A spatialtemporal gene expression database for human aging muscle regeneration
About the human aging muscle regeneration model
The human skeletal muscle injury and regeneration clinical trial (ID) was induced in a dynamometer by 200 involuntary muscle contractions initiated by electrical stimulation of the vastus lateralis part of the quadriceps femoris muscle simultaneously with a greater opposite force applied by the dynamometer arm (eccentric muscle work). Skeletal muscle biopsies were obtained from the vastus lateralis part of the quadriceps femoris muscle with manual suction under local analgesics (Xylocain 10 mg/ml, AstraZeneca, Stockholm, Sweden) in sterile conditions. A minimum distance of 3 cm was kept between each incision to minimize the effect of repeated sampling before injury (pre), and at 2, 8, 30 days post injury.
Spatial transcriptomics analysis
Spatial transcriptomics analysis of skeletal muscle was carried out on samples from three subjects. Biopsies from pre, 2, 8, and 30 days post injury were embedded with OCT and 10 µm thick cryosections were used for analysis. The cryosections were placed directly on Visium slides (cat. no.: PN-1000184 , 10X Genomics) with one slide containing pre, 2, 8, and 30 days post injury samples from the same donor. The spatial sequencing libraries were prepared following the manufacturer’s instructions of Visium Spatial Gene expression reagent kits guide (CG000239, 10X Genomics).
About the database
The HuMdb database was generated using the ShinyCell Framework, but modified for interactive exploration of spatial transcriptomics. HuMdb enables the exploration of gene and geneset expression score at different levels:
| Spatial plot | Spatial gene expression plots provide normalized gene or geneset expression at the spatially resoved levels. |
| UMAP plot | UMAP plot provides interactive and comparative analysis for expression levels between spatially resolved clusters, deconvoluted cell types, and genes |
| Violin/box plot | These plots provide interactive analysis of gene expression according to muscle injury and regeneration timecourse at individual or grouped levels. |
| Heatmap/bubble plot | This allows more advanced analysis (clustering) of a group of genes according to muscle injury and regeneration timecourse at individual or grouped levels. |