The human-induced pluripotent stem cell initiative-data resources for cellular genetics

Area of Science:

• Stem Cell Biology
• Genomics
• Bioinformatics

Background:

• The Human Induced Pluripotent Stem Cell Initiative (HipSci) is building a large, well-characterized collection of human induced pluripotent stem cell (iPSC) lines.
• Existing resources often lack comprehensive multi-omics data or easy accessibility for researchers.

Purpose of the Study:

• To establish and characterize a substantial collection of human iPSC lines for research purposes.
• To create a user-friendly portal for discovering, selecting, and reusing iPSC lines and their associated assay data.
• To deposit data in public EMBL-EBI archives for broad accessibility.

Main Methods:

• Generation and characterization of human iPSC lines from healthy individuals and patients with rare genetic diseases.
• Comprehensive data generation including genomic, transcriptomic, proteomic, and cellular phenotyping assays.
• Data deposition into EMBL-EBI archives (ENA, EGA, ArrayExpress, PRIDE) and presentation via the HipSci data portal.
• Development of a Track Hub for visualizing analysis results alongside public genomic annotations.

Main Results:

• As of August 2016, 238 iPSC lines are available, with a goal of 500 lines from healthy donors and 150 from patients.
• The HipSci portal provides a summary matrix of cell lines and data types, with individual pages detailing metadata, quality, and links to archived data.
• Data is accessible through the HipSci portal and FTP site, with analysis results available in a Track Hub for genomic context visualization.

Conclusions:

• The HipSci initiative provides an invaluable, well-characterized resource of human iPSC lines and multi-omics data.
• The data portal and associated archives enhance data discoverability, accessibility, and reusability for the scientific community.
• This resource supports research in stem cell biology, regenerative medicine, and disease modeling.