Fig 1: a Workflow depicting single-cell isolation by epithelial and mesenchymal markers, followed Hi-C library construction from the single cells isolated from the “PEO1+HEYA8” mixed population of cells. Single cells isolated from the “PEO1+HEYA8” mixed population were classified into (i) Epithelial (EpCAM+/VIM–), (ii) Hybrid (EpCAM+/VIM+), and (iii) Mesenchymal (EpCAM–/VIM+) clusters. Profiles of the 3 clusters: b Staining of EpCAM (PE, red) and Vimentin (FIT-C, green); c Heatmap of single-cell Hi-C matrix at ± 500 kb of EPCAM or VIM; and d genome structures at chromosome 2 and 10. Hierarchical clustering heatmap based on the cell-cell r.m.s.d values at chromosomes 2 and 10 are shown on the right of the genome structures. e Workflow depicting single-cell isolation by epithelial and mesenchymal markers, following which Hi-C library construction from the single cells isolated from OVCA429 shGRHL2 Tet-inducible cell line treated with doxycycline to induce GRHL2 expression. The single cells from OVCA429 shGRHL2 Tet-inducible were classified into (i) low GRHL2/EpCAM, (ii) mid GRHL2/EpCAM, and (iii) high GRHL2/EpCAM as differentiated by the staining intensity of GRHL2 (APC, green) and EpCAM (PE, red). Profiles of the GRHL2 groups: f staining profiles. EMT spectrum (orange-purple gradient rectangle) alongside GRHL2 staining intensity (triangle with white-black gradient) indicates how the 3 groups of cells correspond to their EMT states in the spectrum; and g genome structures of chromosome 2 and 10. Heatmap of the cell-cell r.m.s.d values at chromosome 2 and 10 of the OVCA429 shGRHL2 Tet-inducible single cells are shown below the genome structures. In b and f, cell IDs are shown to the left of staining images. In d and g, color = purple-to-red spectrum denotes chromosome start-to-end. Cells are arranged according to the dendrogram derived from hierarchical clustering of the cell-cell r.m.s.d values