Fig. 1: Enhancer change in the process of hMSCs differentiation.

A Pipeline for SEs identification. The H3K27ac peaks from each sample were merged to generate a consistent peak set comprise 149217 peaks. After excluding of 17609 promoter regions, remained enhancers within a genome distance of 12.5 kb were stitched together and resulted in a total of 34922 stitched enhancers. Next, ROSE algorithm was applied to each sample to determine a primary SE number. The mean value of primary number from all samples was used to redefine the SE number for each sample. The enhancers with a mean rank of 1700 or higher (<1700) in each cell type were considered as SEs for this cell type. B Scatter plots display SE signal and rank of hMSCs, adipocytes and osteoblasts from the first replication of differentiation experiment. The intersection points of dashed line corresponding to the cut-off point of SEs and TEs, in X-axis, it corresponding to 1700. Colored points indicate SEs with a mean rank of 1700 or higher (<1700) in two replications, while gray points indicate SEs with a mean rank lower (>1700) in two replications. C Upset plot display the SE number for each cell type and the overlap among three or between two cell types. D Scatter plots display SE signal alteration between differentiated cells and hMSCs: up panel showed the signal alteration of SEs between adipocytes and hMSCs, the lower panel showed the signal alteration of SEs between osteoblasts and hMSCs. Blue dots indicate a significant higher (FDR ≤ 0.1, equivalent to the original P ≤ 0.0228) signal in adipocytes cells, green dots indicate a significant higher signal in osteoblasts, red dots indicate a significant higher signal in hMSCs. E Bar plots display the percentage of enhancers with significant signal change after differentiation into adipogenic and osteogenic lineage.