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Skin sc-RNASeq from seven body sites (face, scalp, axilla, palmoplantar, arm, leg, and back)
This sc-RNAseq dataset is composed of samples from 96 skin biopsies from seven body sites (face, scalp, axilla, palmoplantar, arm, leg, and back). The skin biopsies were separated into epidermis and dermis before dissociated and enriched for various cell fractions (keratinocytes, fibroblasts, and endothelial cells) and immune cells (myeloid and lymphoid cells) to up sample rare cell types. In total, across body sites, 274,834 cells were profiled, including 96,194 keratinocytes. Seurat v3.0. was utilized to normalize, scale, and reduce the dimensionality of the data. Low quality cells containing less than 200 genes per cell as well as greater than 5,000 genes per cell were filtered out. Cells containing more mitochondrial genes than the permitted quantile of 0.05 were removed. Ambient RNA was removed using R package SoupX v1.6.2. Doublets were removed using scDblFinder v1.12.0. Principal components (PC) were obtained from the topmost 2,000 variable genes, and the Uniform Manifold Approximation and Projection (UMAP) dimensional reduction technique was applied to the 30 topmost variable PC-reduced dataset. Batch effect correction was performed utilizing harmony v1.0, using donor as batch. After batch correction, cells were clustered using shared nearest neighbor modularity optimization-based clustering. Cluster marker genes were identified with FindAllMarkers; cluster corresponding cell type was identified by comparing marker genes to curated cell-type signature genes. Differential expression by keratinocyte subtype was performed with Seurat (v4.3.0) FindMarkers function by comparing keratinocyte subtype to non-keratinocyte clusters. The log fold-change of the average expression between a keratinocyte subtype cluster compared to the rest of clusters is utilized as keratinocyte-subtype gene expression statistic. Biopsy sample details, curated cell-type signature genes and processed Seurat object are provided herein. Raw data are available in SRA (id PRJNA1054546)
Funding
University of Michigan Skin Biology and Diseases Resource-based Center
National Institute of Arthritis and Musculoskeletal and Skin Diseases
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Research Institution(s)
AbbVie Inc. University of MichiganContact email
alextsoi@med.umich.eduAssociated Preprint DOI
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