The human-induced pluripotent stem cell initiative-data resources for cellular genetics
Open accessAbstract
The Human Induced Pluripotent Stem Cell Initiative (HipSci) isf establishing a large catalogue of human iPSC lines, arguably the most well characterized collection to date. The HipSci portal enables researchers to choose the right cell line for their experiment, and makes HipSci's rich catalogue of assay data easy to discover and reuse. Each cell line has genomic, transcriptomic, proteomic and cellular phenotyping data. Data are deposited in the appropriate EMBL-EBI archives, including the European Nucleotide Archive (ENA), European Genome-phenome Archive (EGA), ArrayExpress and PRoteomics IDEntifications (PRIDE) databases. The project will make 500 cell lines from healthy individuals, and from 150 patients with rare genetic diseases; these will be available through the European Collection of Authenticated Cell Cultures (ECACC). As of August 2016, 238 cell lines are available for purchase. Project data is presented through the HipSci data portal (http://www.hipsci.org/lines) and is downloadable from the associated FTP site (ftp://ftp.hipsci.ebi.ac.uk/vol1/ftp). The data portal presents a summary matrix of the HipSci cell lines, showing available data types. Each line has its own page containing descriptive metadata, quality information, and links to archived assay data. Analysis results are also available in a Track Hub, allowing visualization in the context of public genomic annotations (http://www.hipsci.org/data/trackhubs).
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The quality of the numerical differential expression analysis was validated using HipSci data and iPSCpoweR tools, and all analyses identified very low number of spurious DEGs.
“To validate the quality of our numerical differential expression analysis, we took advantage of HipSci data (55, 56) and iPSCpoweR tools (29).”
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Examining iPSC derived motor neuron variability and genome stability monitoring as a solution
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- Authors
- Streeter, I., Harrison, P. W., Faulconbridge, A., The HipSci Consortium, Flicek, P., Parkinson, H., & Clarke, L.
- Affiliations
- European Bioinformatics Institute (GB)
- Corresponding author
- Clarke, Laura
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2016-10-12
- Volume
- 45
- Issue
- D1
- Pages
- D691-D697
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC5210631
- OpenAlex
- W2530086808
- Cited by
- 92
- References
- 20
- Citations by year
- 2026: 4 · 2025: 7 · 2024: 11 · 2023: 4 · 2022: 6 · 2021: 17 · 2020: 12 · 2019: 11 · 2018: 10 · 2017: 9
- FWCI
- 5.37
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- HighWire Press Open Archive (submittedVersion)
- Funders
- Wellcome Trust (WT-098503/D/12, 098503)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Pluripotent Stem Cells Research
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
- Keywords
- human induced pluripotent stem cells, data portal, rare genetic disorders, genomic data, transcriptomic data, proteomics data, cellular phenotyping, data reuse, European Nucleotide Archive, European Genome-phenome Archive, ArrayExpress, pride, cell line authentication
- MeSH terms
- Cell Line, Humans, Software, Computational Biology, Proteome, Genomics, Databases, Genetic, Genetic Association Studies, Induced Pluripotent Stem Cells, Transcriptome
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