Fig. 1: Comparing single-cell trajectories of reprogramming and transformation.
a, Schematic of the repro-transformable mouse model. Reprogramming (repro; doxycycline-induced OSKM expression) or transformation (transfo; tamoxifen-induced K-rasG12D expression combined with c-Myc overexpression) gave rise to iPS cells or transformed cells (TCs), respectively. b, Immunofluorescence staining of repro-induced iPS cells for Ssea1 and Nanog. Scale bar, 100 µm. c, Histological analysis of teratomas derived from iPS cells. Scale bar, 1 mm. d, Tumour generated by transformed cells injected into nude mice. Scale bar, 0.2 mm. e, Proliferation curves of MEFs upon induction of repro, transfo and repro plus transfo. The data from one representative experiment out of two are shown. f,g, T-SNE visualization of scRNA-Seq profiles integrating the replicate values of 30,146 preprocessed cells (individual dots), corresponding to two biological replicates run in one sequencing experiment. The cells are coloured by sample (f) or by cluster (g). h,i, Diffusion maps of scRNA-Seq profiles where the cells are coloured by sample (h) or by cluster (i). The trajectories defined by Slingshot are represented by red (repro) and blue lines (transfo). The intersection area is indicated by a red box. j, Composition of samples in the intersection area. k,l, Patterns of the MEF identity signature score using gene lists from Schiebinger et al.13, with the score represented on the diffusion map (k) or on the calculated pseudotime trajectories (l).
