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Series GSE110544 Query DataSets for GSE110544
Status Public on Feb 13, 2018
Title Impact of regulatory variation across human iPSCs and differentiated cells [methylation]
Organism Homo sapiens
Experiment type Methylation profiling by array
Summary Induced pluripotent stem cells (iPSCs) are an essential tool for studying cellular differentiation and cell types that are otherwise difficult to access. We investigated the use of iPSCs and iPSC-derived cells to study the impact of genetic variation on gene regulation across different cell types and as models for studies of complex disease. To do so, we established a panel of iPSCs from 58 well-studied Yoruba lymphoblastoid cell lines (LCLs); 14 of these lines were further differentiated into cardiomyocytes. We characterized regulatory variation across individuals and cell types by measuring gene expression levels, chromatin accessibility and DNA methylation. Our analysis focused on a comparison of inter-individual regulatory variation across cell types. While most cell type-specific regulatory quantitative trait loci (QTLs) lie in chromatin that is open only in the affected cell types, we found that 20% of cell type-specific regulatory QTLs are in shared open chromatin. This observation motivated us to develop a deep neural network to predict open chromatin regions from DNA sequence alone. Using this approach, we were able to use the sequences of segregating haplotypes to predict the effects of common SNPs on cell type-specific chromatin accessibility.
 
Overall design Bisulfite converted DNA from feeder free iPSCs for meQTL analysis.
 
Contributor(s) Banovich NE, Li YI, Raj A, Ward MC, Tung P, Burnett JE, Myrthil M, Thomas SM, Calderon D, Greenside P, Kundaje A, Pritchard JK, Gilad Y
Citation(s) 29208628
Submission date Feb 13, 2018
Last update date Jan 20, 2019
Contact name Nicholas E Banovich
Organization name University of Chicago
Department Human Genetics
Lab Gilad
Street address 920 E. 58th Street, CLSC 317
City Chicago
State/province IL
ZIP/Postal code 60453
Country USA
 
Platforms (1)
GPL21145 Infinium MethylationEPIC
Samples (58)
GSM2995445 NA18486_methylation
GSM2995446 NA18498_methylation
GSM2995447 NA18502_methylation
This SubSeries is part of SuperSeries:
GSE89895 Impact of regulatory variation across human iPSCs and differentiated cells
Relations
BioProject PRJNA433959

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
GSE110544_RAW.tar 974.1 Mb (http)(custom) TAR (of IDAT)
Processed data included within Sample table

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