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| Status |
Public on Jun 17, 2015 |
| Title |
Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics [ChIP-Seq] |
| Platform organism |
Pan troglodytes |
| Sample organisms |
Pan troglodytes; Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Third-party reanalysis
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| Summary |
Comparative genomics studies in primates are extremely restricted due to our limited access to samples from non-human apes. In order to gain better insight into the genetic processes that underlie variation in complex phenotypes in primates, we must have access to faithful model systems for a wide range of cell types. To facilitate this, we have generated a panel of 7 fully characterized chimpanzee induced pluripotent stem cell (iPSC) lines derived from healthy donors. To begin demonstrating the utility of comparative iPSC panels, we collected RNA-sequencing and DNA methylation data from the chimpanzee iPSCs and the corresponding fibroblast lines, as well as from 7 human iPSCs and their source lines, which encompass multiple populations and cell types. We observe much less within-species variation in iPSCs than in somatic cells, indicating that the reprogramming process erases many inter-individual differences. The low within-species regulatory variation in iPSCs allowed us to identify many novel inter-species regulatory differences of small magnitude.
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| Overall design |
We used ChIP-seq to characterize the genome-wide distribution of two types of histone modifications (H3K27me3 and H3K27ac) in three of our chimpanzee iPSCs and compared them to histone modification data from three human iPSC lines from the Roadmap Epigenomics project:
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| Contributor(s) |
Gallego Romero I, Pavlovic BJ, Hernando-Herraez I, Zhou X, Ward MC, Banovich NE, Kagan CL, Burnett JE, Huang CH, Mitrano A, Chavarria CI, Ben-Nun IF, Li Y, Sabatini KJ, Leonardo TR, Parast M, Marques-Bonet T, Laurent LC, Loring JF, Gilad Y |
| Citation(s) |
26102527 |
| Submission date |
Jun 16, 2015 |
| 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 (1) |
| GPL19148 |
Illumina HiSeq 2500 (Pan troglodytes) |
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| Samples (9)
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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 |
| Reanalysis of |
GSM773033 |
| Reanalysis of |
GSM772935 |
| Reanalysis of |
GSM773024 |
| Reanalysis of |
GSM772848 |
| Reanalysis of |
GSM772847 |
| Reanalysis of |
GSM772863 |
| Reanalysis of |
GSM752967 |
| Reanalysis of |
GSM752971 |
| Reanalysis of |
GSM752993 |
| BioProject |
PRJNA287133 |
| SRA |
SRP059542 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE69919_HiPSC18a_H3K27ac_peaks_peaks.xls.bed.gz |
508.9 Kb |
(ftp)(http) |
BED |
| GSE69919_HiPSC18a_H3K27me3.merged.nochrM.rmdup.filter_HiPSC18a_input.merged.nochrM.rmdup.filter-domains.bed.gz |
436.9 Kb |
(ftp)(http) |
BED |
| GSE69919_HiPSC20b_H3K27ac_peaks_peaks.xls.bed.gz |
718.0 Kb |
(ftp)(http) |
BED |
| GSE69919_HiPSC20b_H3K27me3.merged.nochrM.rmdup.filter_HiPSC20b_input.merged.nochrM.rmdup.filter-domains.bed.gz |
603.4 Kb |
(ftp)(http) |
BED |
| GSE69919_HiPSCDF6-9_H3K27ac_peaks_peaks.xls.bed.gz |
737.7 Kb |
(ftp)(http) |
BED |
| GSE69919_HiPSCDF6-9_H3K27me3.merged.nochrM.rmdup.filter_HiPSCDF6-9_input.merged.nochrM.rmdup.filter-domains.bed.gz |
78.0 Kb |
(ftp)(http) |
BED |
| GSE69919_RAW.tar |
4.6 Mb |
(http)(custom) |
TAR (of BED) |
| GSE69919_all_samples_enrichment_scores.txt.gz |
878.3 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
| Raw data are available in SRA |
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