Extended Data Fig. 1: Comparing single-cell trajectories of reprogramming & transformation.
(a) Foci obtained from repro-transformable MEFs colored with cresyl-violet. (b) Soft agar colonies. (c) Immunofluorescent staining. One representative experiment (from three independent experiments). Scale bar: 100 µm. (d) Counting of γH2AX-positive cells depicted in (c). n = 3 independent experiments. One-way ANOVA followed by a Tukey’s post hoc test. (e) Counting of H2AX-positive cells after 3 days of transformation with alternative oncogenic cocktails. n = 2 independent experiments. (f) FACS of cell cycle analysis. (g) Countings. Data presents one experiment representative of three independent experiments. (h) FACS profile PI/AnnexinV after 3 days of Repro, Transfo or Repro+Transfo compared to control MEFs. One representative experiment (from two independent experiments). (i) Percentage of total apoptosis depicted in (h). n = 2 independent experiments. (j-k) T-distributed stochastic neighbor embedding (t-SNE) visualization of sc-RNA-seq profiles (individual dots). Cells are colored by samples (j) or by clusters (k). (l-m) Patterns of MEF identity signature score using gene lists from Nefzger et al., 2017. (l) Score represented on the diffusion map. (m) Score represented on the calculated pseudo-time trajectories. (n) MEF identity score during reprogramming and transformation. The score from Schiebinger et al., 2019 is assessed in MEFs, repro, transfo samples alongside iPS and transformed cells obtained from MEFs. (o) Patterns of gene signature scores on the diffusion map using gene lists.
