scMuscle

The Single-Cell Muscle Project (scMuscle) aims to collect, analyze, and provide to the research community skeletal muscle transcriptomic data.

Click one of the tabs above to begin viewing the data...

Current data version: 1.1 (details found here )

This resource was developed by the Cosgrove and De Vlaminck Labs at Cornell University.

Code for this web app is available here . To report errors or request new features, please post an issue on the Github page or email scmuscle@cornell.edu

Please cite this paper when using this resource:

McKellar, D.W., Walter, L.D., Song, L.T. et al. Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration. Commun Biol 4, 1280 (2021). https://doi.org/10.1038/s42003-021-02810-x

Click here to load entire dataset. (opens with 10% of all cells) Re-draw plots to see additional data once loaded.

Plot 1: Gene expression UMAP... Select gene

Plot 2: Cell type UMAP... Select reduction

Plot 3: Metadata feature UMAP... Select feature

Select gene

Select feature

Select a gene to plot

Select cell type IDs:

Select feature

Click to apply input changes below

Select gene(s) to display:

Select feature

Download Specifications

file type:

horizontal dimension (inches)

vertical dimension (inches)

Download

Visualize gene expression in myogenic cells alone...

Choose a dimensional reduction to display:

Group cells by metadata features...

Metadata Features:

Click to generate new violin plots

Select gene(s) to plot

Download Specifications

file type:

horizontal dimension (inches)

vertical dimension (inches)

Download

Visualize spatial gene expression across injury response

Select gene(s) to plot:

Visualize cell type distributions across injury response

Select cell type(s) to plot:

Download Specifications

file type:

horizontal dimension (inches)

vertical dimension (inches)

Download

scMuscle

The Single-Cell Muscle Project (scMuscle) aims to collect, analyze, and provide to the research community skeletal muscle transcriptomic data.

Click one of the tabs above to begin viewing the data...

Current data version: 1.1 (details found here )

This resource was developed by the Cosgrove and De Vlaminck Labs at Cornell University.

Code for this web app is available here . To report errors or request new features, please post an issue on the Github page or email scmuscle@cornell.edu

Please cite this paper when using this resource:

McKellar, D.W., Walter, L.D., Song, L.T. et al. Large-scale integration of single-cell transcriptomic data captures transitional progenitor states in mouse skeletal muscle regeneration. Commun Biol 4, 1280 (2021). https://doi.org/10.1038/s42003-021-02810-x

Click here to load entire dataset. (opens with 10% of all cells) Re-draw plots to see additional data once loaded.

Seurat object downloads can be found here.

Supplemetal resources from our preprint may be found here.

If you wold like to download the raw sequencing data (.fastq files), you can find GEO/SRA download info here.