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

doi:10.1016/j.isci.2018.08.016

Single-Cell Profiling Identifies Key Pathways Expressed by iPSCs Cultured in Different Commercial Media

iScience. 2018 Sep 28:7:30-39. doi: 10.1016/j.isci.2018.08.016. Epub 2018 Aug 23.

Authors

Maciej Daniszewski¹, Quan Nguyen², Hun S Chy³, Vikrant Singh⁴, Duncan E Crombie¹, Tejal Kulkarni¹, Helena H Liang¹, Priyadharshini Sivakumaran¹, Grace E Lidgerwood¹, Damián Hernández¹, Alison Conquest¹, Louise A Rooney¹, Sophie Chevalier¹, Stacey B Andersen², Anne Senabouth², James C Vickers⁵, David A Mackey⁶, Jamie E Craig⁷, Andrew L Laslett³, Alex W Hewitt⁸, Joseph E Powell⁹, Alice Pébay¹⁰

Affiliations

¹ 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.
² Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia.
³ Commonwealth Scientific and Industrial Research Organisation (CSIRO) Manufacturing, Clayton, VIC 3168, Australia; Australian Regenerative Medicine Institute, Monash University, Clayton, VIC 3168, Australia.
⁴ School of Medicine, Menzies Institute for Medical Research, University of Tasmania, Hobart, TAS 7000, Australia.
⁵ Wicking Dementia Research and Education Centre, University of Tasmania, Hobart, TAS 7000, Australia.
⁶ Centre for Ophthalmology and Visual Science, Lions Eye Institute, University of Western Australia, Perth, WA 6009, Australia.
⁷ Flinders University, Adelaide, SA 5042, Australia.
⁸ 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.
⁹ Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia; Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia.
¹⁰ 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. Electronic address: apebay@unimelb.edu.au.

Abstract

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.

Keywords: Automation; Stem Cells Research; Transcriptomics.