Extended Data Fig. 4: Chromatin accessibility and transcriptomic changes during reprogramming & transformation.
(a) Principal component analysis of ATAC-seq signal of the control cells, cellular intermediates (BLTL and BHTH) and the final product of each process (iPS and transformed cells). (b) Heatmap of differentially accessible peaks in ATAC-seq data. Peaks are scaled per row and annotated by cluster labels. (c) Top 10 motifs enriched in the ATAC-seq clusters defined in the main text. (d) Q-RTPCR of FosL1 levels. Data, normalized to control, are the mean + /- sd of 3 independent experiments. Two-sided Student T-test. (e) Western blot for FosL1 in similar settings as (d). (f) Foci staining of immortalized cells. One representative experiment (from three independent experiments). (g) Counting of foci depicted in (f). n = 3 independent experiments. Two-tailed Student’s t-test. (h) Alkaline phosphatase (AP) staining of iPS colonies. One representative experiment (from five independent experiments). (i) Counting of AP-positive colonies depicted in (h). n = 5 independent experiments. Two-tailed Student’s t-test. (j) Ssgsea analysis of the MEF identity score using independent datasets from Nefzger et al., 2017 and Schiebinger et al., 2019. n = 2 independent experiments. (k) Itga4 and Nt5e expression in cellular intermediates. RNA-seq data from Fig. 4 are used. n = 2 independent experiments. (l) Gene expression levels in MEFs and cellular intermediates. Stromal and MET fate genes, as defined in Schiebinger et al., 2019, were analyzed in the RNA-seq dataset. n = 2 independent experiments.
