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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of human induced pluripotent stem cells free of exogenous DNA are derived with episomal vectors (super series)

ABSTRACT: Human induced pluripotent stem (iPS) cells have previously been derived from somatic cells using viral vectors that integrate transgenes into the genome. Genomic integration, however, can allow persistent leaky expression of the transgenes and can create insertional mutations, thus limiting the utility of these cells for both research and clinical applications. Here, we describe the derivation of human iPS cells free of vector and transgene sequences using non-integrating oriP/EBNA1-based episomal vectors. The resulting iPS cells are similar to human embryonic stem (ES) cells in both proliferative and developmental potential. These results demonstrate that reprogramming of human somatic cells does not require genomic integration or the continued presence of exogenous reprogramming factors, and removes one important obstacle to the clinical applications of these cells. This SuperSeries is composed of the following subset Series:; GSE15175: Human induced pluripotent stem cells free of exogenous DNA are derived with episomal vectors (fig 1.c); GSE15176: Human induced pluripotent stem cells free of exogenous DNA are derived with episomal vectors (fig 4.a) Experiment Overall Design: Total 21 samples were analyzed to confirm the similarity of human iPS cells derived with episomal vectors with human ES cells, and a dissimilarity with fibroblasts. Experiment Overall Design: Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Victor Ruotti

PROVIDER: E-GEOD-15148 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Transcription profiling of human induced pluripotent stem cells free of exogenous DNA derived with episomal vectors

Project description:Human induced pluripotent stem (iPS) cells have previously been derived from somatic cells using viral vectors that integrate transgenes into the genome. Genomic integration, however, can allow persistent leaky expression of the transgenes and can create insertional mutations, thus limiting the utility of these cells for both research and clinical applications. Here, we describe the derivation of human iPS cells free of vector and transgene sequences using non-integrating oriP/EBNA1-based episomal vectors. The resulting iPS cells are similar to human embryonic stem (ES) cells in both proliferative and developmental potential. These results demonstrate that reprogramming of human somatic cells does not require genomic integration or the continued presence of exogenous reprogramming factors, and removes one important obstacle to the clinical applications of these cells. Experiment Overall Design: Total of 5 es, 1 fibr, 2 parental, 4 ips sub clones

2009-04-04 | E-GEOD-15176 | biostudies-arrayexpress

Transcription profiling of human induced pluripotent stem cells free of exogenous DNA are derived with episomal vectors (fig 1.c)

2009-04-04 | E-GEOD-15175 | biostudies-arrayexpress

Human induced pluripotent stem cells free of exogenous DNA are derived with episomal vectors (fig 4.a)

2009-03-27 | GSE15176 | GEO

Human induced pluripotent stem cells free of exogenous DNA are derived with episomal vectors (fig 1.c)

2009-03-27 | GSE15175 | GEO

Human induced pluripotent stem cells free of exogenous DNA are derived with episomal vectors

Project description:Human induced pluripotent stem (iPS) cells have previously been derived from somatic cells using viral vectors that integrate transgenes into the genome. Genomic integration, however, can allow persistent leaky expression of the transgenes and can create insertional mutations, thus limiting the utility of these cells for both research and clinical applications. Here, we describe the derivation of human iPS cells free of vector and transgene sequences using non-integrating oriP/EBNA1-based episomal vectors. The resulting iPS cells are similar to human embryonic stem (ES) cells in both proliferative and developmental potential. These results demonstrate that reprogramming of human somatic cells does not require genomic integration or the continued presence of exogenous reprogramming factors, and removes one important obstacle to the clinical applications of these cells. This SuperSeries is composed of the SubSeries listed below.

2009-03-27 | GSE15148 | GEO

Transcription profiling of human fibroblast cell line CCD27SK before and after pluripotent reprogramming by lentiviral-mediated insertion of SOX2 C-MYC and TCL-1A

Project description:Reprogramming of somatic cells to pluripotency, thereby creating induced pluripotent stem (iPS) cells, promises to boost cellular therapy. Most instances of direct reprogramming have been achieved by forced expression of defined exogenous factors using multiple viral vectors. The most used four transcription factors, OCT4, SOX2, KLF4 and C-MYC, can induce pluripotency in mouse and human fibroblasts. Here we report that a forced expression of a new combination of transcription factors (TCL-1A, C-MYC and SOX2) is sufficient to promote the reprogramming of human fibroblast into pluripotent cells. These three-factor pluripotent cells are similar to human embryonic stem cells (hESC) in morphology, in the ability to differentiate into cells of the three embryonic layers, and at the level of global gene expression. Induced pluripotent human cells generated by combination of other factors will be of great help for the understanding of reprogramming pathways. This in turn will allow us to better control cell-fate and apply this knowledge to cell therapy.

2010-10-26 | E-MEXP-2422 | biostudies-arrayexpress

Homo sapiens

Project description:Human induced pluripotent stem cells free of exogenous DNA are derived with episomal vectors (fig 1.c)

| PRJNA123127 | ENA

Homo sapiens

Project description:Human induced pluripotent stem cells free of exogenous DNA are derived with episomal vectors (fig 4.a)

| PRJNA123129 | ENA

Chromatin Structure and Gene Expression Programs of Human Embryonic and Induced Pluripotent Stem Cells (Affymetrix)

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

Uniform, integration-free iPS cells with a safeguard system using human artificial chromosome vectors

Project description:Human artificial chromosomes (HACs) have unique characteristics as gene-delivery vector, e.g., episomal transmission and transfer of multiple, large transgenes. Here, we demonstrate the advantages of HAC vectors for reprogramming mouse embryonic fibroblasts (MEFs) to induced pluripotent stem (iPS) cells. Two HAC vectors (iHAC1 and iHAC2) were constructed. Both carried four reprogramming factors, and iHAC2 also encoded a p53-knockdown construct (see Kazuki et al 2011). The iHAC1 partially reprogrammed MEFs, and the iHAC2 efficiently reprogrammed MEFs. Global gene expression showed that the iHACs, unlike other vectors, generated relatively uniform iPS cells. We established iHAC-free iPS cells by isolating cells that spontaneously lost the iHAC2. Analyses of pluripotent markers, teratomas, and chimeras confirmed that these iHAC-free iPS cells were pluripotent. Moreover, iHAC-free iPS cells with a re-introduced HAC encoding Herpes Simplex Virus Thymidine Kinase were eliminated by Ganciclovir treatment; therefore, the HAC safeguard system functioned in iPS cells. Thus, the HAC vector could generate uniform, integration-free iPS cells with a safeguard system.

2011-10-16 | GSE29441 | GEO

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