Muscle Atlas

Why this app?

Skeletal muscle is composed primarily of muscle fibres, but also encompasses blood and lymph vessels, nerves and immune cells. Samples extracted from whole muscle biopsies are therefore a mix of the expression levels of all the different cells composing the tissue. As each of these cell types can potentially respond to experimental conditions, it is difficult to decipher the contribution of muscle cells to the overall tissue response.

This tool allows the estimation of mRNA levels of genes in muscle tissue and its comparison to isolated muscle fibers and several primary cell types present in muscle tissue in vivo. Because approaches using primary cells are useful to investigate the specific response of myotubes, this tool aims at providing a first estimation of the relative expression level of genes in muscle cells compared to other cells types present in muscle biopsies.

As an example, the surface marker CD14 is know to be expressed on circulating monocytes. Indeed, the tool estimates that the mRNA expression of CD14 is higher in blood and primary macrophages compared to other cell types. The expression of endothelin (EDN1) is restricted to endothelia and the tool indeed finds it much higher in endothelial cells compared to muscle or blood. On opposite, the mRNA levels of myosin heavy chain 2 (MYH2) are very high in muscle biopsies, fibres and cells and almost absent in blood, immune and endothelial cells.

In conclusion, this tool is useful to quickly compare the enrichment of your favorite gene in one cell type compared to another. However, the data should be confirmed in your own cells and under your conditions using qPCR or Western blot.

From public datasets to expression atlas

This tool was created by collecting publicly available gene array data on mRNA expression levels in human tissues and cells. For each array, only basal/control conditions were kept and processed to determine baseline expression levels. The data was then coded and uploaded in a shiny app created for easier interrogation of the database.

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