title: Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivatives.
abstract: The use of induced pluripotent stem cells (iPSC) derived from independent patients and sources holds considerable promise to improve the understanding of development and disease. However, optimized use of iPSC depends on our ability to develop methods to efficiently qualify cell lines and protocols, monitor genetic stability, and evaluate self-renewal and differentiation potential. To accomplish these goals, 57 stem cell lines from 10 laboratories were differentiated to 7 different states, resulting in 248 analyzed samples. Cell lines were differentiated and characterized at a central laboratory using standardized cell culture methodologies, protocols, and metadata descriptors. Stem cell and derived differentiated lines were characterized using RNA-seq, miRNA-seq, copy number arrays, DNA methylation arrays, flow cytometry, and molecular histology. All materials, including raw data, metadata, analysis and processing code, and methodological and provenance documentation are publicly available for re-use and interactive exploration at https://www.synapse.org/pcbc. The goal is to provide data that can improve our ability to robustly and reproducibly use human pluripotent stem cells to understand development and disease.
authors.affiliation: Sage Bionetworks, Seattle, Washington 98109, USA.
authors.forename: Kenneth
authors.identifier: 0000-0001-5729-7376
authors.initials: K
authors.lastname: Daily
authors.affiliation: Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA.
authors.forename: Shannan J
authors.initials: SJ
authors.lastname: Ho Sui
authors.affiliation: Institute for Genome Sciences and Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.
authors.forename: Lynn M
authors.initials: LM
authors.lastname: Schriml
authors.affiliation: Department of Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, Ohio 45229, USA.
authors.forename: Phillip J
authors.initials: PJ
authors.lastname: Dexheimer
authors.affiliation: Department of Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, Ohio 45229, USA.
authors.forename: Nathan
authors.initials: N
authors.lastname: Salomonis
authors.affiliation: Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, Ohio 45229, USA.
authors.forename: Robin
authors.initials: R
authors.lastname: Schroll
authors.affiliation: Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, Ohio 45229, USA.
authors.forename: Stacy
authors.initials: S
authors.lastname: Bush
authors.affiliation: Division of Human Genetics, Cincinnati Children's Hospital, Cincinnati, Ohio 45229, USA.
authors.forename: Mehdi
authors.initials: M
authors.lastname: Keddache
authors.affiliation: Division of Developmental Biology, Cincinnati Children's Hospital, Cincinnati, Ohio 45229, USA.
authors.forename: Christopher
authors.initials: C
authors.lastname: Mayhew
authors.affiliation: Gladstone Institutes, San Francisco, California 94158, USA.
authors.forename: Samad
authors.initials: S
authors.lastname: Lotia
authors.affiliation: Sage Bionetworks, Seattle, Washington 98109, USA.
authors.forename: Thanneer M
authors.initials: TM
authors.lastname: Perumal
authors.affiliation: Sage Bionetworks, Seattle, Washington 98109, USA.
authors.forename: Kristen
authors.initials: K
authors.lastname: Dang
authors.affiliation: Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA.
authors.forename: Lorena
authors.initials: L
authors.lastname: Pantano
authors.affiliation: Gladstone Institutes, San Francisco, California 94158, USA.
authors.forename: Alexander R
authors.initials: AR
authors.lastname: Pico
authors.affiliation: Translational Trials Development and Support Laboratory Field Service, Cincinnati Children's Hospital, Cincinnati, Ohio 45229, USA.
authors.forename: Elke
authors.initials: E
authors.lastname: Grassman
authors.affiliation: Cell Manipulation Laboratory, Cincinnati Children's Hospital, Cincinnati, Ohio 45229, USA.
authors.forename: Diana
authors.initials: D
authors.lastname: Nordling
authors.affiliation: Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, USA.|Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield S10 2HQ, UK.|Harvard Stem Cell Institute, Cambridge, Massachusetts 02138, USA.
authors.forename: Winston
authors.initials: W
authors.lastname: Hide
authors.affiliation: Departments of Medicine and Cell and Developmental Biology, Division of Cardiovascular Medicine, Vanderbilt University, Nashville, Tennessee 37232, USA.
authors.forename: Antonis K
authors.initials: AK
authors.lastname: Hatzopoulos
authors.affiliation: Institute for Genome Sciences and Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA.
authors.forename: Punam
authors.initials: P
authors.lastname: Malik
authors.affiliation: Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, Ohio 45229, USA.
authors.forename: Jose A
authors.initials: JA
authors.lastname: Cancelas
authors.affiliation: Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital, Cincinnati, Ohio 45229, USA.
authors.forename: Carolyn
authors.initials: C
authors.lastname: Lutzko
authors.affiliation: Department of Biomedical Informatics, Cincinnati Children's Hospital, Cincinnati, Ohio 45229, USA.
authors.forename: Bruce J
authors.initials: BJ
authors.lastname: Aronow
authors.affiliation: Sage Bionetworks, Seattle, Washington 98109, USA.
authors.forename: Larsson
authors.initials: L
authors.lastname: Omberg
mesh_terms: D000818:Animals; D018929:Cell Culture Techniques; D006801:Humans; D057026:Induced Pluripotent Stem Cells; D039904:Pluripotent Stem Cells