Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genetic Variation, Not Cell Type of Origin, Underlies Regulatory Differences in iPSCs [Expression]

ABSTRACT: Analysis of contribution of cell type of origin and individual to gene expression differences in iPSCs. The hypothesis tested in the present study was that cell type of origin affects iPSC gene expression. Results show that individual has a much stronger effect than cell type of origin on differences between iPSCs derived from multiple individuals.

ORGANISM(S): Homo sapiens

PROVIDER: GSE65035 | GEO | 2015/01/16

SECONDARY ACCESSION(S): PRJNA272742

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Genetic Variation, Not Cell Type of Origin, Underlies Regulatory Differences in iPSCs [Methylation]

Project description:Analysis of contribution of cell type of origin and individual to gene expression differences in iPSCs. The hypothesis tested in the present study was that cell type of origin affects iPSC gene expression. Results show that individual has a much stronger effect than cell type of origin on differences between iPSCs derived from multiple individuals.

2015-01-19 | GSE65078 | GEO

Genetic Variation, Not Cell Type of Origin, Underlies Regulatory Differences in iPSCs [Methylation]

2015-01-19 | E-GEOD-65078 | biostudies-arrayexpress

Genetic Variation, Not Cell Type of Origin, Underlies Regulatory Differences in iPSCs [Expression]

2015-01-16 | E-GEOD-65035 | biostudies-arrayexpress

Genetic Variation, Not Cell Type of Origin, Underlies Regulatory Differences in iPSCs

Project description:Genetic Variation, Not Cell Type of Origin, Underlies Regulatory Differences in iPSCs

| PRJNA272898 | ENA

Genetic Variation, Not Cell Type of Origin, Underlies Regulatory Differences in iPSCs

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-01-19 | E-GEOD-65079 | biostudies-arrayexpress

Genetic Variation, Not Cell Type of Origin, Underlies the Majority of Identifiable Regulatory Differences in iPSCs.

Project description:The advent of induced pluripotent stem cells (iPSCs) revolutionized human genetics by allowing us to generate pluripotent cells from easily accessible somatic tissues. This technology can have immense implications for regenerative medicine, but iPSCs also represent a paradigm shift in the study of complex human phenotypes, including gene regulation and disease. Yet, an unresolved caveat of the iPSC model system is the extent to which reprogrammed iPSCs retain residual phenotypes from their precursor somatic cells. To directly address this issue, we used an effective study design to compare regulatory phenotypes between iPSCs derived from two types of commonly used somatic precursor cells. We find a remarkably small number of differences in DNA methylation and gene expression levels between iPSCs derived from different somatic precursors. Instead, we demonstrate genetic variation is associated with the majority of identifiable variation in DNA methylation and gene expression levels. We show that the cell type of origin only minimally affects gene expression levels and DNA methylation in iPSCs, and that genetic variation is the main driver of regulatory differences between iPSCs of different donors. Our findings suggest that studies using iPSCs should focus on additional individuals rather than clones from the same individual.

| S-EPMC4727884 | biostudies-literature

Impact of regulatory variation across human iPSCs and differentiated cells [methylation]

Project description: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.

2018-02-13 | GSE110544 | GEO

Genetic Variation, Not Cell Type of Origin, Underlies Regulatory Differences in iPSCs

Project description:This SuperSeries is composed of the SubSeries listed below.

2015-01-19 | GSE65079 | GEO

Impact of regulatory variation across human iPSCs and differentiated cells [ATAC-seq iPSC]

2017-12-23 | GSE108458 | GEO

Impact of regulatory variation across human iPSCs and differentiated cells [ATAC-seq LCL]

2017-12-23 | GSE108460 | GEO