Fig 1: Differential gene expression highlight basal stem cell heterogeneity.a Heatmap showing top 300 differentially expressed genes per cluster. Dotted lines outline differentially expressed genes. b Violin plots of relative expression of marker genes split by cell cohorts and color-coded by cell community as in A. c Library 3 violin plots of relative expression of GJB2 and RHCG. d Feature plots showing expression of select basal and granular cell marker genes. e Immunostaining of KRT14 (red), KRT10 (green), and DAPI (blue) in human neonatal skin. Scale bar 100 µm. n = 3. Immunostaining of differentially expressed proteins (red) from the (f) BAS-III cluster (ASS1 [n = 6] and COL17A1 [n = 4]), (g) BAS-III/IV clusters (KRT19 [n = 3] and GJB2 [n = 4]), (h) BAS-I cluster (PTTG1 [n = 6] and CDC20 [n = 6]), (i) BAS-II cluster (RRM2 [n = 6] and PCLAF [n = 2]), (j) GRN cluster (SPINK5 [n = 3] and CALML5 [n = 2]), and (k) the MEL (MLANA [n = 2]) and LAN (CD74 [n = 2]) clusters in human neonatal skin. COL7A1 (green) and DAPI (blue) are costained. Dotted lines denote position of basement membrane where COL7A1 staining is absent. Scale bar 100 µm. l Quantification of ASS1 (n = 14 ridges) and KRT19 (n = 10 ridges) staining intensity at the top and bottom of Rete ridges. ***p < 0.0001. m Quantification of PTTG1 (n = 102 cells) and RRM2 (n = 104 cells) distance from the basement membrane, with KRT14 + basal cell (n = 167 cells) or KRT10+ suprabasal cell (n = 142 cells) distance shown as controls. Black stars represent significance compared with basal cell position whereas green stars represent significance compared with suprabasal position. ***p < 0.0001. Box represents 25th to 75th percentiles. Whiskers represent minimum and maximum data points. Bar represents mean. Significance was determined by unpaired two-tailed t test.