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Identification of stable reference genes in differentiating human pluripotent stem cells
University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden. (Bioinformatics)ORCID iD: 0000-0002-0402-1437
University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. Department of Clinical Chemistry/Transfusion Medicine, Sahlgrenska University Hospital, Gothenburg, Sweden. (Bioinformatics)ORCID iD: 0000-0003-2942-6702
Buck Institute for Research on Aging, Buck Institute, Novato, California, USA.
University of Skövde, School of Bioscience. University of Skövde, The Systems Biology Research Centre. (Bioinformatics)
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2015 (English)In: Physiological Genomics, ISSN 1094-8341, E-ISSN 1531-2267, Vol. 47, no 6, 232-239 p.Article in journal (Refereed) Published
Abstract [en]

Reference genes, often referred to as housekeeping genes (HKGs), are frequently used to normalize gene expression data based on the assumption that they are expressed at a constant level in the cells. However, several studies have shown that there may be a large variability in the gene expression levels of HKGs in various cell types. In a previous study, employing human embryonic stem cells (hESCs) subjected to spontaneous differentiation, we observed that the expression of commonly used HKG varied to a degree that rendered them inappropriate to use as reference genes under those experimental settings. Here we present a substantially extended study of the HKG signature in human pluripotent stem cells (hPSC), including nine global gene expression datasets from both hESC and human induced pluripotent stem cells (hiPSCs), obtained during directed differentiation towards endoderm-, mesoderm-, and ectoderm derivatives. Sets of stably expressed genes were compiled and a handful of genes (e.g., EID2, ZNF324B, CAPN10, and RABEP2) were identified as generally applicable reference genes in hPSCs across all cell lines and experimental conditions. The stability in gene expression profiles was confirmed by quantitative PCR (RT-qPCR) analysis. Taken together, the current results suggest that differentiating hPSCs have a distinct HKG signature, which in some aspects is different from somatic cell types, and underscore the necessity to validate the stability of reference genes under the actual experimental setup used. In addition, the novel putative HKGs identified in this study can preferentially be used for normalization of gene expression data obtained from differentiating hPSCs.

Place, publisher, year, edition, pages
American Physiological Society , 2015. Vol. 47, no 6, 232-239 p.
Keyword [en]
Differentiation, Endogenous controls; Gene expression, Housekeeping genes, Human pluripotent stem cells, Normalization, Reference genes
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Identifiers
URN: urn:nbn:se:his:diva-11419DOI: 10.1152/physiolgenomics.00130.2014ISI: 000357489400005PubMedID: 25852171ScopusID: 2-s2.0-84930975405OAI: oai:DiVA.org:his-11419DiVA: diva2:848550
Available from: 2015-08-25 Created: 2015-08-25 Last updated: 2016-03-18Bibliographically approved

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Holmgren, GustavGhosheh, NidalSartipy, PeterSynnergren, Jane
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