Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Gene expression in soleus muscle of mouse inbred strains LG/J and SM/J

ABSTRACT: Variability in muscle mass significantly impacts energy expenditure, influencing preponderance to obesity and recently it has been reported that there is a positive association between muscle mass and longevity in older adults. Muscle fibre cross-sectional area (CSA) and proportion of different fibre types are important determinants of muscle mass, function and overall metabolism. Genetic variation plays a substantial role in phenotypic variation of these traits but the underlying genes remain poorly understood. We identified QTL associated with these muscle fibre phenotypes and hypothesized that if the phenotypic effect of the QTL was brought about by the allele specific abundance of transcripts encoded by genes within the QTL, such genes would be differentially expressed in the transcriptome between the parental strains. In this experiment, the expressed transcriptome in soleus muscle of mouse LG/J and SM/J strains was examined by measurement of gene expression on microarrays to facilitate nomination of candidate genes within identified QTL. Hypothesis driven analysis of differential expression in soleus muscle was performed between LG/J and SM/J strains for the genes in the most robust QTLs affecting fibre CSA or % Type I fibres.

INSTRUMENT(S): FS450, GCS3000

ORGANISM(S): Mus musculus

SUBMITTER: Elaina Collie-Duguid

PROVIDER: E-MTAB-5290 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

Fine-mapping of genes determining extrafusal fiber properties in murine soleus muscle.

Carroll A M AM Cheng R R Collie-Duguid E S R ES Meharg C C Scholz M E ME Fiering S S Fields J L JL Palmer A A AA Lionikas A A

Physiological genomics 20170113 3

Muscle fiber cross-sectional area (CSA) and proportion of different fiber types are important determinants of muscle function and overall metabolism. Genetic variation plays a substantial role in phenotypic variation of these traits; however, the underlying genes remain poorly understood. This study aimed to map quantitative trait loci (QTL) affecting differences in soleus muscle fiber traits between the LG/J and SM/J mouse strains. Fiber number, CSA, and proportion of oxidative type I fibers we ...[more]

PMID: 28087756

Similar Datasets

Project description:Ectopic calcification in synovial tissues is devastating to diarthrodial joints. While some forms of synovial ectopic calcification have genetically simple basis, most cases manifest as complex traits with environmental and multigenic components. The location of causal loci or the physiological processes affected by allelic variants is poorly understood. Here, we report on genetic susceptibility to ectopic calcification in the LG/J and SM/J advanced intercross mice. Using 347 mice in 98 full-sibships, destabilization of medial meniscus was performed to induce joint injury. We performed quantitative trait locus (QTL) analysis to map calcification phenotypes to discrete genomic locations. To validate the functional significance of the selected QTL candidate genes, we compared mRNA expression between parental LG/J and SM/J inbred strains. Our findings showed that joint destabilization instigated ectopic calcifications as detected and quantified by micro-CT. Overall, we detected 20 QTLs affecting synovial and meniscus calcification phenotypes with 11 QTLs linked to synovial calcification. Functional and bioinformatic analyses of single nucleotide polymorphism identified functional classifications relevant to angiogenesis (Myo1e, Kif26b, Nprl3, Stab2, Fam105b), bone metabolism/calcification (Tle3, Tgfb2, Lipc, Nfe2l1, Ank, Fam105b), arthritis (Stab2, Tbx21, Map4k4, Hoxb9, Larp6, Col1a2, Adam10, Timp3, Nfe2l1, Trpm3), and ankylosing-spondylitis (Ank, Pon1, Il1r2, Tbkbp1) indicating that ectopic calcification involves multiple mechanisms. Furthermore, the expression of 11 candidate genes was significantly different between LG/J and SM/J. Correlation analysis showed that Aff3, Fam81a, Syn3, and Ank were correlated with synovial calcification. Our findings of multiple genetic loci affecting the phenotype suggest the involvement of multiple genes contributing to its pathogenesis. We collected tissue lysates from the formalin-fixed paraffin-embedded sections from mouse knee joints and analyzed the expression of several genes by Affymetrix QuantiGene Plex assay.

Dataset Information

Gene expression in soleus muscle of mouse inbred strains LG/J and SM/J

Publications

Fine-mapping of genes determining extrafusal fiber properties in murine soleus muscle.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure