Epidermal basal domains organization highlights skin robustness to environmental exposure [scRNA-seq]

Purpose: To unravel the molecular heterogeneity and characterise cell states of LRC/Non-LRC domains in interfollicular epidermis in vivoMethods: We performed 10x genomics single-cell RNA sequencing (scRNA-seq) of FACS purified basal (Sca1+/alpha6-integrin+) IFE cells as H2BGFP LRCs, mid-LRCs, and non-LRCs from K5-tTA x pTRE-H2BGFP mice. Single-cell suspension from back (2-week chase) and tail skin (3-week chase) was processed for the barcoded single-cell 3â€2 cDNA libraries generation using Chromium Single Cell 3â€2 gel bead and library Kit v3. The final libraries were quantified using Agilent Bioanalyzer high sensitivity DNA chip and sequenced using an Illumina NextSeq-500. The raw data files were demultiplexed to generate the sample-specific FASTQ files, which were aligned to the mouse reference genome (mm10-3.0.0) using the 10x Genomics Cell Ranger pipeline (v3.1.0). The raw scRNA-seq data was processed using Cell Ranger from the 10x platform to generate an expression matrix that was further analyzed in R using the Seurat package version 3.1. Only high-quality cells that had between 200 and 5000 genes expressed and had under 10% of the UMIs mapped to mitochondrial genes were retained.Results: We obtained a total of 13484 and 14884 high quality cells from two different skin types after combining two datasets each from LRCs/mid-LRCs/Non-LRCs for further analysis by Seurat workflowConclusions: Obtained high quality single cell transcriptomic data to dissect molecular and proliferative heterogeneity of interfollicular epidermis (IFE)

Single cell RNA-seq profiles of sorted IFE LRC/Non-LRC domains from back and tail skin of wild type (WT) mice