronal subpopulation transcriptome
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Project description:Every day, we sleep for a third of the day. Sleep is important for cognition, brain waste clearance, metabolism, and immune responses. Homeostatic regulation of sleep is maintained by progressively rising sleep need during wakefulness, which then dissipates during sleep. The molecular mechanisms governing sleep are largely unknown. Here, we used a combination of single-cell RNA sequencing and cell-type specific proteomics to interrogate the molecular and functional underpinnings of sleep. Different cell-types in the brain regions show similar transcriptional response to sleep need whereas sleep deprivation changes overall expression indicative of altered antigen processing, synaptic transmission and cellular metabolism in brainstem, cortex and hypothalamus, respectively. Increased sleep need enhances expression of transcription factor Sox2, Mafb, and Zic1 in brainstem; Hlf, Cebpb and Sox9 in cortex, and Atf3, Fosb and Mef2c in hypothalamus. Results from cell-type proteome analysis suggest that sleep deprivation changes abundance of proteins in cortical neurons indicative of altered synaptic vesicle cycles and glucose metabolism whereas in astrocytes it alters the abundance of proteins associated with fatty acid degradation. Similarly, phosphoproteomics of each cell type demonstrates large shifts in site-specific protein phosphorylation in neurons and astrocytes of sleep deprived mice. Our results indicate that sleep deprivation regulates transcriptional, translational and post-translational responses in a cell-specific manner and advances our understanding of the cellular and molecular mechanisms that govern sleep-wake homeostasis in mammals.
2022-10-13 | PXD018334 | Pride
Project description:To gain insight into the molecular changes of sleep need, this study addresses gene expression changes in a subpopulation of neurons selectively activated by sleep deprivation. Whole brain expression analyses after 6h sleep deprivation clearly indicate that Homer1a is the best index of sleep need, consistently in all mouse strains analyzed. Transgenic mice expressing a FLAG-tagged poly(A)-binding protein (PABP) under the control of Homer1a promoter were generated. Because PABP binds the poly(A) tails of mRNA, affinity purification of FLAG-tagged PABP proteins from whole brain lysates, is expected to co-precipitate all mRNAs from neurons expressing Homer1a. Three other activity-induced genes (Ptgs2, Jph3, and Nptx2) were identified by this technique to be over-expressed after sleep loss. All four genes play a role in recovery from glutamate-induced neuronal hyperactivity. The consistent activation of Homer1a suggests a role for sleep in intracellular calcium homeostasis for protecting and recovering from the neuronal activation imposed by wakefulness. Experiment Overall Design: Experiments were performed on male mice, 12 weeks of age +/- 1 week. Animals were housed in polycarbonate cages (31x18x18cm) in an experimental room with an ambient temperature varying from 23° to 25°C under a 12:12 hrs light/dark cycle. Food and water were available ad libitum. At light onset mice were either sleep deprived by gentle handling (n=10) or left undisturbed (n=10) for 6 hrs. Animals were then randomly sacrificed by cervical dislocation. Total RNA from the whole brain was isolated for control (n=4) and sleep deprived (n=4) using a commercial RNA extraction kit (RNeasy Lipid Tissue Kit, Quiagen). Specific Homer1a-expressing cells polyA RNAs were immunoprecipitated following the total brain crosslinking (1% formaldehyde perfusion) for sleep deprived (n=6) and control (n=6) animals. The total RNA from the pull-down supernatants were also harvested (n=4). To test for transcriptional changes after sleep deprivation Homer1a-expressing cells, we proceeded in 2 steps: (1) identify probe sets enriched in the pull-down extracts, (2) among those probe sets compare sleep deprivation to control condition in both pull-down (6 vs. 6 chip comparison) and whole-brain (4 vs. 4 chip comparison) extracts. 4728 probe sets were significantly enriched at 5% FDR when pull-downs were compared to both supernatant and whole-brain extracts.
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