Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Homo sapiens

ABSTRACT: Culture-induced recurrent epigenetic aberrations in human pluripotent stem cells [RNA-seq]

PROVIDER: PRJNA389212 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR5644212.fastq.gz	Fastqsanger.gz
	SRR5644213.fastq.gz	Fastqsanger.gz
	SRR5644214.fastq.gz	Fastqsanger.gz
	SRR5644215.fastq.gz	Fastqsanger.gz
	SRR5644216.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 6

Similar Datasets

Culture-induced recurrent epigenetic aberrations in human pluripotent stem cells

Project description:Culture-induced recurrent epigenetic aberrations in human pluripotent stem cells

| PRJNA389209 | ENA

Homo sapiens

Project description:Culture-induced recurrent epigenetic aberrations in human pluripotent stem cells [methylation]

| PRJNA389213 | ENA

NextGen/GENESiPS

Project description:<p>Variability in induced pluripotent stem cell (iPSC) lines remains a roadblock for disease modeling and regenerative medicine. Through linear mixed models we have described different sources of gene expression variability from RNA sequencing data in 317 human iPSC lines from 101 individuals. We found that ~50% of genome-wide expression variability is explained by variation across individuals and identified a set of expression quantitative trait loci that contribute to this variation. These analyses coupled with allele specific expression show that iPSCs retain a subject-specific gene expression pattern. Pathway enrichment and key driver analyses, based on predictive causal gene networks, found that Polycomb targets explain a significant part of the non-genetic variability present in iPSCs within and across individuals. These publically available iPSC lines and genetic datasets will be a resource to the scientific community and will open new avenues to reduce variability in iPSCs and improve their utility in disease modeling.</p> <p>SNP array data from individuals included in RNA-seq transcriptome profiling study of human induced pluripotent stem cells to characterize gene expression variation across individuals and within multiple iPSC lines from the same individual. Genotyping was performed on patient blood.</p> Data availability: <ul> <li>SNP-genotyping: dbGaP - current study</li> <li>RNA-seq counts: <a href="http://www.ncbi.nlm.nih.gov/geo/">GEO</a> - GSE79636</li> <li>FASTQ files: <a href="http://www.ncbi.nlm.nih.gov/sra">SRA</a> - SRP072417</li> </ul>

| phs001139 | dbGaP

The Role of SQSTM1 (P62) in Mitochondrial Function and Clearance in Human Cortical Neurons

Project description:We have assessed the importance of SQSTM1 in human induced pluripotent stem cell (iPSC)-derived cortical neurons with and without SQSTM1. By combining high-content imaging, RNA-Seq, and functional mitochondrial readouts, we showed that SQSTM1 depletion causes aberrations in mitochondrial gene expression and functionality in iPSC-derived neurons.

2021-01-18 | E-MTAB-9383 | biostudies-arrayexpress

Homo sapiens

Project description:Epigenetic and transcriptional aberrations in human pluripotent stem cells reflect differences in reprogramming mechanisms [RNA-Seq]

| PRJNA230824 | ENA

Coding mutations and loss-of-imprinting in human pluripotent cells derived by nuclear transfer and defined factors [RNA-Seq]

Project description:Human pluripotent stem cells can be derived from somatic cells by forced expression of defined factors, and more recently by nuclear-transfer into human oocytes, revitalizing a debate on whether one reprogramming approach might be advantageous over the other. Here we compared the genetic and epigenetic stability of human nuclear-transfer embryonic stem cell (NT-ESC) lines and isogenic induced pluripotent stem cell (iPSC) lines, derived from the same somatic cell cultures of fetal, neonatal and adult origin. Both cell types shared similar genome-wide gene expression and DNA methylation profiles. Importantly, NT-ESCs and iPSCs have comparable numbers of de novo coding mutations but significantly higher than parthenogenetic ESCs. Similar to iPSCs NT-ESCs displayed clone- and gene-specific aberrations in DNA methylation and allele-specific expression of imprinted genes, similarly to iPSCs. The occurrence of these genetic and epigenetic defects in both NT-ESCs and iPSCs suggests that they are inherent to reprogramming, regardless of the underlying technique. RNA sequencing analysis was performed on a total of 12 human cell lines, including: an isogenic set of 3 nuclear-transfer embryonic stem cell (NT-ESC) lines, 2 RNA-reprogrammed induced pluripotent stem cell (iPSC) lines and their parental neonatal fibroblast cell line; an isogenic set of 1 NT-ESC line, 3 iPSC lines and their parental adult fibroblast cell line (derived from a type 1 diabetic subject); as well as 1 control embryonic stem cell (ESC) line.

2014-11-06 | E-GEOD-61656 | biostudies-arrayexpress

StemNet - in vitro differentiation of human hepatocytes

Project description:Integrative epigenomic and transcriptomic characterization of hepatocyte-like cells differentiated in vitro from human induced pluripotent stem cells in comparison with primary human hepatocytes. This study comprises single cell RNA-seq, bulk mRNA-seq, ATAC-seq and RRBS.

| EGAS00001004201 | EGA

Dynamic Changes in the Copy Number of Pluripotency and Cell Proliferation Genes in Human ES and iPS Cells during Reprogramming and Time in Culture

Project description:Human embryonic and induced pluripotent stem cells (hESCs and iPSCs) are being considered as sources of differentiated cells for drug development and cell therapy. Genomic stability of these cells is important for in vitro studies, and is critical for clinical applications. Of particular concern for cell therapy is the known association between genetic aberrations and tumorigenicity. Our results highlight the dynamic nature of genomic abnormalities in pluripotent stem cell culture and the need for frequent genomic monitoring of pluripotent stem cells destined for transplantation in order to determine the impact of specific genomic changes on phenotypic stability and clinical safety.

2011-02-15 | GSE25925 | GEO

Coding mutations and loss-of-imprinting in human pluripotent cells derived by nuclear transfer and defined factors [DNA methylation profiling]

Project description:Human pluripotent stem cells can be derived from somatic cells by forced expression of defined factors, and more recently by nuclear-transfer into human oocytes, revitalizing a debate on whether one reprogramming approach might be advantageous over the other. Here we compared the genetic and epigenetic stability of human nuclear-transfer embryonic stem cell (NT-ESC) lines and isogenic induced pluripotent stem cell (iPSC) lines, derived from the same somatic cell cultures of fetal, neonatal and adult origin. Both cell types shared similar genome-wide gene expression and DNA methylation profiles. Importantly, NT-ESCs and iPSCs have comparable numbers of de novo coding mutations but significantly higher than parthenogenetic ESCs. Similar to iPSCs NT-ESCs displayed clone- and gene-specific aberrations in DNA methylation and allele-specific expression of imprinted genes, similarly to iPSCs. The occurrence of these genetic and epigenetic defects in both NT-ESCs and iPSCs suggests that they are inherent to reprogramming, regardless of the underlying technique. Genome-wide DNA methylation profiling by Illumina Infinium HumanMethylation 450K Beadchip was performed on a total of 21 human cell lines, including: an isogenic set of 3 nuclear-transfer embryonic stem cell (NT-ESC) lines, 2 RNA-reprogrammed induced pluripotent stem cell (iPSC) lines and their parental neonatal fibroblast cell line; an isogenic set of 1 NT-ESC line, 6 iPSC lines and their parental adult fibroblast cell line (derived from a type 1 diabetic subject); as well as 7 control embryonic stem cell (ESC) lines.

2014-11-06 | E-GEOD-61461 | biostudies-arrayexpress