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Series GSE69919 Query DataSets for GSE69919
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
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.
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:
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
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)
GPL19148 Illumina HiSeq 2500 (Pan troglodytes)
Samples (9)
GSM1712810 C2_H3K27ac
GSM1712811 C2_H3K27me3
GSM1712812 C2_input
This SubSeries is part of SuperSeries:
GSE61343 Generation of a Panel of Induced Pluripotent Stem Cells From Chimpanzees: a Resource for Comparative Functional Genomics
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

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
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 SelectorHelp
Processed data provided as supplementary file
Processed data are available on Series record
Raw data are available in SRA

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