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Series GSE61342 Query DataSets for GSE61342
Status Public on Sep 11, 2014
Title Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics (methylation array)
Platform organism Homo sapiens
Sample organisms Pan troglodytes; Homo sapiens
Experiment type Methylation profiling by array
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 realise the potential of iPSCs, and in combination with genomic technologies, transform studies of comparative evolution in primates.
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.
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 11, 2014
Last update date Mar 22, 2019
Contact name Irene Gallego Romero
Phone 773 834 1984
Organization name University of Chicago
Department Human Genetics
Lab Gilad
Street address 920 E 58th St, CLSC 317
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
Platforms (1)
GPL13534 Illumina HumanMethylation450 BeadChip (HumanMethylation450_15017482)
Samples (28)
GSM1502695 C3647_iPSC
GSM1502696 C3649_iPSC
GSM1502697 C3651_iPSC
This SubSeries is part of SuperSeries:
GSE61343 Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics
BioProject PRJNA260817

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE61342_RAW.tar 183.1 Mb (http)(custom) TAR
GSE61342_raw_intensities.txt.gz 45.9 Mb (ftp)(http) TXT
Processed data included within Sample table

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