Welcome to the non-diseased Human Skin Reference Atlas

This atlas integrates publicly available single-cell RNA-sequencing data from non-diseased human skin across multiple studies, individuals, and anatomical sites. It provides a standardised reference for exploring skin cell populations and supporting annotation and hypothesis generation.

Human Skin Atlas — UMAP and cell type hierarchy
UMAP embedding coloured by cell type (left) and hierarchical organisation of skin cell populations across three annotation levels (right).
Explore Cell Populations
Each card below is one cell compartment. Use the two buttons on each card:
Open App → Launches the interactive Shiny application for that compartment — browse gene expression, markers, and cell type annotations directly in your browser.
↓ h5 and rds Downloads the processed atlas files for that compartment in HDF5 (.h5) and .rds format.
Main Atlas
All cell types

Full integrated atlas across all five major compartments. Atlas-wide UMAP, cross-population comparisons, and marker gene exploration.

Open App → ↓ .h5ad ↓ .rds
Epithelial Cells
Epithelial

Keratinocytes and rarer epithelial cell populations, such as eccrine gland cells and hair follicles–related subtypes.

Open App → ↓ .h5 ↓ .rds
Immune Cells
Immune

Major lymphoid and myeloid immune resident immune cell populations.

Open App → ↓ .h5 ↓ .rds
Mesenchymal Cells
Mesenchymal

Fibroblast subtypes, smooth muscle cells, and vasculature-related mesenchymal cell populations.

Open App → ↓ .h5 ↓ .rds
Endothelial Cells
Endothelial

Major blood and lymphatic endothelial cell populations, including venous, arterial, capillary, and lymphatic subsets.

Open App → ↓ .h5 ↓ .rds
Neural Crest-Derived Cells
Neural Crest

Melanocyte and Schwann cell populations.

Open App → ↓ .h5 ↓ .rds
Citation

Please cite this work if you use this atlas in your research:

"[Publication to come…] Celine Pattaroni & Johannes Kern - CUTaneous Immunology and Systems lab (CUTIS). Department of Immunology at Monash University