A single-cell spatial census of human skin anatomy

This repository contains the processed data and container environments for the paper titled "A single-cell spatial analysus of human skin anatomy". Raw MERFISH data including transcripts.csv files, cell segmentation masks, and MERFISH stain images are available at EMBL-EBI BioImage under the accession S-BIAD2376. Analysis code is also available on Github at https://github.com/paularstrpo/ns-atlas-analysis. Abstract The skin is the largest human organ and a site of significant disease burden, yet its cellular and molecular organization across the body are largely undefined. Here, we construct a single-cell spatial atlas of ~1.2 million cells from normal adult human skin, resolving the location of 45 cell types across 15 anatomic sites. We define principles of organ-wide cell composition, including axes of cell diversity and specialization, and distinct site-enriched cell types. Each body site zonates into 10 multicellular neighborhoods, including a perivascular neighborhood enriched for immune-stromal crosstalk, which serves as a pan-disease domain of immune modulation from analysis of public spatial transcriptomics data encompassing healthy and diseased skin. We present a framework for the multiscale spatial organization of the largest human organ at unprecedented molecular, cellular, microanatomic, and macroanatomic detail. This browsable resource advances our understanding of skin cellular organization and communication, and its architectural disruption in disease.