Expression data from undifferentiated and induced human pluripotent stem cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Uri Ben-David
PROVIDER: E-GEOD-21262 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Expression data from undifferentiated human induced pluripotent stem cells total RNA was isolated from undifferentiated induced pluripotent stem cells grown in standard HESC growth conditions on mouse embryonic fibroblast feeder layer.
2010-04-09 | E-GEOD-21243 | biostudies-arrayexpress
Project description:Expression data from undifferentiated human embryonic stem cells and induced pluripotent stem cells total RNA was isolated from undifferentiated pluripotent stem cells grown in standard HESC growth conditions on mouse embryonic fibroblast feeder layer.
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Project description:Three parthenogenetic induced pluripotent stem cell (PgHiPSCs) lines were generated from each of the ovarian teratoma cell lines (two distinct individuals). Two normal iPS cell lines were generated from normal fibroblasts. Three biological replicates of normal embryonic stem cells (H9, HESCs) were perfomed. We used microarrays to study the gene expression profiles of the PgHiPSCs, and compared the expression of genes to both embryonic and induced pluripotent stem cell, to identify paternally expressed genes that are down-regulated in the PgHiPSC lines. All parthenogenetic and normal iPS cell lines, were tested for pluripotency assays (inclusing, morphology, immuno stanings and qRT-PCR for known pluripotency markers, differentiation capacity in vivo and in vitro)
2011-05-31 | E-GEOD-27362 | biostudies-arrayexpress
Project description:Using global gene expression and proteomic analyses, we identified a molecular signature in human embryonic and induced pluripotent stem cells that suggested a central regulatory role for RNA splicing in self-renewal. Through genetic and biochemical approaches, we established reciprocal functional links between the master regulatory factor OCT4 and SFRS2, a member of the serine/arginine-rich family of splicing factors. SFRS2 regulates expression of two isoforms of the methyl-CpG-binding protein MBD2 that play opposing roles in human ESC and during the reprogramming of fibroblasts. Both the MBD2a isoform expressed in fibroblasts and the MBD2c isoform found in pluripotent cells bind OCT4 and NANOG promoters in human ESC, but only MBD2a interacts with NuRD chromatin remodeling factors. Members of the miR-301 and miR-302 families provide additional regulation by targeting SFRS2 and the somatic specific MBD2a isoform. These data are consistent with a model in which OCT4, SFRS2, and MBD2 participate in a positive feedback loop to regulate proteome diversity in support of self-renewal in pluripotent cells. We isolated RNA from human iPS cells, different human fibroblasts and human embryonic stem cells for hybridization to the Affymetrix gene expression microarrays.
2014-04-18 | E-GEOD-55673 | biostudies-arrayexpress
Project description:TrxG and PcG complexes play key roles in the epigenetic regulation of development through H3K4me3 and H3K27me3 modification at specific sites throughout the human genome, but how these sites are selected is poorly understood. We find that in pluripotent cells, clustered CpG islands at genes predict occupancy of H3K4me3 and H3K27me3, and these "bivalent" chromatin domains precisely span the boundaries of CpG island clusters. Examination of two histone modifications (H3K4me3 and H3K27me3) in human induced pluripotent stem (hiPS) M23F cells.
2012-07-06 | E-GEOD-39137 | biostudies-arrayexpress
Project description:Recently, various groups managed to isolate naïve human embryonic stem cell (hESC) state in vitro has come into acceptance. However, a thorough epigenetic characterization of this human ground state, defined as a state without any epigenetic restrictions, and how that compares to mouse is currently lacking. Also, the epigenomic remodeling required to obtain the ground state, and the important transient processes occurring during the remodeling, have remained elusive in human. Here, we address these issues by using an untargeted mass spectrometry-based (MS) approach to profile the histone epigenome in a time-resolved experimental design. Special care was given to defining the naïve hESC state that was reached over 12 passages (P12, 37 days) in feeder-free conditions in this study. We found that conversion is a multi-staged process with a prominent cellular disturbance after stimulation (P3), an increase in cell proliferation between P3 and P6 and a naïve cell state stabilizing between P9 and P12. In total, 20 different histone post-translational modifications (hPTMs) changed significantly over time from primed to naïve hESCs. Most notably, H3K27me3 is the most prominently increasing hPTM in naïve hESCs, in line with what we recently described in mouse. Essentially, we present a first roadmap of the changing human histone epigenome from primed to naïve state and emphasize that the overlap with mouse hints at a conserved Mammalian epigenetic signature of the ground state.
