RNA sequencing of FACS purified HFSCs, total epidermal cells and cultured HFSCs. Mus musculus

We sequenced mRNA from HFSCs that were FACS purified (CD34+alpha-6 Integrin+ cells) from p21 mouse epidermis, total epidermal cells from p21 mice and HFSCs cultured for 14 days in 3C cultures, 3 biological replicates each. We sequenced mRNA from different cell populations that were FACS-purified from HFSC cultures (also known as 3C cultures), 3 biological replicates each. We performed two independent comparisons: 1. Comparison of FACS-purified cells grown in standard 3C cultures: HFSCs (CD34+ alpha-6 Integrin+) and non-HFSCs (CD34neg alpha-6 Integrin+). 2. Comparison of total cells in 3C cultures treated for 48 hours with dorsomorphin (BMP inhibitor that causes depletion of CD34+ alpha-6 integrin+ cells in 3C cultures) or with cyclopamine Shh inhibitor that causes enrichment of CD34+ alpha-6 integrin+ cells in 3C cultures). Overall design: Examination of transcriptomes from bona fide HFSCs, total epidermal cells and cultured HFSCs. The aim of the experiment was to determine: for the first comparison (1.) the identity of the two populations of cells that grow in 3C cultures (CD34+ alpha-6 Integrin+ and CD34neg alpha-6 Integrin+); and for the second comparison (2.) the early transcriptional changes that lead to a fate change in cells grown in 3C cultutres to drive depletion (with dorsomorphin treatment) or enrichment (with cyclopamine treatment) of HFSCs.