Skin Sole-Boldo Skin Cell Track Settings
 
Skin single cell RNA binned by cell type from Sole-Boldo et al 2020

Track collection: Skin single cell data from Sole-Boldo et al 2020

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+  All tracks in this collection (4)

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Label: Name or ID of item    Alternative name for item   

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

Categories:  
 keratinocyte
 epidermal stem (EpSC) and progenitor cell
 erythrocyte
 endothelial lymphatic cell
 macrophage/dendritic cell
 melanocyte
 fibroblast (mesenchymal)
 pericyte
 fibroblast (pro-inflammatory)
 fibroblast (secretory-papilliary)
 fibroblast (secretory-reticular)
 T cell
 endothelial vascular cell
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Data last updated at UCSC: 2022-05-12 17:35:44

Description

This track displays data from Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming. Single cell RNA sequencing (scRNA-seq) was performed on sun-protected skin samples prepared using droplet-sequencing (drop-seq). RNA profiles were generated for 15,457 cells after quality control and subsequent clustering identified 17 clusters with distinct expression profiles as found in Solé-Boldo et al., 2020.

This track collection contains four bar chart tracks of RNA expression in the human skin where cells are grouped by cell type (Skin Cell), age (Skin Age), donor (Skin Donor), and cell type and donor's age (Skin Cell+Age). The default track displayed is Skin Cell.

Display Conventions

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

Color Cell classification
fibroblast
immune
epithelial
endothelial

Cells that fall into multiple classes will be colored by blending the colors associated with those classes. The colors will be purest in the Skin Cell 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.

Method

Healthy skin samples were obtained from whole-skin specimens belonging to 5 male donors (ages 25-70) with fair skin. Donors underwent full body skin examinations by a dermatologist and medical records were checked for skin diseases and/or comorbidities that affect the skin. 4-mm punch biopsies were taken from surgically removed skin belonging to the inguinal region of the body also known as the groin. Skin samples were kept in MACS Tissue Storage Solution for less than 1 hour to avoid necrosis and apoptosis. Enzymatical and mechanical dissociation was done using the Miltenyi Biotec Whole Skin Dissociation kit for human material and the Miltenyi Biotec Gentle MACS dissociator. Drop-seq libraries were prepared using a 10x Genomics 3' v2 kit and sequenced on an Illumina HiSeq4000.

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.

Credit

Thanks to Llorenç Solé-Boldo 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 by Gerardo Perez. The UCSC work was paid for by the Chan Zuckerberg Initiative.

References

Solé-Boldo L, Raddatz G, Schütz S, Mallm JP, Rippe K, Lonsdorf AS, Rodríguez-Paredes M, Lyko F. Single-cell transcriptomes of the human skin reveal age-related loss of fibroblast priming. Commun Biol. 2020 Apr 23;3(1):188. PMID: 32327715; PMC: PMC7181753