2019-11-27 | PXD013067 | Pride
Project description:Clinical application of induced pluripotent stem (iPS) cells is limited by low efficiency of iPS derivation, and protocols that permanently modify the genome to effect cellular reprogramming. Moreover, safe and effective means of directing the fate of patient-specific iPS cells towards clinically useful cell types are lacking. Here we describe a simple, non-mutagenic strategy for reprogramming cell fate based on administration of synthetic mRNA modified to overcome innate anti-viral responses. We show that this approach can reprogram multiple human cell types to pluripotency with efficiencies that greatly surpass established protocols. We further show that the same technology can be used to efficiently direct the differentiation of RNA-induced pluripotent stem (RiPS) cells into terminally differentiated myogenic cells. Our method represents a safe, efficient strategy for somatic cell reprogramming and directing cell fates that has broad applicability for basic research, disease modeling and regenerative medicine. We isolated RNA from human RNA derived iPS cells, viral derived iPS cells, different human fibroblasts and human embryonic stem cells for hybridization to the Affymetrix gene expression microarrays.
2010-09-30 | E-GEOD-23583 | biostudies-arrayexpress
Project description:Human induced pluripotent stem (iPS) cells derived from somatic cells of patients hold great promise for modelling human diseases. Dermal fibroblasts are frequently used for reprogramming, but require an invasive skin biopsy and a prolonged period of expansion in cell culture prior to use. Here, we report the derivation of iPS cells from multiple human blood sources including peripheral blood mononuclear cells (PBMCs) harvested by routine venipuncture. Peripheral blood-derived human iPS lines are comparable to human embryonic stem (ES) cells with respect to morphology, expression of surface antigens, activation of endogenous pluripotency genes, DNA methylation and differentiation potential. Analysis of Immunoglobulin and T-cell receptor gene rearrangement revealed that some of the PBMC iPS cells were derived from T-cells, documenting derivation of iPS cells from terminally differentiated cell types. Importantly, peripheral blood cells can be isolated with minimal risk to the donor and can be obtained in sufficient numbers to enable reprogramming without the need for prolonged expansion in culture. Reprogramming from blood cells thus represents a fast, safe and efficient way of generating patient-specific iPS cells. We isolated RNA from multiple human blood sources including peripheral blood mononuclear iPS cells, multiple somatic cells and iPS cells and human embryonic cells and hybridized them to Affymetrix gene expression microarrays.
2010-06-23 | E-GEOD-22167 | biostudies-arrayexpress
Project description:Three induced pluripotent stem (iPS) cell lines were generated from pancreatic BCD (beta-cell-derived cells). One iPS cell clone was derived from pancreatic non-beta cells. We used microarrays to study the gene expression profiles of beta-iPSCs, and compared the expression of genes in their somatic parental cells and other ES and iPS cells. All BiPSC lines were tested in pluripotency assays (including morphology, immunostainings and qRT-PCR) for known pluripotency markers, as well as differentiation capacity in vivo and in vitro.
2011-07-31 | E-GEOD-29880 | biostudies-arrayexpress
Project description:Knowledge of both the global chromatin structure and the gene expression programs of human embryonic stem (ES) cells and induced pluripotent stem (iPS) cells should provide a robust means to assess whether the genomes of these cells have similar pluripotent states. Recent studies have suggested that ES and iPS cells represent different pluripotent states with substantially different gene expression profiles. We describe here a comparison of global chromatin structure and gene expression data for a panel of human ES and iPS cells. Genome-wide maps of nucleosomes with histone H3K4me3 and H3K27me3 modifications indicate that there is little difference between ES and iPS cells with respect to these marks. Gene expression profiles confirm that the transcriptional programs of ES and iPS cells show very few consistent differences. Although some variation in chromatin structure and gene expression was observed in these cell lines, these variations did not serve to distinguish ES from iPS cells. Examination of gene expression in 7 human ES cell lines, 8 human iPS cell lines, and 2 fibroblast cell line2.
2010-08-09 | E-GEOD-23402 | biostudies-arrayexpress