Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA213319 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The equivalency of human induced pluripotent stem cells (hiPSCs) with human embryonic stem cells (hESCs) remains controversial. Here, we devised a strategy to assess the contribution of clonal growth, reprogramming method and genetic background to transcriptional patterns in hESCs and hiPSCs. Surprisingly, transcriptional variation originating from two different genetic backgrounds was dominant over variation due to the reprogramming method or cell type of origin of pluripotent cell lines. Moreover, the few differences we detected between isogenic hESCs and hiPSCs neither predicted functional outcome, nor distinguished an independently derived, larger set of unmatched hESC/hiPSC lines. We conclude that hESCs and hiPSCs are transcriptionally and functionally highly similar and cannot be distinguished by a consistent gene expression signature. Our data further imply that genetic background variation is a major confounding factor for transcriptional comparisons of pluripotent cell lines, explaining some of the previously observed expression differences between unmatched hESCs and hiPSCs. Expression profiling of human embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs) and fibroblasts, mostly in triplicates.
2015-10-26 | E-GEOD-73211 | biostudies-arrayexpress
Project description:The Human Induced Pluripotent Stem Cells Initiative (HipSci) is generating a large, high-quality reference panel of human IPSC lines. This is a submission of mass-spectrometry analyses from 6 induced pluripotent stem cell lines generated by the HipSci project.
2017-05-15 | MSV000081088 | MassIVE
Project description:The Human Induced Pluripotent Stem Cells Initiative (HipSci) is generating a large, high-quality reference panel of human IPSC lines. This is a submission of mass-spectrometry analyses from 6 induced pluripotent stem cell lines generated by the HipSci project.
2017-05-12 | PXD005506 | Pride
Project description:The equivalency of human induced pluripotent stem cells (hiPSCs) with human embryonic stem cells (hESCs) remains controversial. Here, we devised a strategy to assess the contribution of clonal growth, reprogramming method and genetic background to transcriptional patterns in hESCs and hiPSCs. Surprisingly, transcriptional variation originating from two different genetic backgrounds was dominant over variation due to the reprogramming method or cell type of origin of pluripotent cell lines. Moreover, the few differences we detected between isogenic hESCs and hiPSCs neither predicted functional outcome, nor distinguished an independently derived, larger set of unmatched hESC/hiPSC lines. We conclude that hESCs and hiPSCs are transcriptionally and functionally highly similar and cannot be distinguished by a consistent gene expression signature. Our data further imply that genetic background variation is a major confounding factor for transcriptional comparisons of pluripotent cell lines, explaining some of the previously observed expression differences between unmatched hESCs and hiPSCs.
2015-10-26 | GSE73211 | GEO
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
Project description:Human pluripotent cells were reset to ground state pluripotency by transient overexpression of NANOG and KLF2 and subsequent inhibition of ERK and protein kinase C. Transcriptional profiling of H9 parental and clonal lines, and induced pluripotent stem cells derived from adult fibroblast and adipose cell types was carried out in reset and conventional culture conditions.
2014-09-10 | E-MTAB-2856 | biostudies-arrayexpress
Project description:The variation among induced pluripotent stem cells (iPSCs) in their differentiation capacity to specific lineages is frequently attributed to somatic memory. In this study, we compared hematopoietic differentiation capacity of 35 human iPSC lines derived from four different tissues and four embryonic stem cell lines. The analysis revealed that hematopoietic commitment capacity (PSCs to hematopoietic precursors) is correlated with the expression level of the IGF2 gene independent of the iPSC origins. In contrast, maturation capacity (hematopoietic precursors to mature blood) is affected by iPSC origin; blood-derived iPSCs showed the highest capacity. However, some fibroblast-derived iPSCs showed higher capacity than blood-derived clones. Tracking of DNA methylation changes during reprogramming reveals that maturation capacity is highly associated with aberrant DNA methylation acquired during reprogramming, rather than the types of iPSC origins. These data demonstrated that variations in the hematopoietic differentiation capacity of iPSCs are not attributable to somatic memories of their origins. Methyl-seq analysis for undifferentiated induced pluripotent stem cell (iPSC) lines (n = 21), human dermal fibroblast (HDF, n = 1), human peripheral blood (n = 1), and human keratinocyte (n = 1), and ATAC-seq analysis for 2 iPSC lines and an embryonic stem cell (ESC) line with two different culture conditions. CTCF-ChIP-seq analysis for an ESC line.
