The skeletal muscle cell type enriched transcriptome

The main function of skeletal muscle is to provide stability, posture and movement throughout the body. It handles this by contracting and relaxing in a manner coordinated directly by impulses from the brain, i.e., it is under voluntary control, as opposed to cardiac and smooth muscle, where movement is involuntary. Another important function of skeletal muscle is to regulate body temperature. The heat is generated when the muscles contract and cause blood vessels in the skin to dilate.

1225 genes were predicted to have cell type specificity in the skeletal muscle.

  • 9 cell types profiled
  • 131 very highly enriched genes
  • 305 highly enriched genes
  • 811 moderately enriched genes


Skeletal muscle cell type enriched transcriptome: Summary

Genes with predicted cell type specificity within skeletal muscle are detailed in Table 1. Identified genes are subdivided into 3 specificity categories, based on the difference between the enrichment score in the corresponding cell type, compared to the other cell types profiled in the tissue (see Methods Summary page for details):

  • Predicted specificity: ยดVery highยด - Differential score vs. other profiled cell types within the tissue >0.35
  • Predicted specificity: ยดHighยด - Differential score vs. other profiled cell types within the tissue >0.25
  • Predicted specificity: ยดModerateยด - Differential score vs. other profiled cell types within the tissue >0.15


Table 1. Number of genes in each specificity category in the skeletal muscle cell types.

Cell type
Very high
High
Moderate
Total enriched
Skeletal myocytes 63 107 180 328
Endothelial cells 4 37 196 237
Smooth muscle cells 3 12 26 41
Fibroblasts 0 53 285 338
Macrophages 25 55 98 178
Neutrophils 13 9 12 34
Plasma cells 23 32 14 69
All cell types 131305811 1225


Figure 1. Bar plot of the number of enriched genes in the cell types of the skeletal muscle, divided by specificity category

0.050100150200250300genesSkeletal myocytes_1Skeletal myocytes_2Skeletal myocytes_3Endothelial cellsSmooth muscle cellsFibroblastsMacrophagesNeutrophilsPlasma cellsVery highHighModerate

Skeletal muscle cell type enriched transcriptome: Illustrative examples

Skeletal myocytes

Skeletal muscle cells consist of many individual striated muscle cells that are fused together into long, multinuclear myofibers. The contractile function of muscle cells is controlled by actin and myosin myofilaments, which form small repeating subunits known as sarcomeres which are then arranged together and aligned to form very long, repeating myofibrils, which give skeletal muscle its distinctive striated or striped pattern. Skeletal muscle myofibers can be separated into two main types, termed fast-twitch and slow-twitch.

Myocyte 1

Genes classified as having specificity in the Myocyte_1 group include the contractile protein Myosin light chain 6B (MYL6B), the regulatory protein Troponin C1, slow type (TNNC1), as well as the uncharacterized protein C12orf75, with unknown function.

0.30.40.50.60.70.80.91.0Enrichment
MYL6B - Skeletal muscle

MYL6B
0.30.40.50.60.70.80.91.0Enrichment
TNNC1 - Skeletal muscle

TNNC1
0.30.40.50.60.70.80.91.0Enrichment
C12orf75 - Skeletal muscle

C12orf75

Myocyte 2

Genes classified as having specificity in the Myocyte_2 group include the sarcoglycan complex subunit Sarcoglycan gamma (SGCG), which links the myocyte cytoskeleton to the extracellular matrix, as well as Calcium voltage-gated channel subunit alpha1 S (CACNA1S), involved in calcium regulation, and Protein phosphatase 1 regulatory subunit 3A (PPP1R3A), which is important for the metabolism of glycogen in muscle fibers.

0.30.40.50.60.70.80.91.0Enrichment
SGCG - Skeletal muscle

SGCG
0.30.40.50.60.70.80.91.0Enrichment
CACNA1S - Skeletal muscle

CACNA1S
0.30.40.50.60.70.80.91.0Enrichment
PPP1R3A - Skeletal muscle

PPP1R3A

Myocyte 3

Genes classified as having specificity in the Myocyte_3 group include the regulatory proteins Troponin C2, fast type (TNNC2), Myosin binding protein C2, fast isoform (MYBPC2), and ATPase sarcoplasmic/endoplasmic reticulum Ca2+ transporting 1 (ATP2A1), responsible for calcium reuptake into the sarcoplasmic reticulum.

0.30.40.50.60.70.80.91.0Enrichment
TNNC2 - Skeletal muscle

TNNC2
0.30.40.50.60.70.80.91.0Enrichment
MYBPC2 - Skeletal muscle

MYBPC2
0.30.40.50.60.70.80.91.0Enrichment
ATP2A1 - Skeletal muscle

ATP2A1