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SarcoAtlas: plot and analyze gene expression in skeletal muscles during aging

About SarcoAtlas:

SarcoAtlas is an interactive application for studying changes in the gene expression occurring in multiple skeletal muscles of mice and rats during aging and in response to a genetic intervention and/or drug treatment and/or physiological treatment.

SarcoAtlas is based on five high-throughput data sets obtained by mRNA profiling of skeletal muscles of male C57BL/6JRj mice and male Wistar rats and offers three possibilities to analyze these data sets.

Mouse data sets:

- 'TSCmKO' data set (GEO accession number: GSE139213) describes mRNA profiling of Extensor digitorum longus muscle of 3 and 9 months old wild type mice and TSCmKO mice untreated and treated with rapamycin at a dose of ~8 mg/kg/day for 3 days. It was previously demonstrated that sustained muscle fiber-specific mTORC1 activity, by deleting the mTORC1 upstream inhibitor Tsc1 in mice (TSCmKO), drives progressive muscle wasting and weakness reminiscent of sarcopenia (see Castets, P. et al. Cell Metab 17, 731-744).
- 'Aging-CR-RM' data set (GEO accession number: GSE139204) describes mRNA profiling of skeletal muscles Soleus, Tibialis anterior, Triceps brachii and Gastrocnemius of 10 and 30 months old wild type mice and mice daily treated with rapamycin (RM) or undergoing calorie restriction (CR) for 15 months from the age of 15 months. Rapamycin treatment was at a dose of ~4 mg/kg/day. This dose of rapamycin has been shown to maximally extend lifespan in male C57BL/6 mice (see Miller, R. A. et al. Aging Cell 13, 468-477). Mice undergoing calorie restriction were fed according to 70% of AIN93M diet with 1.43x(vitamins + minerals).
- 'NMJ' data set (GEO accession number: GSE139209) contains mRNA profiles of synaptic (NMJ) and extra-synaptic (xNMJ) regions of Tibialis anterior muscle of 10 and 30 months old wild type mice. NMJ (neuromuscular junction) instability is a common feature of sarcopenic muscle and is thought to play a central role in how a muscle responds to age-related perturbations (see Valdez, G. et al. Proc Natl Acad Sci U S A 107, 14863-14868).
- 'Time course' data set (GEO accession number: GSE145480) contains mRNA profiles of Gastrocnemius muscle of 8, 18, 22, 24, 26 and 28 months old wild type mice.

Rat data set:

- 'Time course' data set (GEO accession number: GSE78702 and GSE146976) contains mRNA profiles of Gastrocnemius muscle of 8, 18, 20, 22 and 24 months old wild type rats (see Pannerec, A. et al. AGING 8, 3).

Analysis tools:

- Click Expression to plot the gene expression.
- Click DE to compare gene expression between two conditions.
- Click PCA to perform principal component analysis.

If you use SarcoAtlas in your work, please cite:

Ham, D. J. et al. The neuromuscular junction is a focal point of mTORC1 signaling in sarcopenia. Nat. Commun. 11, 1–21 (2020)
A. Boersch et al. Molecular and phenotypic analysis of rodent models reveals conserved and species-specific modulators of human sarcopenia. Commun Biol 4, 194 (2021)
Ham, D. J. et al. Distinct and additive effects of calorie restriction and rapamycin in aging skeletal muscle. Submitted
GEO accession number to raw data sets will be provided after the publication.
If you have any questions about the resource, please contact us:
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