Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivatives

Kenneth Daily,Bruce J Aronow,Antonis K Hatzopoulos,Lynn M Schriml,Diana Nordling,Shannan Ho Sui ,Nathan Salomonis,Phillip Dexheimer ,Carolyn Lutzko,Alexander Pico ,Kristen K Dang ,Lorena Pantano,José A Cancelas ,Elke Grassman,Punam Malik,Thanneer M Perumal,Stacy Bush,Robin Schroll,Samad Lotia,Christopher N Mayhew ,Mehdi Keddache,Winston Hide,Larsson Omberg

doi:10.1038/sdata.2017.30

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.

Highlights

Background & SummaryThe development of methods to transform adult somatic cells into induced pluripotent stem cells have lead to new opportunities for disease modeling and clinical translation[1,2,3]
Human embryonic stem cells have been considered to be the functional, genetic and epigenetic ‘gold standard’ in this field[6]. Such analyses are needed to ensure the reproducible use of existing induced pluripotent stem cells (iPSC) lines for laboratory research purposes
The 64 stem cell lines (58 iPSC and 6 human embryonic stem cells (hESC)) selected were obtained from a diverse set of somatic cell of origins, gene reprogramming combinations, culturing methods and reprogramming vectors for both distinct and common genetic donors. These lines were sent to a centralized core laboratory for cell culturing, mycoplasma testing, growth characterization, flow cytometry analysis, and in vivo and in vitro differentiation potential

Summary

Background & Summary

The development of methods to transform adult somatic cells into induced pluripotent stem cells (iPSC) have lead to new opportunities for disease modeling and clinical translation[1,2,3]. Human embryonic stem cells (hESC) have been considered to be the functional, genetic and epigenetic ‘gold standard’ in this field[6] Such analyses are needed to ensure the reproducible use of existing iPSC lines for laboratory research purposes. The 64 stem cell lines (58 iPSC and 6 hESC) selected were obtained from a diverse set of somatic cell of origins, gene reprogramming combinations, culturing methods (e.g., stromal priming) and reprogramming vectors for both distinct and common genetic donors. These lines were sent to a centralized core laboratory for cell culturing, mycoplasma testing, growth characterization, flow cytometry analysis, and in vivo and in vitro differentiation potential. We encourage other researchers and members of the public to download and critically analyze this resource

Methods

Findings

Data Records Data availability overview