Global transcriptional profiles of abdominal skin epidermis during perinatal period

We report global transcriptional alteration and transcriptional heterogeneity of epidermal cells in remodeling mouse abdominal skin during perinatal period. By RNA-sequencing of FACS-isolated interfollicular epidermal (IFE) basal cells from abdominal skin of wildtype (WT) non-pregnant (NP) mice, pregnant mice, and Tbx3 cKO pregnant mice, we revealed pregnancy-associated genes and a key role of Tbx3 in regulating the pregnancy-associated transcriptome. To resolve the transcriptional heterogeneity of epidermal cells at single cell resolution, we performed single cell RNA sequencing of epidermal cells isolated from the abdominal skin of NP mice, pregnant mice, and post-partum mice by using Tbx3creERT2;R26H2B-EGFP mice. By unsupervised evaluation of clustering-based cell identities of total samples on the Seurat platform, we identified 14 main clusters, where the IFE1 cluster was appeared to be enriched in Dpc16 samples, and further revealed the pseudotime differentiation of Tbx3cre labeled cells during perinatal period. For RNAseq, mRNA profiles of FACS-isolated interfollicular basal cells (CD49f+, CD34-) from abdominal skin of wildtype (WT) non-pregnant (NP) mice, pregnant mice at dpc16, and K14creERT2;Tbx3flox/flox (Tbx3 cKO) pregnant mice at dpc16 were generated by deep sequencing, in triplicate, using Illumina NextSeq500. For scRNAseq, we treated the mice with tamoxifen during pregnancy and harvested abdominal skin at dpc16, dpp6, and dpp40. For the control, abdominal skin was harvested from non-pregnant (NP) mice treated with tamoxifen for 3 days. After dissociation of the epidermis into single cells, we generated chromium single cell 3′ v2 libraries from randomly captured epidermal cells and sequenced them using Illumina NextSeq500. We profiled 36,912 cells (NP: 6,485 cells; Dpc16: 12,846 cells; Dpp6: 9,029 cells; Dpp40: 8,552 cells) with a range of 20,000–40,000 mean reads per cell for each sample, whereby approximately 1,400–1,600 median genes per cell for each sample were detected.