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| Status |
Public on Sep 10, 2014 |
| Title |
Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics (RNA-Seq) |
| Organisms |
Pan troglodytes; Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Comparative studies in primates are extremely restricted because we only have access to a few types of cell lines from non-human apes and to a limited collection of frozen tissues. In order to gain better insight into regulatory processes that underlie variation in complex phenotypes, we must have access to faithful model systems for a wide range of tissues and cell types. To facilitate this, we have generated a panel of 7 fully characterized chimpanzee (Pan troglodytes) induced pluripotent stem cell (iPSC) lines derived from fibroblasts of healthy donors. All lines are free of integration from exogenous reprogramming vectors, can be maintained using standard iPSC culture techniques, and have proliferative and differentiation potential similar to human and mouse lines. To begin demonstrating the utility of comparative iPSC panels, we collected RNA-seq data and methylation profiles from the chimpanzee iPSCs and their corresponding fibroblast precursors, as well as from 7 human iPSCs and their precursors, which were of multiple cell type and population origins. Overall, we observed much less regulatory variation within species in the iPSCs than in the somatic precursors, indicating that the reprogramming process has erased many of the differences observed between somatic cells of different origins. We identified 4,918 differentially expressed genes and 1,986 differentially methylated regions between iPSCs of the two species, many of which are novel inter-species differences and not observed between the somatic cells of the two species. Our panel will help realize the potential of iPSCs, and in combination with genomic technologies, transform studies of comparative evolution in primates.
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| Overall design |
We obtained RNA sequencing and methylation profiles from 7 chimpanzee iPSCs and the fibroblasts used to generate them, as well as 7 human iPSCs and the LCLs and fibroblasts used to generate them.
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| Contributor(s) |
Gallego Romero I, Pavlovic BJ, Hernando-Herraez I, Banovich NE, Kagan CL, Burnett JE, Huang CH, Mitrano A, Chavarria CI, Ben-Nun IF, Li Y, Sabatini K, Leonardo TR, Parast M, Marques-Bonet T, Laurent LC, Loring JF, Gilad Y |
| Citation(s) |
26102527 |
| Submission date |
Sep 02, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Irene Gallego Romero |
| E-mail(s) |
ireneg@uchicago.edu
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| Phone |
773 834 1984
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| Organization name |
University of Chicago
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| Department |
Human Genetics
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| Lab |
Gilad
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| Street address |
920 E 58th St, CLSC 317
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| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platforms (2) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL19148 |
Illumina HiSeq 2500 (Pan troglodytes) |
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| Samples (28)
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| This SubSeries is part of SuperSeries: |
| GSE61343 |
Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics |
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| Relations |
| BioProject |
PRJNA260053 |
| SRA |
SRP045999 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE60996_all_samples_RPKM.txt.gz |
3.4 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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