Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1010398 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25782270.fastq.gz | Fastqsanger.gz | |||
| SRR25782271.fastq.gz | Fastqsanger.gz | |||
| SRR25782272.fastq.gz | Fastqsanger.gz | |||
| SRR25782273.fastq.gz | Fastqsanger.gz | |||
| SRR25782274.fastq.gz | Fastqsanger.gz |
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Project description:We report RNA-Seq experiments of eye and retinal tissues from Ground Squirrel (Ictidomys tridecemlineatus)
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Project description:Mammalian hibernation is a dramatic physiological transition that involves the controlled reduction of regulated body temperature and the consequent depression of all physiological processes. The resulting reduction of metabolism and associated energy expenditure permits survival during extended periods of poor food availability in winter. To date our understanding of the molecular events that give rise to the hibernating phenotype is fragmentary and incomplete. Here, we present a large-scale gene expression screen to explore the transcriptional changes that are associated with the torpid phenotype of the hibernating golden-mantled ground squirrel, Spermophilus lateralis. Expression profiles for liver, cardiac tissue, and brain isolated from summer active, torpid, and interbout aroused animals were generated by hybridization to a squirrel microarray composed of >12,000 cDNA probes. We reveal that the transcriptional changes associated with torpor are modest and generally involve less than 2-fold changes in mRNA level. By profiling the distribution of gene ontological terms in the lists of differentially expressed genes we were able to identify the functional themes that distinguish the summer awake and hibernating phenotypes. In all tissues, the pattern of differential gene expression is consistent with a switch to lipid metabolism during hibernation. In liver, we detected an expression signature suggestive of a profound depression in urea metabolism and detoxification pathways. This expression signature was reproduced in transcript data collected from liver of the13-lined ground squirrel, S. tridecemlineatus, suggesting that this phenotype is conserved between closely related species. The transcriptional changes in cardiac tissue were interpreted as a component of the bradycardia associated with torpor. The function of the differentially expressed transcripts in brain is less transparent, likely due to heterogeneity among the responses of different cell populations in this complex organ.
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Project description:Ictidomys tridecemlineatus isolate:GS200 Genome sequencing and assembly
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Project description:We report the application of the Illumina/Solexa sequencing-by-synthesis platform to analysis differential expression genes of two key tissues (brain and adipose tissue) during hibernation vs. aroused state, with a hibernating bat species (Myotis ricketti) as model. Total of 12272 genes were identified including 11291 genes in brain and 10691 genes in adipose tissue. Chi-square test indicated that 1943 and 3673 genes in brain and adipose tissues respectively reached the significant level (P ⤠0.01), including 1243 up-regulated and 700 down-regulated genes in hibernating brain and 2621 up-regulated and 1052 down-regulated genes in hibernating adipose tissue. This study provide opportunity to in-deep analysis the molecular mechanism of hibernating regualtion.
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Project description:Small RNA-Seq of Ictidomys tridecemlineatus white adipose tissue from adult males
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Project description:Hibernating mammals such as the thirteen-lined ground squirrel (Ictidomys tridecemlineatus) experience significant reductions in oxidative metabolism and body temperature when entering a state known as torpor. Animals entering or exiting torpor do not experience permanent loss of brain function or other injuries, and the processes that enable such neuroprotection are not well understood. To gain insight into changes in protein function that occur in dramatically different physiological states, we performed quantitative phosphoproteomics experiments on thirteen-lined ground squirrels that are summer active, winter torpid, and spring active. An important aspect of our approach was the use of focused microwave irradiation of the brain to sacrifice the animals and rapidly inactivate phosphatases and kinases to preserve the native phosphoproteome. Overall, our results showed pronounced changes in phosphorylated proteins for the transitions into and out of torpor, including for proteins involved in gene expression and DNA repair, cellular plasticity, and human disease. In contrast, the transition between active states showed minimal changes. This study offers valuable insight into the global changes of brain phosphorylation in hibernating mammals, the results of which may be relevant to the future therapeutic strategies for brain injury.
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