Skip to main content
Fig. 5 | Genome Biology

Fig. 5

From: scMC learns biological variation through the alignment of multiple single-cell genomics datasets

Fig. 5

scMC reveals integrated epidermal and dermal trajectories by simultaneous integration across replicates and time points during skin embryonic development. a, b UMAP of the corrected data from scMC on the time-course scRNA-seq datasets from E13.5 to E14.5. a Cells are colored by the replicates and time points. b Cells are colored by the identified cell subpopulations from the corrected data. Cells inside the dashed line were identified as dermal and epidermal cells based on their known markers. c Overlay the expression levels of markers of dermal (Col1a1 and Lum) and epidermal cells (Krt14 and Krt10) onto the UMAP space. Dark red and gray colors represent the high and zero expression, respectively. d PHATE visualizations for the epidermal cells from both E13.5 and E14.5, only E13.5, and only E14.5, respectively. e Overlay the expression levels of markers of epidermal cells (Krt5, Krt14, Krt10, and Lor) onto the PHATE space. f PHATE visualizations for the dermal cells from both E13.5 and E14.5, only E13.5, and only E14.5, respectively. g Overlay the expression levels of markers of dermal cells (Lox and Col1a1) and DC cells (Sox2 and Bmp4) onto the PHATE space. h Comparison of the recovered trajectories by computing Pearson correlation coefficients between the pseudotime values of cells from each replicate sample before and after integration. i, j Pseudotemporal dynamics of un-differentiation and differentiation marker genes reconstructed from the integrated trajectories. Cells are colored based on the pseudotime values. Blue lines represent the locally weighted smoothing expression. Color bar represents the scaled pseudotime values

Back to article page