title: A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics.
abstract: Comparative genomics studies in primates are restricted due to our limited access to samples. In order to gain better insight into the genetic processes that underlie variation in complex phenotypes in primates, we must have access to faithful model systems for a wide range of cell types. To facilitate this, we generated a panel of 7 fully characterized chimpanzee induced pluripotent stem cell (iPSC) lines derived from healthy donors. To demonstrate the utility of comparative iPSC panels, we collected RNA-sequencing and DNA methylation data from the chimpanzee iPSCs and the corresponding fibroblast lines, as well as from 7 human iPSCs and their source lines, which encompass multiple populations and cell types. We observe much less within-species variation in iPSCs than in somatic cells, indicating the reprogramming process erases many inter-individual differences. The low within-species regulatory variation in iPSCs allowed us to identify many novel inter-species regulatory differences of small magnitude.
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, United States.
authors.forename: Irene
authors.identifier: http://orcid.org/0000-0003-1613-8998
authors.initials: I
authors.lastname: Gallego Romero
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, United States.
authors.forename: Bryan J
authors.initials: BJ
authors.lastname: Pavlovic
authors.affiliation: Parc Recerca Biomèdica de Barcelona, Barcelona, Spain.
authors.forename: Irene
authors.initials: I
authors.lastname: Hernando-Herraez
authors.affiliation: Department of Biostatistics, University of Michigan, Ann Arbor, United States.
authors.forename: Xiang
authors.initials: X
authors.lastname: Zhou
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, United States.
authors.forename: Michelle C
authors.initials: MC
authors.lastname: Ward
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, United States.
authors.forename: Nicholas E
authors.initials: NE
authors.lastname: Banovich
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, United States.
authors.forename: Courtney L
authors.initials: CL
authors.lastname: Kagan
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, United States.
authors.forename: Jonathan E
authors.initials: JE
authors.lastname: Burnett
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, United States.
authors.forename: Constance H
authors.initials: CH
authors.lastname: Huang
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, United States.
authors.forename: Amy
authors.initials: A
authors.lastname: Mitrano
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, United States.
authors.forename: Claudia I
authors.initials: CI
authors.lastname: Chavarria
authors.affiliation: Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States.
authors.forename: Inbar
authors.initials: I
authors.lastname: Friedrich Ben-Nun
authors.affiliation: Department of Pathology, University of California San Diego, San Diego, United States.
authors.forename: Yingchun
authors.initials: Y
authors.lastname: Li
authors.affiliation: Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States.
authors.forename: Karen
authors.initials: K
authors.lastname: Sabatini
authors.affiliation: Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States.
authors.forename: Trevor R
authors.initials: TR
authors.lastname: Leonardo
authors.affiliation: Department of Pathology, University of California San Diego, San Diego, United States.
authors.forename: Mana
authors.initials: M
authors.lastname: Parast
authors.affiliation: Parc Recerca Biomèdica de Barcelona, Barcelona, Spain.
authors.forename: Tomas
authors.initials: T
authors.lastname: Marques-Bonet
authors.affiliation: Sanford Consortium for Regenerative Medicine, La Jolla, United States.
authors.forename: Louise C
authors.initials: LC
authors.lastname: Laurent
authors.affiliation: Center for Regenerative Medicine, Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States.
authors.forename: Jeanne F
authors.initials: JF
authors.lastname: Loring
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, United States.
authors.forename: Yoav
authors.initials: Y
authors.lastname: Gilad
mesh_terms: D000818:Animals; D002454:Cell Differentiation; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D023281:Genomics / Q000379:methods*; D006801:Humans; D057026:Induced Pluripotent Stem Cells; D008969:Molecular Sequence Data; D002679:Pan troglodytes; D017422:Sequence Analysis, DNA
keywords: Pan troglodytes; cell panel; chimpanzee; developmental biology; evolutionary biology; genomics; human; iPSC; induced pluripotent stem cells; stem cells