Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Comparative analysis of mouse muscles types

ABSTRACT: The dataset presents FASP- and LC-MS/MS-based analysis of whole lysates of tree types of mouse muscle tissue: white and red muscle fibers and heart muscle. The measurements were performed using five biological replicates for each tissue type. The dataset cover 7200 proteins. The data were used for calculation of protein titers using the 'total protein method' (TPA) method.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Mus Musculus (ncbitaxon:10090)

SUBMITTER: Jacek R Wisniewski

PROVIDER: MSV000084934 | MassIVE | Fri Feb 07 14:01:00 GMT 2020

SECONDARY ACCESSION(S): PXD002152

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Publications

Proteomics Unveils Fibroblast-Cardiomyocyte Lactate Shuttle and Hexokinase Paradox in Mouse Muscles.

Rakus Dariusz D Rakus Dariusz D Gizak Agnieszka A Wiśniewski Jacek R JR

Journal of proteome research 20160624 8

Quantitative mapping, given in biochemically interpretable units such as mol per mg of total protein, of tissue-specific proteomes is prerequisite for the analysis of any process in cells. We applied label- and standard-free proteomics to characterize three types of striated muscles: white, red, and cardiac muscle. The analysis presented here uncovers several unexpected and novel features of striated muscles. In addition to differences in protein expression levels, the three muscle types substan ...[more]

PMID: 27302655

Similar Datasets

Comparative analysis of mouse muscles types

Project description:The dataset presents FASP- and LC-MS/MS-based analysis of whole lysates of tree types of mouse muscle tissue: white and red muscle fibers and heart muscle. The measurements were performed using five biological replicates for each tissue type. The dataset cover 7200 proteins. The data were used for calculation of protein titers using the 'total protein method' (TPA) method.

2016-06-21 | PXD002152 | Pride

Absolute protein quantification allows differentiation of cell specific metabolic routes and functions

Project description:Total protein approach (TPA) is a proteomic method which allows calculation of concentrations of individual proteins and groups of functionally related proteins in any protein mixture without spike-in standards. Using the two step digestion filter aided sample preparation method and LC-MS/MS analysis we generated comprehensive quantitative datasets of mouse intestinal mucosa, liver, red muscle fibers, brain, and of human plasma, erythrocytes, and tumor cells lines. We show that the TPA based quantitative data reflect well-defined and specific physiological functions of different organs and cells, for example nutrient absorption and transport in intestine, amino acid catabolism and bile secretion in liver, and contraction of muscle fibers. Focusing on key metabolic processes we compared metabolic capacities in different tissues and cells. In addition, we demonstrate quantitative differences in the mitochondrial proteomes. Providing insight into the abundances of mitochondrial metabolite transporters we demonstrate that their titers are well tuned to cell specific metabolic requirements. This study provides for the first time a comprehensive overview of the protein hardware mediating metabolism in different mammalian organs and cells. The presented approach can be applied to any other system to study biological processes.

2014-12-15 | PXD001352 | Pride

RNAseq from neonatal mouse hindlimb muscles

Project description:During neonatal development, skeletal muscle grows dramatically by myonuclei accretion to existing fibers and hypertophic growth of fibers with protein synthesis. To understand molecular mechanism underlying neonatal muscle growth, we used RNAseq to profile the global program of gene expressions especially involved in myoblast fusion, migration, and muscle fiber growth by itself. We used two biological replicates for each time point.

2015-12-10 | E-GEOD-75832 | biostudies-arrayexpress

RNAseq from neonatal mouse hindlimb muscles

Project description:During neonatal development, skeletal muscle grows dramatically by myonuclei accretion to existing fibers and hypertophic growth of fibers with protein synthesis.

2015-12-10 | GSE75832 | GEO

Expression data from mouse neonatal hindlimb muscles

2015-12-08 | GSE75774 | GEO

Expression data from mouse neonatal hindlimb muscles

Project description:During neonatal development, skeletal muscle grows dramatically by myonuclei accretion to existing fibers and hypertophic growth of fibers with protein synthesis. To understand molecular mechanism underlying neonatal muscle growth, we used microarray to profile the global program of gene expressions especially involved in myoblast fusion, migration, and muscle fiber growth by itself. Mouse hindlimb muscles at postnatal day (P) 2, 7, and 14 were isolated and used for RNA extraction and hybridyzation on microarrays. We used three biological replicates for each time point.

