Dataset Information

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.

SUBMITTER: Daily K

PROVIDER: S-EPMC5369318 | biostudies-literature | 2017 Mar

REPOSITORIES: biostudies-literature

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

Daily Kenneth K Ho Sui Shannan J SJ Schriml Lynn M LM Dexheimer Phillip J PJ Salomonis Nathan N Schroll Robin R Bush Stacy S Keddache Mehdi M Mayhew Christopher C Lotia Samad S Perumal Thanneer M TM Dang Kristen K Pantano Lorena L Pico Alexander R AR Grassman Elke E Nordling Diana D Hide Winston W Hatzopoulos Antonis K AK Malik Punam P Cancelas Jose A JA Lutzko Carolyn C Aronow Bruce J BJ Omberg Larsson L

Scientific data 20170328

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, resul ...[more]

PMID: 28350385

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Project description:Introduction: The Minimum Information About BIobank data Sharing (MIABIS) was initiated in 2012. MIABIS aims to create a common biobank terminology to facilitate data sharing in biobanks and sample collections. The MIABIS Core terminology consists of three components describing biobanks, sample collections, and studies, in which information on samples and sample donors is provided at aggregated form. However, there is also a need to describe samples and sample donors at an individual level to allow more elaborate queries on available biobank samples and data. Therefore the MIABIS terminology has now been extended with components describing samples and sample donors at an individual level. Materials and Methods: The components were defined according to specific scope and use cases by a large group of experts, and through several cycles of reviews, according to the new MIABIS governance model of BBMRI-ERIC (Biobanking and Biomolecular Resources Research Infrastructure-European Research Infrastructure Consortium). The guiding principles applied in developing these components included the following terms: model should consider only samples of human origin, model should be applicable to all types of samples and all sample donors, and model should describe the current status of samples stored in a given biobank. Results: A minimal set of standard attributes for defining samples and sample donors is presented here. We added an "event" component to describe attributes that are not directly describing samples or sample donors but are tightly related to them. To better utilize the generic data model, we suggest a procedure by which interoperability can be promoted, using specific MIABIS profiles. Discussion: The MIABIS sample and donor component extensions and the new generic data model complement the existing MIABIS Core 2.0 components, and substantially increase the potential usability of this terminology for better describing biobank samples and sample donors. They also support the use of individual level data about samples and sample donors to obtain accurate and detailed biobank availability queries.

Dataset Information

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

Publications

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

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