Expression data from mouse integration-free iPS cells
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ABSTRACT:
ORGANISM(S): Mus musculus
PROVIDER: GSE61403 | GEO | 2015/09/14
SECONDARY ACCESSION(S): PRJNA261009
REPOSITORIES: GEO
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Project description:Reprogramming process can bring in genetic and epigenetic abnormalities, and these abnormalities can endow effect on gene expression of obtained iPSCs. We used Microarray to detect obvious gene expression differences between iPS cells ,which were induced using one episomal plasmid from C57BL/6 mouse embryonic fibroblasts, and one normal ES cell line from C57BL/6 inbred strain mice. iPS cells and control ES cells were selected in early passage for RNA extraction and hybridization on Affymetrix microarrays. To reduce the effect of in vitro culture, we chose iPS cells and ES cells in passage 7 to 10 for analysis.
2015-09-14 | E-GEOD-61403 | biostudies-arrayexpress
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
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. Total RNA from mouse embryonic fibroblasts, two control ES cells (TT2 and B6ES), retrovirus vector-derived iPS cells (20D17), and twelve HAC-derived iPS clones were hybridized to the Agilent Whole Mouse Genome microarrays.
2011-10-15 | E-GEOD-29441 | biostudies-arrayexpress
Project description:Epstein-Barr virus (EBV)-based episomal vector system enables persistent transgene expression, which is advantageous for efficient derivation of transgene-free induced pluripotent stem cells (iPSCs) without viral transduction. Here, we report establishment of an iPSC line from somatic fibroblasts of a neonatal common marmoset monkey (marmoset; Callithrix jacchus) using an all-in-one episomal vector that we newly developed. The established iPSC line, named NM-iPS, showed standard characteristics of pluripotency such as pluripotency-related marker expression, three germ layer differentiation, and normal karyotype (2n = 46). The novel iPSC line would be a useful resource for stem cell research using non-human primates.
2021-01-10 | GSE164497 | GEO
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2013-07-23 | GSE49082 | GEO
Project description:Disease-specific induced pluripotent stem (iPS) cells have been used for a model to analyze pathogenesis of the disease. In this study, we generated iPS cells derived from a fibroblastic cell line of ataxia telangiectasia (AT-iPS cells), a neurodegenerative, inherited disease with chromosomal instability and hypersensitivity to ionizing radiation. AT-iPS cells exhibited hypersensitivity to X-ray irradiation, one of the characteristics of the disease. Surprisingly, while parental ataxia telangiectasia cells exhibited significant chromosomal abnormalities, AT-iPS cells did not show any chromosomal instability in vitro, i.e. maintenance of intact chromosomes at least by 80 passages (560 days) probably due to robust stability of pluripotent stem cells such as iPS cells and embryonic stem cells. The whole exome analysis also showed comparable nucleotide substitution speed in AT-iPS cells. Interestingly, after longer period of AT-iPS implantation into immunodeficient mice, teratoma generated by AT-iPS cells exhibited telangiectasia and carcinogenesis that are two characteristic symptoms of ataxia telangiectasia. Taken together, AT-iPS cells would be a good model for ataxia telangiectasia to clarify pathogenesis of the disease, and may allow us to facilitate development of drugs that inhibit ataxia and hypersensitivity to ionizing radiation for therapeutic application.
2013-06-22 | GSE47498 | GEO
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 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
2009-04-04 | E-GEOD-15148 | biostudies-arrayexpress
Project description:The generation of induced pluripotent stem cells (iPSCs) often results in aberrant silencing of the imprinted Dlk1-Dio3 gene cluster, which compromises their ability to generate entirely iPSC-derived mice (âall-iPSC miceâ). Here, we show that reprogramming in the presence of ascorbic acid attenuates hypermethylation of Dlk1-Dio3 by enabling a chromatin configuration at its imprint control region that interferes with abnormal binding of the DNA methyltransferase Dnmt3a. This approach allowed us to generate adult all-iPSC mice from mature B cells, which have thus far failed to support the development of exclusively iPSC-derived postnatal mice. Our data demonstrate that factor-mediated reprogramming can endow a defined, terminally differentiated cell type with a developmental potential equivalent to that of embryonic stem cells. More generally, these findings indicate that the choice of culture conditions used for transcription factor-mediated reprogramming can strongly influence the epigenetic and biological properties of resultant iPSCs. This series consists of quadruplicated mRNA expression microarray data (Affymetrix mouse 430_2 3'-IVT array) for iPS cells derived from MEF cells under cell culture conditions with or without ascorbic acid supplementation. iPS cells were generated from MEFs of the Col-OKSM reprogrammable mice. In the presence of doxycycline, the reprogramming transcription factors Oct4, Sox2, Klf4, and cMyc were induced in MEFs to derivate iPS cells. Total RNA was isolated from iPS cells derivated in the presence or absence of ascorbic acid in culture medium.
2012-02-01 | E-GEOD-34761 | biostudies-arrayexpress
Project description:Disease-specific induced pluripotent stem (iPS) cells have been used for a model to analyze pathogenesis of the disease. We generated iPS cells derived from a fibroblastic cell line of ataxia telangiectasia (AT-iPS cells). In analysis of AT-iPS cells, the human wild-type iPS cell line (MRC5-iPS) was generated and cultured in the same conditions as the diseased iPS cell lines. It is an ideal control cell line for the disease and patient-specific iPS cell lines. Because MRC5-iPS cells exhibited considerable chromosomal abnormalities in vitro, we performed a structural alteration analysis by using a SNP genotyping array for MRC5-iPS cell line, Tic, at passage 15, passage 30, and passage 37. The parental MRC-5 fibroblast cells and MRC-iPS 25 (Tic) were subjected to Illumina HumanCytoSNP-12 v2.1 BeadChip analysis.
2013-07-23 | E-GEOD-49082 | biostudies-arrayexpress
Project description:Establishing a common marmoset induced pluripotent stem cell line NM-iPS by an all-in-one episomal vector approach
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