Sample isolation and overall miRNA expression patterns. (A) Collection of the Thy1- population from day 5 cultures of OSKM-infected MEFs. MEFs were transduced with OSKM virus supernatants for 5 days, harvested, and stained with phycoerythrin (PE)-conjugated anti-mouse Thy1 antibody. Wt, wild type (B) Collection of the SSEA1+ population from day 10 cultures of OSKM-infected MEFs. OSKM-transduced MEFs were stained with APC-conjugated anti-mouse SSEA1 antibody. (C) Collection of the GFP + population from day 14 cultures of OSKM-infected MEFs. Cells were sorted based on endogenous expression of GFP driven by the Oct4 promoter. (D) Principal component (PC) analysis of the 290 most variant miRNAs. Replicate 1 is in black, replicate 2 is in blue. Arrows show the trajectory of reprogramming in each replicate. (E) miRNAs differentially expressed (false discovery rate of 5%) during reprogramming in stage to stage transitions. (F) Histogram and overlaid density plot of distribution of log2 fold changes (FC) calculated by edgeR for the differentially expressed miRNAs in E). The fraction of upregulated miRNAs with a log2 fold change >5 in each transition is shown. See also Figures S1 and S2 in Additional file 1.