Muscle De Micheli Muscle Cells Track Settings
Muscle RNA binned by cell type from De Micheli et al 2020

Track collection: Muscle single cell data from De Micheli et al 2020

+  Description
+  All tracks in this collection (2)

Display mode:      Duplicate track

Label: Name or ID of item    Alternative name for item   

Log10(x+1) transform:    View limits maximum: UMI/cell (range 0-10000)

Cell type:  
 skeletal muscle cell ACTA1+
 smooth muscle cell ACTA2+ MYH11+ MYL9+
 adipocyte APOD+ CFD+ PLAC9+
 macrophage C1QA+ CD74+
 platelet CD36+ VWF+
 endothelial cell CLDN5+ PECAM1+
 fibroblast COL1A1+
 fibroblast DCN+ GSN+ MYOC+
 fibroblast FBN1+ MFAP5+ CD55+
 erythroblast HBA1+
 endothelial cell HBA1+
 B/T/NK cell IL7R+ PTPRC+ NKG7+
 muscle stem cell PAX7+ DLK1+ (MuSC1)
 muscle stem cell PAX7- MYF5+ (MuSC2)
 pericyte RGS5+ MYL9+
 macrophage (inflammatory) S100A9+ LYZ+
Data schema/format description and download
Assembly: Human Dec. 2013 (GRCh38/hg38)
Data last updated at UCSC: 2022-05-12 04:20:12


This track displays data from A reference single-cell transcriptomic atlas of human skeletal muscle tissue reveals bifurcated muscle stem cell populations. Muscle tissue was analyzed using single-cell RNA-sequencing (scRNA-seq) and subsequent clustering distinguished 16 muscle-resident cell types based on their identified marker genes found in De Micheli et al., 2020. Muscle samples were from surgically discarded tissue taken from a wide variety of anatomical sites.

This track collection contains two bar chart tracks of RNA expression in the human muscle where cells are grouped by cell type (Muscle Cells) or biosample (Muscle Sample). The default track displayed is Muscle Cells.

Display Conventions

The cell types are colored by which class they belong to according to the following table.

Color Cell classification
stem cell

Cells that fall into multiple classes will be colored by blending the colors associated with those classes. The colors will be purest in the Muscle Cells subtrack, where the bars represent relatively pure cell types. They can give an overview of the cell composition within other categories in other subtracks as well. Note that the Muscle Sample subtrack is colored based on colors provided from Figure 1 from De Micheli et al., 2020.

Relevant Figures From De Micheli et al. 2020

Muscle tissue cell type populations.

Muscle Tissue Cell
De Micheli et al. Skelet Muscle. 2020. / CC BY 4.0


Muscle samples were taken from 10 healthy donors of ages ranging from 41-81 years old from different sections of the face (F), trunk (T), and leg (L). Excessive fat and connective tissue were removed from the muscle samples prior to enzymatic dissociation. Next, libraries were prepared using the 10x Genomics 3' v2 or v3 library kit and sequenced on the Illumina NextSeq 500. This resulted in libraries with 200-250 million reads which were processed using Cell Ranger version 3.1. In total, over 22,000 RNA transcriptomic profiles were generated from all of the samples after quality control filtering. The single cell transcriptomes from all 10 datasets were integrated using a scRNA-seq integration method called Scanorama as described in the reference below.

The cell/gene matrix and cell-level metadata was downloaded from the UCSC Cell Browser. The UCSC command line utility matrixClusterColumns, matrixToBarChart, and bedToBigBed were used to transform these into a bar chart format bigBed file that can be visualized. The coloring was done by defining colors for the broad level cell classes and then using another UCSC utility, hcaColorCells, to interpolate the colors across all cell types. The UCSC utilities can be found on our download server.

Data Access

The raw bar chart data can be explored interactively with the Table Browser or the Data Integrator. For automated analysis, the data may be queried from our REST API. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.


Thanks to Andrea De Micheli of the Cosgrove Laboratory at Cornell University and to the many authors who worked on producing and publishing this data set. The data were integrated into the UCSC Genome Browser by Jim Kent and Brittney Wick then reviewed Luis Nassar. The UCSC work was paid for by the Chan Zuckerberg Initiative.


De Micheli AJ, Spector JA, Elemento O, Cosgrove BD. A reference single-cell transcriptomic atlas of human skeletal muscle tissue reveals bifurcated muscle stem cell populations. Skelet Muscle. 2020 Jul 6;10(1):19. PMID: 32624006; PMC: PMC7336639