Fig. 3

Integration of single-cell RNA sequencing datasets from MCF-7 cells cultured in standard 2D conditions and MS. A 5592 single-cell transcriptomes derived from 2D- and MS-cultured MCF-7 cells were integrated and represented bi-dimensionally. B The distribution of 2D- and MS-cultured MCF-7 cells in each cluster relative to the total cell number is indicated. C, D FEA was performed for the gene signatures derived from the DEGs of the original MS Cluster 1 (C) and MS Cluster 2 (D) on the integrated dataset. E Cell cycle distribution for each cluster as the percent of total cell number is indicated. F QPCR for the top DEGs of MS Cluster 1 and MS Cluster 2 was performed in MCF-7 cells cultured in 2D vs MS conditions. Data are presented as fold change (FC) normalized to 2D cells on a per gene basis. *P < 0.05, **P < 0.005, ***P < 0.001, ns not significant