2016-07-27 | E-GEOD-74967 | biostudies-arrayexpress
Project description:<p>Hematopoietic stem cell (HSC) mutations can result in clonal hematopoiesis (CH) with heterogeneous clinical outcomes. Here, we investigated how the cell state preceding <em>Tet2</em> mutation impacts the pre-malignant phenotype. Using an inducible system for clonal analysis of myeloid progenitors, we found that the epigenetic features of clones at similar differentiation status were highly heterogeneous and functionally responded differently to <em>Tet2</em> mutation. Cell differentiation stage also influenced <em>Tet2</em> mutation response indicating that the cell of origin's epigenome modulates clone-specific behaviors in CH. Molecular features associated with higher risk outcomes include <em>Sox4</em> that sensitized cells to <em>Tet2</em> inactivation, inducing dedifferentiation, altered metabolism and increasing the <em>in vivo</em> clonal output of mutant cells, as confirmed in primary GMP and HSC models. Our findings validate the hypothesis that epigenetic features can predispose specific clones for dominance, explaining why identical genetic mutations can result in different phenotypes.</p>
1970-01-01 | MTBLS9914 | MetaboLights
Project description:Hematopoiesis generated from human embryonic stem cells (ES) and induced pluripotent stem cells (iPS) are unprecedented resources for cell therapy. We compared hematopoietic differentiation potentials from ES and iPS cell lines originated from various donors and derived them using integrative and non-integrative vectors. Significant differences in differentiation toward hematopoietic lineage were observed among ES and iPS. The ability of engraftment of iPS or ES-derived cells in NOG mice varied among the lines with low levels of chimerism. iPS generated from ES cell-derived mesenchymal stem cells (MSC) reproduce a similar hematopoietic outcome compared to their parental ES cell line. We were not able to identify any specific hematopoietic transcription factors that allow to distinguish between good versus poor hematopoiesis in undifferentiated ES or iPS cell lines. However, microarray analysis showed genes differentially expressed in ES and iPS cell lines according to their hematopoietic potential. These results demonstrate the influence of genetic background in variation of hematopoietic potential rather than the reprogramming process.
2015-11-17 | GSE75051 | GEO
Project description:Induced pluripotent stem cells (iPSCs) have become an essential tool for both modeling how causal genetic variants impact cellular function in disease, as well as being an emerging source of tissue for transplantation medicine. Unfortunately the preparation of somatic cells, their reprogramming and the subsequent verification of iPSC pluripotency are laborious, manual processes that limit the scale and level of reproducibility of this technology. Here we describe a modular, robotic platform for iPSC reprogramming that enables automated, high-throughput conversion of skin biopsies into iPSCs and differentiated cells with minimal manual intervention. Using this platform, we demonstrate that automated reprogramming and the pooled selection of pluripotent cells results in high quality, stable, iPSCs. These lines display less line-to-line variation than either manually produced lines or lines produced through automation followed by single colony-subcloning. The robotic platform we describe will enable the application of iPSCs to population-scale biomedical problems including the study of complex genetic diseases and the development of personalized medicines. Two independent human fibroblast lines were reprogrammed, using modified mRNA, into induced pluripotent stem cells (iPSCs). The genomic stability of several cell lines was evaluated using SNP arrays. Three iPSCs originating from one fibroblast line were tested at passages 8 and 20, with two of these derived as picked (clonal) lines and the third being a pooled population. Five iPSCs originating from a second fibroblast line were tested at passages 8 and 20, with three of these derives derived as picked (clonal) lines and two derived as pooled populations. The iPSCs were compared against the original parental fibroblasts.
2015-08-03 | E-GEOD-69868 | biostudies-arrayexpress