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PXD003188

DataSet Summary

  • HostingRepository: PRIDE
  • AnnounceDate: 2018-07-11
  • AnnouncementXML: Submission_2018-07-11_08:13:04.xml
  • DigitalObjectIdentifier:
  • ReviewLevel: Peer-reviewed dataset
  • DatasetOrigin: Original data
  • RepositorySupport: Unsupported dataset by repository
  • PrimarySubmitter: Kyle Anderson
  • Title: Proteogenomic analysis in hibernating mammal suggests contribution of skeletal muscle physiology to hibernation phenotype
  • Description: Mammalian hibernation is a strategy employed by many species to survive fluctuations in resource availability and environmental conditions. Hibernating mammals endure conditions of dramatically depressed heart rate, body temperature, and oxygen consumption; yet show no typical pathological response. Because of the high abundance and metabolic cost of skeletal muscle, not only must it adjust to the constraints of hibernation, but is positioned to play a more active role in the initiation and maintenance of the hibernation phenotype. In this study, MS/MS proteomic data were searched against a custom database of transcriptomic and genomic protein predictions built using the platform GalaxyP. This proteogenomic approach allows for a thorough investigation of skeletal muscle protein expression throughout the circannual cycle of the 13-lined ground squirrel. Of the 1,563 proteins identified by these methods, 232 were differentially expressed. Not only do these data support previously reported physiological transitions, they also offer insight into specific mechanisms of how their muscles might be reducing nitrogenous waste, preserving mass and function, and signaling to other tissues. Additionally, the combination of proteomic and transcriptomic data provides unique opportunities for determining the level of post-transcriptional regulation throughout the year and improving the genomic annotation of this non-model organism.
  • SpeciesList: scientific name: Spermophilus tridecemlineatus (Thirteen-lined ground squirrel); NCBI TaxID: 43179;
  • ModificationList: iTRAQ8plex-116 reporter+balance reagent acylated residue; methyl methanethiosulfonate
  • Instrument: LTQ Orbitrap Velos

Dataset History

VersionDatetimeStatusChangeLog Entry
02015-11-16 01:26:56ID requested
12018-07-11 08:13:06announced

Publication List

  1. Anderson KJ, Vermillion KL, Jagtap P, Johnson JE, Griffin TJ, Andrews MT, Proteogenomic Analysis of a Hibernating Mammal Indicates Contribution of Skeletal Muscle Physiology to the Hibernation Phenotype. J Proteome Res, 15(4):1253-61(2016) [pubmed]
  2. Vermillion KL, Jagtap P, Johnson JE, Griffin TJ, Andrews MT, Characterizing Cardiac Molecular Mechanisms of Mammalian Hibernation via Quantitative Proteogenomics. J Proteome Res, 14(11):4792-804(2015) [pubmed]

Keyword List

  1. curator keyword: Biological
  2. submitter keyword: iTRAQ, Galaxy-P, proteomics, hibernation, skeletal muscle, AMP –deaminsase 1, fibromodulin

Contact List

    Matthew T. Andrews
    • contact affiliation: Biology University of Minnesota Duluth
    • contact email: mandrews@d.umn.edu
    • lab head:
    Kyle Anderson
    • contact affiliation: University of Minnesota Duluth
    • contact email: kander47@gmail.com
    • dataset submitter:

Full Dataset Link List

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  2. PRIDE project URI
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