Fig 2: Reprogramming trajectories of cocktails containing Oct4, Oct6, Oct4defSox2, or GFP in chemically defined medium. a The cartoons represent the preferences of the POU proteins for the DNA-dependent homodimerization on MORE versus heterodimerization with Sox2 on SoxOct elements determined using quantitative biochemical assays14. MORE DNA is shown in orange and SoxOct DNA in blue; m1 is monomer 1 and m2 is monomer2. The thickness of the arrows illustrates the DNA binding preferences. b Experimental design of reprogramming and RNA-seq, ATAC-seq, and ChIP-seq experiments. c Whole-well scans from a 6-well plate using GFP channel (Oct4-GFP), Nanog immunofluorescence and merged panels; for OG2-MEF cells reprogrammed with Oct4-SK at day 8; scale 5 mm. d Whole-well scans (upper panel) of wells from 12-well plate using GFP channel for three POU factors (Oct4, Oct4defSox2, and Oct6); scale 5 mm. Representative phase contrast (middle panel) and corresponding Oct4-GFP fluorescence (lower panel) images of reprogramming experiments; time-point: day 8 post transduction; scale 200 µm. e Hierarchically clustered heatmap based on r2 correlation coefficients using RNA-seq reads as input. iPSCs and ESCs expression data are from GSE9302942. f Mean gene expression trajectories for indicated categories (upper panel) or a representative gene from each category (lower panel) in four reprogramming conditions. See Supplementary Fig. 1E for a larger panel of genes for each category. g Fraction of E-cadherin positive (Cdh1 + ve) cells at different stages of reprogramming in indicated cocktails. FACS was performed in technical duplicates (n = 2). Source data for FACS experiment are provided as a Source Data file

Fig 3: Reprogramming Enhancement and Acceleration by TGF-ß Inhibitors(A) Nanog-GFP- and GFP+ colony numbers on day 12 of reprogramming.(B) Flow cytometry analysis of E-CADHERIN (E-CAD) expression during reprogramming.(C) Numbers of mOrange+ MKOS expressing transgenic (Tg) cells (left) and mOrange- wild-type feeder MEFs (right) during the first 4 days.(D) Real-time RT-PCR for p19Arf with mOrange+ cells on days 4 and 8.(E) Immunofluorescence for p19ARF on day 4.(F) CD44/ICAM1/Nanog-GFP expression throughout reprogramming. Red, Nanog-GFP-; green, Nanog-GFP+ Tg cells.Cont and A83 indicate in the absence and presence of A83, respectively. See also Figure S1.

Fig 4: Epithelial-to-Mesenchymal Transition Reported by Historical Lineage-Tracing Reporter and Current E-Cadherin Status in Murine Metastatic Mammary Carcinoma Model(A) Schematic of fluorescent transgenic mouse model, carrying polyoma middle-T (PyMT) oncogene driven by the mammary gland specific MMTV promoter, Cre recombinase under the control of the fsp1 promoter, endogenous E-cad labeled with mCFP, and ubiquitous expression from the R26 locus of membranous RFP-STOP, which is flanked by loxP sites, leading to excision and subsequent expression of membranous GFP upon Cre expression.(B) Top panel: representative multi-photon images of the fluorescent PyMT mammary tumors from recipient mice. Scale bar, 100 µm. Bottom panel: high-magnification images of the E-cad-mCFP and RFP channel of the boxed area in the top left image. Scale bar, 50 µm.(C) Representative scatterplot from flow cytometry analysis of primary tumor of recipient mice for either absence of endogenous E-cad-mCFP expression and antibody staining (E-cadLO) or presence of high expression of E-cad and staining for Ab (E-cadHI tumor cells) or subdivision of RFP+ or GFP+ cells.(D) Relative mRNA expression of classical EMT marker genes (E-cad, Vimentin [Vim], fibronectin [FN], Zeb1, N-cad [N-cadherin], Slug) determined using qPCR of sorted RFP+E-cadHi, RFP+E-cadLO, RFP+GFP+, and GFP+ cells from primary tumors. Plotted mean and SD of n = 3 mice.(E) Quantification of lung metastases of all transplanted mice.(F) Representative multi-photon image of metastases in lung secetion from recipient mice. Outlining of lung tissue is shown by white dashed line. Scale bar 500 µm.

Fig 5: Mesenchymal E-cadLO Population Exceeds fsp1-Lineage-Traced Population in Primary Tumor and Circulation and Has Metastatic Potential(A) Percentage of GFP+ (green), GFP+ RFP+ (yellow), and RFP+ (red) tumor cells in primary tumors of recipient mice. n = 16 mice.(B) Percentage of E-cadHI (blue), E-cadLO (light blue) tumor cells in primary tumors of recipient mice. n = 16 mice.(C) Comparison of percentage of E-cadLO (light blue) with GFP+ (green) and GFP+ RFP+ (yellow) tumor cells in primary tumors of recipient mice. n = 16 mice.(D) Percentage of GFP+ (green), GFP+ RFP+ (yellow), and RFP+ (red) circulating tumor cells collected from the right cardiac chamber of recipient mice. n = 16 mice.(E) Percentage of E-cadHI (blue), E-cadLO (light blue) circulating tumor cells collected from the right cardiac chamber of recipient mice. n = 16 mice.(F) Comparison of percentage of E-cadLO (light blue) with GFP+ (green) and GFP+ RFP+ (yellow) circulating tumor cells collected from the right cardiac chamber of recipient mice. n = 16 mice.(G) Top panel: schematic overview of experimental setup: fluorescence-activated cell sorting (FACS)-sorted E-cadHI or E-cadLO cells of orthotopically transplanted mice were injected in the tail vein of acceptor mice. Bottom panel: quantification of lung metastases of all transplanted mice. n = 3 mice per condition.(H) Representative multi-photon image of lung metastasis from (G). Scale bar, 500 µm. Right panels: zoom of boxed area showing detected E-cad-mCFP and RFP signal. Scale bar, 100 µm.