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Series GSE50781 Query DataSets for GSE50781
Status Public on Feb 19, 2014
Title Primate iPS cells as tools for evolutionary analyses
Organisms Macaca fascicularis; Macaca mulatta; Gorilla gorilla; Pan paniscus; Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Induced pluripotent stem cells (iPSCs) are regarded as a central tool to understand human biology in health and disease. Similarly, iPSCs from closely related species should be a central tool to understand human evolution and to identify conserved and variable patterns of iPSC disease models. Here, we have generated human, gorilla, bonobo and cynomolgus monkey iPSCs. We show that these cells are well comparable in their differentiation potential and generally similar to human, cynomolgus and rhesus monkey embryonic stem cells (ESCs). RNA sequencing reveals that expression differences among clones, individuals and stem cell type are all of very similar magnitude within a species. In contrast, expression differences between closely related primate species are three times larger and most genes show significant expression differences among the analysed species. However, pseudogenes differ more than twice as much, suggesting that evolution of expression levels in primate stem cells is rapid, but constrained. These patterns in pluripotent stem cells are comparable to those found in other tissues except testis. Hence, primate iPSCs reveal insights into general primate gene expression evolution and should provide a rich source to identify conserved and species-specific gene expression patterns for cellular phenotypes.
Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, Hannover Medical School, 30625 Hannover, Germany
Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
Overall design We used expression profiling to characterize five gorilla, two bonobo and three macaque iPS clones as well as three iPS clones from two human individuals, three human embryonic stem (ES) cell lines and three macaque ES cell lines. We generated tagged RNA-Seq libraries from these 19 samples including four technical replicates (23 samples). Over 100 million single end reads were generated on the Illumina platform.
Citation(s) 24631741
Submission date Sep 11, 2013
Last update date May 15, 2019
Contact name Jay Shendure
Organization name University of Washington
Department Genome Sciences
Lab Shendure
Street address 3720 15th Ave NE
City Seattle
State/province WA
ZIP/Postal code 98195-5065
Country USA
Platforms (5)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
GPL13766 Illumina Genome Analyzer IIx (Macaca mulatta)
GPL13801 Illumina Genome Analyzer IIx (Gorilla gorilla)
Samples (23)
GSM1229057 b_SF_iPS_1
GSM1229058 b_SF_iPS_2
GSM1229059 g_SF_iPS_1
BioProject PRJNA218873
SRA SRP029888

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Supplementary file Size Download File type/resource
GSE50781_genes_reps.tsv.gz 616.6 Kb (ftp)(http) TSV
GSE50781_isoforms_reps.tsv.gz 1.1 Mb (ftp)(http) TSV
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