PXD003188

PXD003188 is an original dataset announced via ProteomeXchange.

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.
HostingRepository	PRIDE
AnnounceDate	2018-07-11
AnnouncementXML	Submission_2018-07-11_08:13:04.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Kyle Anderson
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

Revision	Datetime	Status	ChangeLog Entry
0	2015-11-16 01:26:56	ID requested
⏵ 1	2018-07-11 08:13:06	announced

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]

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]

curator keyword: Biological

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

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

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PRIDE project URI

• PRIDE
  1. PXD003188
     1. Label: PRIDE project
     2. Name: Proteogenomic analysis in hibernating mammal suggests contribution of skeletal muscle physiology to hibernation phenotype