Note: lifted from hg19
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 Donor), and cell type and donor's age
(Skin Cell+Age). The default
track displayed is Skin Cell.
The cell types are colored by which class they belong to according to the following table.
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.
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.
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
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.
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