Ontology highlight
ABSTRACT:
PROVIDER: PRJNA420609 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6336510.fastq.gz | Fastqsanger.gz | |||
| SRR6336520.fastq.gz | Fastqsanger.gz | |||
| SRR6336530.fastq.gz | Fastqsanger.gz | |||
| SRR6336540.fastq.gz | Fastqsanger.gz | |||
| SRR6336550.fastq.gz | Fastqsanger.gz |
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Project description:Identify shifts in gene expression relevant to torpor phenotypes and recovery following torpor in five tissues of the 13-lined ground squirrel. Sampled tissues and time points overlap with prior hibernation RNA-seq studies in 13-lined ground squirrel and other species, allowing for the analysis of conserved gene expression patterns in torpor.
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Project description:Hibernation is a seasonally adaptive strategy that allows hibernators to live through extreme cold condition and was viewed as a highly regulated physiological event. In spite of the profound reduction of blood flow to retina, hibernation causes no lasting retinal injury and hibernators show increased tolerance to ischemic insults during hibernation period. To understand the molecular changes of retina in response to hibernation we applied transcriptomic analysis to explore the changes of gene expression of 13-lined ground squirrel retinas during hibernation.
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Project description:piRNA analysis of the 13-lined ground squirrel
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Project description:miRNAs are 19-25 nucleotides long small RNAs now well-known for their regulatory roles in the development and diseases through post-transcriptional and translational controls in a wide range of species. Mammalian hibernation is a physiological process involving dramatic metabolic suppression and cellular reorganization, during which miRNAs may play an important role. We systematically analyzed the miRNAs in the liver of an extreme hibernating species, arctic ground squirrels (Spermophilus parryii), during two stages of hibernation compared to non-hibernating animals by massively parallel Illumina sequencing technology. We identified more than 200 ground squirrel miRNAs including novel miRNAs specific to ground squirrel and a fast-evolving miRNA cluster that also showed significant differential expression during hibernation. Integrating with Agilent miRNA microarray and Real-time PCR results, we identified that mir-211, mir-378, mir-184, mir-200a, and mir-320 were significantly under-expressed during hibernation, whereas mir-144, mir-486, mir-451, mir-142-5p, and mir-1 were over-expressed. Analyses of the their target genes suggested that these miRNAs could play an important role to suppress tumor progression and cell growth during hibernation. Investigation of microRNA changes in arctic ground squirrel livers during Early Arousal(EA), Late Topor(LT), and Post-Reproduction(PR) stages.
2010-11-30 | E-GEOD-19807 | biostudies-arrayexpress
Project description:miRNAs are 19-25 nucleotides long small RNAs now well-known for their regulatory roles in the development and diseases through post-transcriptional and translational controls in a wide range of species. Mammalian hibernation is a physiological process involving dramatic metabolic suppression and cellular reorganization, during which miRNAs may play an important role. We systematically analyzed the miRNAs in the liver of an extreme hibernating species, arctic ground squirrels (Spermophilus parryii), during two stages of hibernation compared to non-hibernating animals by massively parallel Illumina sequencing technology. We identified more than 200 ground squirrel miRNAs including novel miRNAs specific to ground squirrel and a fast-evolving miRNA cluster that also showed significant differential expression during hibernation. Integrating with Agilent miRNA microarray and Real-time PCR results, we identified that mir-211, mir-378, mir-184, mir-200a, and mir-320 were significantly under-expressed during hibernation, whereas mir-144, mir-486, mir-451, mir-142-5p, and mir-1 were over-expressed. Analyses of the their target genes suggested that these miRNAs could play an important role to suppress tumor progression and cell growth during hibernation. Three total RNA pools from arctic ground squirrel livers in Early Arousal(EA), Late Topor(LT), and Post-Reproduction(PR) stages were hybridized to three Agilent mouse miRNA microarrays.
2010-11-30 | E-GEOD-19427 | biostudies-arrayexpress
Project description:miRNAs are 19-25 nucleotides long small RNAs now well-known for their regulatory roles in the development and diseases through post-transcriptional and translational controls in a wide range of species. Mammalian hibernation is a physiological process involving dramatic metabolic suppression and cellular reorganization, during which miRNAs may play an important role. We systematically analyzed the miRNAs in the liver of an extreme hibernating species, arctic ground squirrels (Spermophilus parryii), during two stages of hibernation compared to non-hibernating animals by massively parallel Illumina sequencing technology. We identified more than 200 ground squirrel miRNAs including novel miRNAs specific to ground squirrel and a fast-evolving miRNA cluster that also showed significant differential expression during hibernation. Integrating with Agilent miRNA microarray and Real-time PCR results, we identified that mir-211, mir-378, mir-184, mir-200a, and mir-320 were significantly under-expressed during hibernation, whereas mir-144, mir-486, mir-451, mir-142-5p, and mir-1 were over-expressed. Analyses of the their target genes suggested that these miRNAs could play an important role to suppress tumor progression and cell growth during hibernation.
2010-11-30 | GSE19807 | GEO
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2010-11-30 | GSE19427 | GEO
Project description:13-lined ground squirrel cecal mucosa Targeted Locus (Loci)
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Project description:13-lined ground squirrel (Spermophilus tridecemlineatus) hibernating liver transcriptome
| PRJNA91845 | ENA
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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