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scMuscle

The Single-Cell Muscle Project (scMuscle) aims to collect, analyze, annotate, and provide to the research community skeletal muscle transcriptomic data. This includes tools to visualize and re-analyze these data in a consistent and repeatable manner.

If you have a dataset that you would like to see included in a future version of this project, please fill out this survey! Any species, any age, any disease, any muscle-related cell line or organoid!

Figure1

We used more than 100 single-cell and single-nucleus RNA sequencing datasets, from 14 different research groups, to build an integrated transcriptomic reference of murine skeletal muscle. The resulting compendium has ~365,000 cell/nucleus, which we have annotated using a suite of existing software tools (see linked preprint for more details).

Here, you'll find all of the R scripts used for the analysis and visualization (R_scripts/) as well as some of the supplemental resources we generated (supplemental_data/). These resources include metadata details, outputs from differential gene expression analysis, and some other useful gene lists.

You will also find the development version of the code used in our web application (web_app/), as well as details on different versions of the data (data_versions/)

Links:

Code and supplemental data from McKellar et al, Communications Biology, 2021:

Web application to explore these data can be found here

Fully processed Seurat and CellChat objects from this study can be downloaded here. Or, you can download individual objects with wget:

  • Full scMuscle atlas dataset:
wget -O scMuscle_mm10_slim_v1-1.RData https://datadryad.org/stash/downloads/file_stream/1113825
  • Subset myogenic data:
wget -O myo_slim_seurat_v1-1.RData https://datadryad.org/stash/downloads/file_stream/1113823
  • CellChat object:
wget -O scMuscle_cellchat_v1-1.RData https://datadryad.org/stash/downloads/file_stream/1113826
  • Preprocessed Visium data:
wget -O vis_slim_v1.RData https://datadryad.org/stash/downloads/file_stream/1113824

Raw data from Spatial RNA sequencing (Visium) can be found here

Raw data from new 10x Chromium datasets can be found here

Projects and manuscripts that have used the scMuscle dataset:

Actions and interactions of IGF-I and MMPs during muscle regeneration
Kok, H.J. & Barton, E.R.
Seminars in Cell & Developmental Biology, 2021
PubMed link
The first figures published of the scMuscle project were actually in this review. Check out Figure 3!

A Tead1-Apelin axis directs paracrine communication from myogenic to endothelial cells in skeletal muscle.
Lee, U., Stuelsatz, P., Karaz, S., McKellar, DW, Russeil, J., Deak, M., de Vlaminck, I., Lepper, C., Deplancke, B., Cosgrove, B. D., Feige, J. N.
iScience, 2022
PubMed link
*Script for this analysis can be found in R_scripts/example_notebooks/Lee_Tead-Apelin_iScience_2022.Rmd

Hedgehog signaling acts as cell fate determinant during adult tissue repair.
Norris AM, Johnson CD, Zhou LY, Appu A, McKellar DW, Cosgrove BD, Kopinke D
bioRxiv, 2022
*Script for this analysis can be found in R_scripts/example_notebooks/hedgehog_Norris_et_al.Rmd