2015-12-08 | E-GEOD-75774 | biostudies-arrayexpress

RNA-seq from tibialis muscles from rats aged 15 months (adult) and 27 months (old)

Project description:To gain new insights into molecular changes in skeletal muscle aging and disease with a special focus on differential alternative splicing and senescence, we performed RNA-seq on tibialis muscles from 15 months old (adult, a) and 27 months old (old, o) rats. Whole (w) muscle samples were prepared for both age groups (w/a and w/o). Additionally, for both age groups, muscle fibers were isolated. For adult rats, this resulted in one group (f/a). For old rats, fibers were subjected to Laser capture microdissection guided by expression of aging markers Tmem158 and Cdkn1a, giving rise to two groups, aging marker-positive fibers (f/o+) and aging marker-negative fibers (f/o-). The entire experiment comprises 5 groups (w/a, w/o, f/a, f/o+, f/o-), with 5 animals per group, ie. 25 samples total.

2021-06-26 | E-MTAB-10582 | biostudies-arrayexpress

Integrating Proteomics and Enzyme Kinetics Reveals Tissue-Specific Types of the Glycolytic and Gluconeogenic Pathways

Project description:Glycolysis is the core metabolic pathway supplying energy to cells. Whereas the vast majority of studies focus on specific aspects of the process, global analyses characterizing simultaneously all enzymes involved in the process are scarce. Here we demonstrate that quantitative label- and standard-free proteomics allows accurate determination of titers of metabolic enzymes and enables simultaneous measurements of titers and maximal enzymatic activities (Amax)c of all glycolytic enzymes and the gluconeogenic fructose 1,6-bisphosphatase in mouse brain, liver and muscle. Despite occurrence of tissue-specific isoenzymes bearing different kinetic properties, the enzyme titers often correlated well with the Amax values. To provide a more general picture of energy metabolism we analyzed titers of the enzymes in additional 7 mouse organs and in human cells. Across the analyzed samples we identified two basic profiles: a 'fast glucose uptake' one in brain and heart, and a 'gluconeogenic rich' one occurring in liver. In skeletal muscles and other organs, we found intermediate profiles. Obtained data highlighted the glucose-flux-limiting role of hexokinase which activity was always 10-100-fold lower than the average activity of all other glycolytic enzymes. A parallel determination of enzyme titers and maximal enzymatic activities allowed determination of kcat values without enzyme purification. Results of our in-depth proteomic analysis of the mouse organs did not support the concepts of regulation of glycolysis by lysine acetylation.

2015-06-22 | PXD002156 | Pride

Notch2 Expressed by Myofibers Influences Muscle Mass and Fiber Types

Project description:Notch receptors play crucial roles in the cell-fate decisions of tissue stem cells during development and regeneration. Notch1-3 receptors are expressed by satellite cells and their progeny. Here we found that Notch2, but not Notch1 or Notch3, was expressed in fully differentiated myofibers. Using transgenic mice that expressed a muscle-specific active form of Notch2 (N2ICD-mTG), we found that Notch2 activation remarkably reduced muscle mass and strength with a shift toward slow fibers. Transcriptome analyses revealed that growth differentiation factor 11 (GDF11) was highly up-regulated in muscles of N2ICD-mTG mice, and crucially, N2ICD-induced muscle atrophy was rescued by siRNA-mediated reduction of GDF11 expression. These data suggest that Notch2 functions in muscle to regulate muscle mass, in part, through induction of GDF11 expression, and reveal a novel aspect of Notch signaling in a terminally differentiated adult tissue.

2020-01-01 | GSE83929 | GEO

Expression data from wild-type single muscle fibers

Project description:The muscle stem cells (or satellite cells (SC)) reside on the muscle fibers tightly wedged between the plasma membrane of the muscle fibers and the basal lamina. The muscle fibers represent a functional niche providing paracrine signals to maintain the tissue resident stem cells. We performed microarrays to depict the global transcriptional profile of single muscle fibers at different time points

2019-08-01 | GSE135163 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data