Systematic assessment of variability in the proteome of iPSC derivatives
The use of induced pluripotent stem cells (iPSC) to model human complex diseases is gaining popularity as it allows investigation of human cells that are otherwise sparsely available. However, due to its laborious and cost intensive nature, iPSC research is often plagued by limited sample size and p...
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doaj-17cd00d645064ceab99c936775f4a01d2021-08-28T04:42:46ZengElsevierStem Cell Research1873-50612021-10-0156102512Systematic assessment of variability in the proteome of iPSC derivativesStephanie D. Beekhuis-Hoekstra0Kyoko Watanabe1Josefin Werme2Christiaan A. de Leeuw3Iryna Paliukhovich4Ka Wan Li5Frank Koopmans6August B. Smit7Danielle Posthuma8Vivi M. Heine9Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, The NetherlandsDepartment of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, The NetherlandsDepartment of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, The NetherlandsDepartment of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, The NetherlandsDepartment of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, The NetherlandsDepartment of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, The NetherlandsDepartment of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, The NetherlandsDepartment of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, The NetherlandsDepartment of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, The Netherlands; Department of Child and Youth Psychiatry, Emma Children’s Hospital, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, The Netherlands; Corresponding authors at: Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, The Netherlands.Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, The Netherlands; Department of Child and Youth Psychiatry, Emma Children’s Hospital, Amsterdam Neuroscience, Amsterdam UMC, Amsterdam, The Netherlands; Corresponding authors at: Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU University Amsterdam, Amsterdam, The Netherlands.The use of induced pluripotent stem cells (iPSC) to model human complex diseases is gaining popularity as it allows investigation of human cells that are otherwise sparsely available. However, due to its laborious and cost intensive nature, iPSC research is often plagued by limited sample size and putative large variability between clones, decreasing statistical power for detecting experimental effects. Here, we investigate the source and magnitude of variability in the proteome of parallel differentiated astrocytes using mass spectrometry. We compare three possible sources of variability: inter-donor variability, inter- and intra-clonal variability, at different stages of maturation. We show that the interclonal variability is significantly smaller than the inter-donor variability, and that including more donors has a much larger influence on statistical power than adding more clones per donor. Our results provide insight into the sources of variability at protein level between iPSC samples derived in parallel and will aid in optimizing iPSC studies.http://www.sciencedirect.com/science/article/pii/S1873506121003597 |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Stephanie D. Beekhuis-Hoekstra Kyoko Watanabe Josefin Werme Christiaan A. de Leeuw Iryna Paliukhovich Ka Wan Li Frank Koopmans August B. Smit Danielle Posthuma Vivi M. Heine |
spellingShingle |
Stephanie D. Beekhuis-Hoekstra Kyoko Watanabe Josefin Werme Christiaan A. de Leeuw Iryna Paliukhovich Ka Wan Li Frank Koopmans August B. Smit Danielle Posthuma Vivi M. Heine Systematic assessment of variability in the proteome of iPSC derivatives Stem Cell Research |
author_facet |
Stephanie D. Beekhuis-Hoekstra Kyoko Watanabe Josefin Werme Christiaan A. de Leeuw Iryna Paliukhovich Ka Wan Li Frank Koopmans August B. Smit Danielle Posthuma Vivi M. Heine |
author_sort |
Stephanie D. Beekhuis-Hoekstra |
title |
Systematic assessment of variability in the proteome of iPSC derivatives |
title_short |
Systematic assessment of variability in the proteome of iPSC derivatives |
title_full |
Systematic assessment of variability in the proteome of iPSC derivatives |
title_fullStr |
Systematic assessment of variability in the proteome of iPSC derivatives |
title_full_unstemmed |
Systematic assessment of variability in the proteome of iPSC derivatives |
title_sort |
systematic assessment of variability in the proteome of ipsc derivatives |
publisher |
Elsevier |
series |
Stem Cell Research |
issn |
1873-5061 |
publishDate |
2021-10-01 |
description |
The use of induced pluripotent stem cells (iPSC) to model human complex diseases is gaining popularity as it allows investigation of human cells that are otherwise sparsely available. However, due to its laborious and cost intensive nature, iPSC research is often plagued by limited sample size and putative large variability between clones, decreasing statistical power for detecting experimental effects. Here, we investigate the source and magnitude of variability in the proteome of parallel differentiated astrocytes using mass spectrometry. We compare three possible sources of variability: inter-donor variability, inter- and intra-clonal variability, at different stages of maturation. We show that the interclonal variability is significantly smaller than the inter-donor variability, and that including more donors has a much larger influence on statistical power than adding more clones per donor. Our results provide insight into the sources of variability at protein level between iPSC samples derived in parallel and will aid in optimizing iPSC studies. |
url |
http://www.sciencedirect.com/science/article/pii/S1873506121003597 |
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