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| 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
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| 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.
Contributors:
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
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| 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.
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| Citation(s) |
24631741 |
| Submission date |
Sep 11, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Jay Shendure |
| Organization name |
University of Washington
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| Department |
Genome Sciences
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| Lab |
Shendure
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| Street address |
3720 15th Ave NE
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195-5065 |
| Country |
USA |
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| Platforms (5)
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| GPL10999 |
Illumina Genome Analyzer IIx (Homo sapiens) |
| GPL13766 |
Illumina Genome Analyzer IIx (Macaca mulatta) |
| GPL13801 |
Illumina Genome Analyzer IIx (Gorilla gorilla) |
| GPL13803 |
Illumina Genome Analyzer IIx (Pan paniscus) |
| GPL17720 |
Illumina Genome Analyzer IIx (Macaca fascicularis) |
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| Samples (23)
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| Relations |
| BioProject |
PRJNA218873 |
| SRA |
SRP029888 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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