RT Journal Article SR Electronic T1 Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics JF bioRxiv FD Cold Spring Harbor Laboratory SP 008862 DO 10.1101/008862 A1 Irene Gallego Romero A1 Bryan J. Pavlovic A1 Irene Hernando-Herraez A1 Nicholas E. Banovich A1 Courtney L. Kagan A1 Jonathan E. Burnett A1 Constance H. Huang A1 Amy Mitrano A1 Claudia I. Chavarria A1 Inbar Friedrich Ben-Nun A1 Yingchun Li A1 Karen Sabatini A1 Trevor Leonardo A1 Mana Parast A1 Tomas Marques-Bonet A1 Louise C. Laurent A1 Jeanne F. Loring A1 Yoav Gilad YR 2014 UL http://biorxiv.org/content/early/2014/09/06/008862.abstract AB Comparative genomics studies in primates are extremely restricted because we only have access to a few types of cell lines from non-human apes and to a limited collection of frozen tissues. In order to gain better insight into regulatory processes that underlie variation in complex phenotypes, we must have access to faithful model systems for a wide range of tissues and cell types. To facilitate this, we have generated a panel of 7 fully characterized chimpanzee (Pan troglodytes) induced pluripotent stem cell (iPSC) lines derived from fibroblasts of healthy donors. All lines appear to be free of integration from exogenous reprogramming vectors, can be maintained using standard iPSC culture techniques, and have proliferative and differentiation potential similar to human and mouse lines. To begin demonstrating the utility of comparative iPSC panels, we collected RNA sequencing data and methylation profiles from the chimpanzee iPSCs and their corresponding fibroblast precursors, as well as from 7 human iPSCs and their precursors, which were of multiple cell type and population origins. Overall, we observed much less regulatory variation within species in the iPSCs than in the somatic precursors, indicating that the reprogramming process has erased many of the differences observed between somatic cells of different origins. We identified 4,918 differentially expressed genes and 3,598 differentially methylated regions between iPSCs of the two species, many of which are novel inter-species differences that were not observed between the somatic cells of the two species. Our panel will help realise the potential of iPSCs in primate studies, and in combination with genomic technologies, transform studies of comparative evolution.