The DNA methylation status of <i>Aid</i>^−/− iPS cells.

<p>(A–D) The DNA methylation status of the <i>Nanog</i> promoter (A), <i>Oct3/4</i> promoter (B), B1 (C) and LINE1 (D) detected by pyrosequencing. The iPS cell clones analyzed were the same as those examined in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0094735#pone-0094735-g002" target="_blank">Fig. 2C</a>. The data are represented as the averages ± SD of the clones. (E) The results of the comprehensive DNA methylation analysis with MBD-sequencing. Pie charts show the comparison of the detected methylated regions between <i>Aid</i>^+/+ iPS cells and <i>Aid</i>^+/+ MEFs (left), <i>Aid</i>^+/+ iPS cells and ES cells (middle), and <i>Aid</i>^+/+ iPS cells and <i>Aid</i>^−/− iPS cells (right). DMRs; Differentially methylated regions, CMRs; Commonly methylated regions.</p

Generation of iPS cells from <i>Aid</i>^−/− mice.

<p>(A) The relative expression of <i>Aid</i> and <i>Gapdh</i>. Total RNA was isolated from three ES cell clones (RF8, B6ES and MG1.19), three <i>Aid</i>^+/+ iPS cell clones (967B2, 967C1 and 979B1), three <i>Aid</i>^−/− iPS cell clones (957F1, 979F1 and 979E1), three parental <i>Aid</i>^+/+ and <i>Aid</i>^−/− MEF clones and primary B cells (pB cells), and was used for the quantitative RT-PCR analysis. The data are shown as the average ± SD. (B) The morphology of <i>Aid</i>^+/+ and <i>Aid</i>^−/− iPS colonies 25 days after the introduction of 4 Fs into MEFs. Phase contrast (left column) and GFP fluorescence (right column) images are shown. Scale bars; 200 μm. (C, D) The number of GFP-positive colonies from <i>Aid</i>^+/+, <i>Aid</i>^+/− and <i>Aid</i>^−/− MEFs induced by 4 Fs (C) and 3 Fs (D). For each genotype, three different lots of MEFs were used in each experiment, and the experiments were repeated four times. Colonies were counted 25 (4 Fs) and 30 (3 Fs) days after the induction. (E) The number of total colonies from <i>Aid</i>^+/+, <i>Aid</i>^+/− and <i>Aid</i>^−/− MEFs subjected to transduction of the 3 Fs with or without Aid. (F) The proportion of GFP-positive colonies out of the total colonies from <i>Aid</i>^+/+, <i>Aid</i>^+/− and <i>Aid</i>^−/− MEFs induced by 3 Fs with or without Aid. (G) The number of GFP-positive colonies from <i>Aid</i>^+/+ and <i>Aid</i>^−/− primary B cells induced with 4 Fs. Experiments were repeated five times.</p