iScience (Sep 2018)
Single-Cell Profiling Identifies Key Pathways Expressed by iPSCs Cultured in Different Commercial Media
- Maciej Daniszewski,
- Quan Nguyen,
- Hun S. Chy,
- Vikrant Singh,
- Duncan E. Crombie,
- Tejal Kulkarni,
- Helena H. Liang,
- Priyadharshini Sivakumaran,
- Grace E. Lidgerwood,
- Damián Hernández,
- Alison Conquest,
- Louise A. Rooney,
- Sophie Chevalier,
- Stacey B. Andersen,
- Anne Senabouth,
- James C. Vickers,
- David A. Mackey,
- Jamie E. Craig,
- Andrew L. Laslett,
- Alex W. Hewitt,
- Joseph E. Powell,
- Alice Pébay
Affiliations
- Maciej Daniszewski
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
- Quan Nguyen
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
- Hun S. Chy
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Manufacturing, Clayton, VIC 3168, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3168, Australia
- Vikrant Singh
- School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
- Duncan E. Crombie
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
- Tejal Kulkarni
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
- Helena H. Liang
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
- Priyadharshini Sivakumaran
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
- Grace E. Lidgerwood
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
- Damián Hernández
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
- Alison Conquest
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
- Louise A. Rooney
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
- Sophie Chevalier
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia
- Stacey B. Andersen
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
- Anne Senabouth
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
- James C. Vickers
- Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7000, Australia
- David A. Mackey
- Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, WA 6009, Australia
- Jamie E. Craig
- Flinders University, Adelaide, SA 5042, Australia
- Andrew L. Laslett
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Manufacturing, Clayton, VIC 3168, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3168, Australia
- Alex W. Hewitt
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia; School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia
- Joseph E. Powell
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia; Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- Alice Pébay
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, University of Melbourne, 32 Gisborne Street, East Melbourne, VIC 3002, Australia; Ophthalmology, Department of Surgery, the University of Melbourne, Melbourne, VIC 3002, Australia; Corresponding author
- Journal volume & issue
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Vol. 7
pp. 30 – 39
Abstract
Summary: We assessed the pluripotency of human induced pluripotent stem cells (iPSCs) maintained on an automated platform using StemFlex and TeSR-E8 media. Analysis of transcriptome of single cells revealed similar expression of core pluripotency genes, as well as genes associated with naive and primed states of pluripotency. Analysis of individual cells from four samples consisting of two different iPSC lines each grown in the two culture media revealed a shared subpopulation structure with three main subpopulations different in pluripotency states. By implementing a machine learning approach, we estimated that most cells within each subpopulation are very similar between all four samples. The single-cell RNA sequencing analysis of iPSC lines grown in both media reports the molecular signature in StemFlex medium and how it compares to that observed in the TeSR-E8 medium. : Stem Cells Research; Transcriptomics; Automation Subject Areas: Stem Cells Research, Transcriptomics, Automation
