Comparative analysis between F- and B-iPSCs was performed using LPE test. p-Value cutoff was <0.05 and the FDR was controlled by adjusting the p value with Benjamini-Hochberg. An interactive tool for comparing lists with Venn diagrams was done at http://bioinfogp.cnb.csic.es/tools/venny/index.html. Gene lists were analyzed with DAVID (Huang da et al., 2009). For pathway analysis we used the PANTHER Classification System (Thomas et al., 2003). Microarray data are available in the ArrayExpress database (www.ebi.ac.uk/arrayexpress) under accession number E-MTAB-3825.
