Phase-contrast images of FIB and IPSC lines used in this report (as labeled).

<p>FIBA and FIBB displayed a flat stellate cytoplasm with irregular edges characteristic of fibroblast cell types (200X). IPSC lines displayed round colonies with regular edges evident in low magnification 40X images that were composed of tightly packed cells with prominent nucleoli (200X, lower panels of IPSC lines) that appeared morphologically homogenous within the center of the colony and flattened toward the edges where they were bounded by the MEF feeder layer. IPSCB1 and IPSB2 are shown only at 40X magnification.</p

Analysis of telomeres in input, pluripotent, and re-differentiated cell lines.

<p>(A) Blue-stained nuclear DNA with punctate red fluorescence indicating telomeres hybridized to the PNA FISH telomere probe for input fibroblasts, IPSCs, or TER cells from lines A and B as labeled. mag. 400X. (B) Quantification of TRFs from cell lines as labeled. Yellow shading indicates significance compared to line FIBA and red shading significance compared to line FIBB. TRF indicates mean length in kilobase pairs (Kb). * = P<0.05, ** = P<0.01, *** = P<.001. Error bars indicate SEM. (C) Example of changes in TRF size in cell lines as labeled. Numbers at left are fragment lengths in kilobases. (D) Mean TRF lengths for all cell lines combined by type. Labeling as in part B. Significance calculated relative to FIB.</p

Indicators of pluripotency and differentiation in IPSC lines.

<p>(A) Representative sections from teratomas generated from IPSC lines as labeled. Arrows in ectodermal (ECTO) tissue indicate neural rosettes, in mesodermal tissue (MESO) indicate cartilage, and in endodermal tissue (ENDO) indicate glandular columnar epithelium. mag. 100X. (B) Morphology of FIB lines and TER lines, as labeled, in phase-contrast images (top row) and stained for fibronectin (red, bottom row). mag. 400X. Blue is DNA stain. (C) Genome-wide methylation heat map and cluster analysis of representative input fibroblasts, IPSCs, TER, and hESC lines indicating that the overall pattern of methylation of IPSCs closely matches HES lines while differentiated TER lines cluster with input fibroblasts. Value indicates the level of methylation ranked from 0 (hypomethylated) to 1 (hypermethylated).</p

Cell lines used in this report.

<p><i>Report name</i>: name used to reference the cell lines in this report. <i>Cell Type</i>: the general cell phenotype.</p><p><i>Pass:</i> passage of cells at time of telomere analysis. <i>Parental Line</i>: name of the input cell line used to produce the corresponding cell line.</p><p><i>Vec/Factors</i>: Reprogramming factor combination used to produce cell line (if applicable). Individual letters represent each of the 6 reprogramming factors as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0008124#pone-0008124-g001" target="_blank">Figure 1</a>. Parentheses indicate coupling of factors into bicistronic pairs in the vector.</p><p><i>Line Ref Name:</i> Official name of each cell line used in the report.</p>*<p>Lines lost to contamination.</p>#<p>--also passage number used for production of IPSCs.</p