Schema for Skin Cell - Skin single cell RNA binned by cell type from Sole-Boldo et al 2020
  Database: hg38    Primary Table: skinSoleBoldoCellType Data last updated: 2022-05-12
Big Bed File: /gbdb/hg38/bbi/skinSoleBoldo/cell_type.bb
Item Count: 22,193
Format description: BED6+5 with additional fields for category count and median values, and sample matrix fields
fieldexampledescription
chromchr1Reference sequence chromosome or scaffold
chromStart166070019Start position in chromosome
chromEnd166166969End position in chromosome
nameFAM78BName or ID of item
score0Score from 0-1000, typically derived from total of median value from all categories
strand-+ or - for strand. Use . if not applicable
name2ENSG00000188859.5Alternative name for item
expCount13Number of categories
expScores0.00214439,0.00084246,0,0,0.0013465,0.00813008,0,0,0.000557724,0.0101493,0.00318134,0.00156128,0.00613497Comma separated list of category values

Sample Rows
 
chromchromStartchromEndnamescorestrandname2expCountexpScores
chr1166070019166166969FAM78B0-ENSG00000188859.5130.00214439,0.00084246,0,0,0.0013465,0.00813008,0,0,0.000557724,0.0101493,0.00318134,0.00156128,0.00613497
chr1166334883166335762RP11-479J7.20+ENSG00000229588.1130,0.00084246,0,0,0,0,0,0,0.00167317,0.00179104,0,0.00078064,0
chr1166840088166854473POGK0+ENSG00000143157.7130.100786,0.11289,0.00645161,0.0782313,0.0359066,0.146341,0.040404,0.0483607,0.0356944,0.0531343,0.0291622,0.0163934,0.0490798
chr1166856509166876327TADA10-ENSG00000152382.5130.0271623,0.0286436,0.00645161,0.0238095,0.0112208,0.0325203,0.00841751,0.0180328,0.0139431,0.0101493,0.00848356,0.0101483,0.013 ...
chr1166989108167022214MAEL0+ENSG00000143194.8130,0.00084246,0,0,0.000448833,0,0,0.00163934,0.00111545,0,0,0,0.000681663
chr1167052835167090631GPA330-ENSG00000143167.7130.000714796,0,0,0,0.00224417,0,0,0,0,0,0,0,0
chr1167219830167220512RP11-277B15.30-ENSG00000272205.1130.00142959,0.00084246,0,0,0,0,0,0,0,0.000597015,0,0.00078064,0.000681663
chr1167220828167427345POU2F10+ENSG00000143190.17130.0557541,0.0606571,0.00645161,0.0782313,0.0251346,0.0813008,0.0505051,0.047541,0.0351366,0.0513433,0.0530223,0.0210773,0.040218 ...
chr1167430639167518538CD2470-ENSG00000198821.6130.00500357,0.00505476,0.00645161,0.00340136,0.00224417,0.0162602,0,0.00491803,0.0022309,0.0041791,0.00318134,0.139735,0.00886162
chr1167457741167459891RP11-104L21.30-ENSG00000273160.1130,0.00084246,0,0,0.0013465,0,0,0.000819672,0,0.000597015,0,0.00624512,0.000681663

Skin Cell (skinSoleBoldoCellType) Track Description
 

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